Research laboratory of William DeGrado, PhD

Publications

  1. Sundaram, A., Chen, C., Khalifeh-Soltani, A., Atakilit, A., Ren, X., Qiu, W., Jo, H., DeGrado, W.F., Huang, X. and Sheppard, D., 2016. Targeting integrin α5β1 ameliorates severe airway hyperresponsiveness in experimental asthma. J Clin Invest. 2016 127(1).
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  2. Liang, R., Swanson, J.M., Madsen, J.J., Hong, M., DeGrado, W.F. and Voth, G.A., 2016. Acid activation mechanism of the influenza A M2 proton channel. Proc Natl Acad Sci U S A. 2016 Oct 24. Epub
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  3. Markiewicz, B.N., Lemmin, T., Zhang, W., Ahmed, I.A., Jo, H., Fiorin, G., Troxler, T., DeGrado, W.F. and Gai, F. Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel. Phys Chem Chem Phys. 2016 Oct 19;18(41):28939-28950.
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  4. Reed, N.I., Tang, Y., McIntosh, J., Wu, Y., Molnar, K.S., Civitavecchia, A., Sheppard, D., DeGrado, W.F. and Jo, H.. Exploring N-Arylsulfonyl-l-proline Scaffold as a Platform for Potent and Selective αvβ1 Integrin Inhibitors. ACS Med Chem Lett. 2016 Aug 30;7(10):902-907
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  5. Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stoehr J, Hong M. Structural Polymorphism of Alzheimer's β-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study. J Am Chem Soc. 2016 Aug 10;138(31):9840-52.
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  6. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions.  Bioorg Med Chem Lett. 2016 Jul 15;26(14):3359-63.
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  7. Kim KH, Ko DK, Kim YT, Kim NH, Paul J, Zhang SQ, Murray CB, Acharya R, DeGrado WF, Kim YH, Grigoryan G. Protein-directed self-assembly of a fullerene crystal. Nat Commun. 2016 Apr 26;7:11429
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  8. Thomaston JL, DeGrado WF. Crystal structure of the drug-resistant S31N influenza M2 proton channel. Prot Sci. 2016 Aug;25(8):1551-4.
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  9. Fong KP, Zhu H, Span LM, Moore DT, Yoon K, Tamura R, Yin HH, DeGrado WF, Bennett JS. Directly Activating αIIbβ3 Initiates Outside-In Signaling by Causing αIIbβ3 Clustering.  JBC. 2016 May 27;291(22):11706-16
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  10. Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF.  Designed metalloprotein stabilizes a semiquinone radical. Nat Chem. 2016 Apr;8(4):354-9.
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    Featured in:  C&EN News
  11. Li F, Ma C, DeGrado WF, Wang J. Discovery of Highly Potent Inhibitors Targeting the Predominant Drug-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel. J Med Chem. 2016 Feb 11;59(3):1207-16.
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  12. Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14260-5.
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  13. Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc. 2015 Jul 29;137(29):9302-14.
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  14. Snyder RA, Betzu J, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Systematic perturbations of binuclear non-heme iron sites: structure and dioxygen reactivity of de novo Due Ferri proteins. Biochemistry. 2015 Aug 4;54(30):4637-51
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  15. Bhate MP, Molnar KS, Goulian M, DeGrado WF. Signal Transduction in Histidine Kinases: Insights from New Structures. Structure. 2015 Jun 2; 23(6):981-994.
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  16. Wu Y, Span LM, Nygren P, Zhu H, Moore DT, Cheng H, Roder H, DeGrado WF, Bennett JS. The Tyrosine Kinase c-Src Specifically Binds to the Active Integrin αIIbβ3 to Initiate Outside-In Signaling in Platelets. J Biol Chem. 2015 Jun 19; 290(25):15825-34
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  17. Reed NI, Jo H, Chen C, Tsujino K, Arnold TD, DeGrado WF, Sheppard D. The αvβ1 integrin plays a critical in vivo role in tissue fibrosis. Sci Transl Med. 2015 May 20; 7(288):288ra79.
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  18. Zhang Y, Bartz R, Grigoryan G, Bryant M, Aaronson J, Beck S, Innocent N, Klein L, Procopio W, Tucker T, Jadhav V, Tellers DM, DeGrado WF. Computational Design and Experimental Characterization of Peptides Intended for pH-Dependent Membrane Insertion and Pore Formation. ACS Chem Biol. 2015 Apr 17; 10(4):1082-93.
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  19. Zhang SQ, Kulp DW, Schramm CA, Mravic M, Samish I, DeGrado WF. The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions. Structure. 2015 Mar 3; 23(3):527-41.
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  20. Huang S, Green B, Thompson M, Chen R, Thomaston J, DeGrado WF, Howard KP. C-terminal juxtamembrane region of full-length M2 protein forms a membrane surface associated amphipathic helix. Protein Sci. 2015 Mar;24(3):426-9
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  21. Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. De novo design of a transmembrane Zn²⁺-transporting four-helix bundle. Science. 2014 Dec 19; 346(6216):1520-4.
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  22. Wu Y, Canturk B, Jo H, Ma C, Gianti E, Klein ML, Pinto LH, Lamb RA, Fiorin G, Wang J, DeGrado WF. Flipping in the Pore: Discovery of Dual Inhibitors That Bind in Different Orientations to the Wild-Type versus the Amantadine-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel. J Am Chem Soc. 2014 Dec 31; 136(52):17987-95.
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  23. Gianti E, Carnevale V, DeGrado WF, Klein ML, Fiorin G. Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based Inhibitors. J Phys Chem B. 2014 Nov 11; In Press.
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  24. Dong H, Fiorin G, DeGrado WF, Klein ML. Proton release from the histidine-tetrad in the M2 channel of the influenza A virus. J Phys Chem B. 2014 Nov 6; 118(44):12644-51.
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  25. Seither KM, McMahon HA, Singh N, Wang H, Cushman-Nick M, Montalvo GL, DeGrado WF, Shorter J. Specific aromatic foldamers potently inhibit spontaneous and seeded Aß42 and Aß43 fibril assembly. Biochem J. 2014 Nov 15; 464(1):85-98.
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  26. Dong H, Fiorin G, DeGrado WF, Klein ML. Proton release from the histidine-tetrad in the m2 channel of the influenza a virus. J Phys Chem B. 2014 Nov 6; 118(44):12644-51.
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  27. Gonzalez G, Hannigan B, DeGrado WF. A real-time all-atom structural search engine for proteins. PLoS Comput Biol. 2014 Jul; 10(7):e1003750.
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  28. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ. Structure. 2014 Sep 2; 22(9):1239-51.
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  29. Stöhr J, Condello C, Watts JC, Bloch L, Oehler A, Nick M, DeArmond SJ, Giles K, DeGrado WF, Prusiner SB. Distinct synthetic Aß prion strains producing different amyloid deposits in bigenic mice. Proc Natl Acad Sci U S A. 2014 Jul 15; 111(28):10329-34.
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  30. Rey-Carrizo M, Barniol-Xicota M, Ma C, Frigolé-Vivas M, Torres E, Naesens L, Llabrés S, Juárez-Jiménez J, Luque FJ, DeGrado WF, Lamb RA, Pinto LH, Vázquez S. Easily Accessible Polycyclic Amines that Inhibit the Wild-Type and Amantadine-Resistant Mutants of the M2 Channel of Influenza A Virus. J Med Chem. 2014 Jul 10; 57(13):5738-47.
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  31. Ghosh A, Wang J, Moroz YS, Korendovych IV, Zanni M, DeGrado WF, Gai F, Hochstrasser RM. 2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel. J Chem Phys. 2014 Jun 21; 140(23):235105.
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  32. Mensa B, Howell GL, Scott R, DeGrado WF. Comparative Mechanistic Studies of Brilacidin, Daptomycin, and the Antimicrobial Peptide LL16. Antimicrob Agents Chemother. 2014 Sep; 58(9):5136-45.
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  33. Pavone V, Zhang SQ, Merlino A, Lombardi A, Wu Y, Degrado WF. Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron. Nat Commun. 2014; 5:3581.
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  34. Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, Degrado WF, Korendovych IV. Short peptides self-assemble to produce catalytic amyloids. Nat Chem. 2014 Apr; 6(4):303-9.
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  35. Montalvo GL, Zhang Y, Young TM, Costanzo MJ, Freeman KB, Wang J, Clements DJ, Magavern E, Kavash RW, Scott RW, Liu D, Degrado WF. De novo design of self-assembling foldamers that inhibit heparin-protein interactions. ACS Chem Biol. 2014 Apr 18; 9(4):967-75.
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  36. Polishchuk AL, Cristian L, Pinto LH, Lear JD, Degrado WF. Mechanistic insights from functional characterization of an unnatural His37 mutant of the influenza A/M2 protein. Biochim Biophys Acta. 2014 Apr; 1838(4):1082-7.
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  37. Montalvo GL, Gai F, Roder H, Degrado WF. Slow Folding-Unfolding Kinetics of an Octameric ß-Peptide Bundle. ACS Chem Biol. 2014 Jan 17; 9(1):276-81.
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  38. Markiewicz BN, Jo H, Culik RM, Degrado WF, Gai F. Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B. 2013 Nov 27; 117(47):14688-96.
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  39. Rey-Carrizo M, Torres E, Ma C, Barniol-Xicota M, Wang J, Wu Y, Naesens L, Degrado WF, Lamb RA, Pinto LH, Vázquez S. 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane Derivatives: From Wild-Type Inhibitors of the M2 Ion Channel of Influenza A Virus to Derivatives with Potent Activity against the V27A Mutant. J Med Chem. 2013 Nov 27; 56(22):9265-74.
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  40. Rudick JG, Laakso MM, Schloss AC, DeGrado WF. Template-constrained cyclic sulfopeptide HIV-1 entry inhibitors. Org Biomol Chem. 2013 Nov 7; 11(41):7096-100.
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  41. Ma C, Fiorin G, Carnevale V, Wang J, Lamb RA, Klein ML, Wu Y, Pinto LH, Degrado WF. Asp44 stabilizes the trp41 gate of the m2 proton channel of influenza a virus. Structure. 2013 Nov 5; 21(11):2033-41.
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  42. Schmidt NW, Mishra A, Wang J, DeGrado WF, Wong GC. Influenza virus A M2 protein generates negative Gaussian membrane curvature necessary for budding and scission. J Am Chem Soc. 2013 Sep 18; 135(37):13710-9.
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  43. Fry HC, Lehmann A, Sinks LE, Asselberghs I, Tronin A, Krishnan V, Blasie JK, Clays K, DeGrado WF, Saven JG, Therien MJ. Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore. J Am Chem Soc. 2013 Sep 18; 135(37):13914-26.
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  44. Koerber JT, Thomsen ND, Hannigan BT, Degrado WF, Wells JA. Nature-inspired design of motif-specific antibody scaffolds. Nat Biotechnol. 2013 Oct; 31(10):916-21.
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  45. Williams JK, Tietze D, Wang J, Wu Y, DeGrado WF, Hong M. Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR. J Am Chem Soc. 2013 Jul 3; 135(26):9885-97.
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  46. Wang J, Ma C, Wang J, Jo H, Canturk B, Fiorin G, Pinto LH, Lamb RA, Klein ML, DeGrado WF. Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. J Med Chem. 2013 Apr 11; 56(7):2804-12.
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  47. Balgi AD, Wang J, Cheng DY, Ma C, Pfeifer TA, Shimizu Y, Anderson HJ, Pinto LH, Lamb RA, DeGrado WF, Roberge M. Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. PLoS One. 2013; 8(2):e55271.
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  48. Lemmin T, Soto CS, Clinthorne G, DeGrado WF, Dal Peraro M. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations. PLoS Comput Biol. 2013; 9(1):e1002878.
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  49. Mao L, Wang J, DeGrado WF, Inouye M. An assay suitable for high throughput screening of anti-influenza drugs. PLoS One. 2013; 8(1):e54070.
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  50. Wang J, Wu Y, Ma C, Fiorin G, Wang J, Pinto LH, Lamb RA, Klein ML, Degrado WF. Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1315-20.
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  51. Hu X, Zhao J, DeGrado WF, Binns AN. Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals. Proc Natl Acad Sci U S A. 2013 Jan 8; 110(2):678-83.
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  52. Love MS, Millholland MG, Mishra S, Kulkarni S, Freeman KB, Pan W, Kavash RW, Costanzo MJ, Jo H, Daly TM, Williams DR, Kowalska MA, Bergman LW, Poncz M, DeGrado WF, Sinnis P, Scott RW, Greenbaum DC. Platelet factor 4 activity against P. falciparum and its translation to nonpeptidic mimics as antimalarials. Cell Host Microbe. 2012 Dec 13; 12(6):815-23.
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  53. Thomaston JL, Nguyen PA, Brown EC, Upshur MA, Wang J, DeGrado WF, Howard KP. Detection of drug-induced conformational change of a transmembrane protein in lipid bilayers using site-directed spin labeling. Protein Sci. 2013 Jan; 22(1):65-73.
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  54. Jo H, Meinhardt N, Wu Y, Kulkarni S, Hu X, Low KE, Davies PL, DeGrado WF, Greenbaum DC. Development of a-helical calpain probes by mimicking a natural protein-protein interaction. J Am Chem Soc. 2012 Oct 24; 134(42):17704-13.
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  55. Hong M, DeGrado WF. Structural basis for proton conduction and inhibition by the influenza M2 protein. Protein Sci. 2012 Nov; 21(11):1620-33.
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  56. Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem. 2012 Nov; 4(11):900-6.
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  57. Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I. Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure. 2012 May 9; 20(5):924-35.
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  58. Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in ß-sheet folding. J Am Chem Soc. 2012 May 16; 134(19):8026-9.
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  59. Lanci CJ, MacDermaid CM, Kang SG, Acharya R, North B, Yang X, Qiu XJ, DeGrado WF, Saven JG. Computational design of a protein crystal. Proc Natl Acad Sci U S A. 2012 May 8; 109(19):7304-9.
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  60. Borza CM, Su Y, Chen X, Yu L, Mont S, Chetyrkin S, Voziyan P, Hudson BG, Billings PC, Jo H, Bennett JS, Degrado WF, Eckes B, Zent R, Pozzi A. Inhibition of integrin a2ß1 ameliorates glomerular injury. J Am Soc Nephrol. 2012 Jun; 23(6):1027-38.
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  61. Montero M, Gulzar N, Klaric KA, Donald JE, Lepik C, Wu S, Tsai S, Julien JP, Hessell AJ, Wang S, Lu S, Burton DR, Pai EF, Degrado WF, Scott JK. Neutralizing epitopes in the membrane-proximal external region of HIV-1 gp41 are influenced by the transmembrane domain and the plasma membrane. J Virol. 2012 Mar; 86(6):2930-41.
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  62. Moore DT, Nygren P, Jo H, Boesze-Battaglia K, Bennett JS, DeGrado WF. Affinity of talin-1 for the ß3-integrin cytosolic domain is modulated by its phospholipid bilayer environment. Proc Natl Acad Sci U S A. 2012 Jan 17; 109(3):793-8.
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  63. Kim YH, Donald JE, Grigoryan G, Leser GP, Fadeev AY, Lamb RA, DeGrado WF. Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5. Proc Natl Acad Sci U S A. 2011 Dec 27; 108(52):20992-7.
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  64. Soto CS, Hannigan BT, DeGrado WF. A photon-free approach to transmembrane protein structure determination. J Mol Biol. 2011 Dec 9; 414(4):596-610.
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  65. Mensa B, Kim YH, Choi S, Scott R, Caputo GA, DeGrado WF. Antibacterial mechanism of action of arylamide foldamers. Antimicrob Agents Chemother. 2011 Nov; 55(11):5043-53.
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  66. Wang J, Ma C, Wu Y, Lamb RA, Pinto LH, DeGrado WF. Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. J Am Chem Soc. 2011 Sep 7; 133(35):13844-7.
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  67. Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS, DeGrado WF. Computational design of a ß-peptide that targets transmembrane helices. J Am Chem Soc. 2011 Aug 17; 133(32):12378-81.
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  68. Wang J, Ma C, Fiorin G, Carnevale V, Wang T, Hu F, Lamb RA, Pinto LH, Hong M, Klein ML, DeGrado WF. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. J Am Chem Soc. 2011 Aug 17; 133(32):12834-41.
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  69. Korendovych IV, Shandler SJ, Montalvo GL, DeGrado WF. Environment- and sequence-dependence of helical type in membrane-spanning peptides composed of ß3-amino acids. Org Lett. 2011 Jul 1; 13(13):3474-7.
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  70. Remorino A, Korendovych IV, Wu Y, DeGrado WF, Hochstrasser RM. Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer. Science. 2011 Jun 3; 332(6034):1206-9.
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  71. Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science. 2011 May 27; 332(6033):1071-6.
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  72. Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado WF. Design of a switchable eliminase. Proc Natl Acad Sci U S A. 2011 Apr 26; 108(17):6823-7.
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  73. Duque MD, Ma C, Torres E, Wang J, Naesens L, Juárez-Jiménez J, Camps P, Luque FJ, DeGrado WF, Lamb RA, Pinto LH, Vázquez S. Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. J Med Chem. 2011 Apr 28; 54(8):2646-57.
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  74. Ghosh A, Qiu J, DeGrado WF, Hochstrasser RM. Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy. Proc Natl Acad Sci U S A. 2011 Apr 12; 108(15):6115-20.
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  75. Rogers JM, Polishchuk AL, Guo L, Wang J, DeGrado WF, Gai F. Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel. Langmuir. 2011 Apr 5; 27(7):3815-21.
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  76. Cady SD, Wang J, Wu Y, DeGrado WF, Hong M. Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy. J Am Chem Soc. 2011 Mar 30; 133(12):4274-84.
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  77. Chakraborty S, Kravitz JY, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL. Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment. Angew Chem Int Ed Engl. 2011 Feb 25; 50(9):2049-53.
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  78. Donald JE, Zhang Y, Fiorin G, Carnevale V, Slochower DR, Gai F, Klein ML, DeGrado WF. Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. Proc Natl Acad Sci U S A. 2011 Mar 8; 108(10):3958-63.
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  79. Wang J, Qiu JX, Soto C, DeGrado WF. Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus. Curr Opin Struct Biol. 2011 Feb; 21(1):68-80.
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  80. Donald JE, Kulp DW, DeGrado WF. Salt bridges: geometrically specific, designable interactions. Proteins. 2011 Mar; 79(3):898-915.
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  81. Grigoryan G, Moore DT, DeGrado WF. Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K? channels, and integrin receptors. Annu Rev Biochem. 2011; 80:211-37.
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  82. Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS, DeGrado WF. NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation. Proc Natl Acad Sci U S A. 2010 Dec 28; 107(52):22481-6.
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  83. Fadeev AY, DeGrado WF. Lipid membranes supported on optically transparent nanosilicas: synthesis and application in characterization of protein-membrane interactions. J Colloid Interface Sci. 2011 Mar 1; 355(1):265-8.
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  84. Jo H, Culik RM, Korendovych IV, Degrado WF, Gai F. Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. Biochemistry. 2010 Dec 14; 49(49):10354-6.
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  85. Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA, Degrado WF. De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex. J Am Chem Soc. 2010 Nov 10; 132(44):15516-8.
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  86. Polishchuk AL, Lear JD, Ma C, Lamb RA, Pinto LH, Degrado WF. A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein. Biochemistry. 2010 Nov 30; 49(47):10061-71.
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  87. Ivankin A, Livne L, Mor A, Caputo GA, Degrado WF, Meron M, Lin B, Gidalevitz D. Role of the conformational rigidity in the design of biomimetic antimicrobial compounds. Angew Chem Int Ed Engl. 2010 Nov 2; 49(45):8462-5.
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  88. Fiorin G, Carnevale V, DeGrado WF. Structural biology. The flu's proton escort. Science. 2010 Oct 22; 330(6003):456-8.
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  89. Korendovych IV, Kim YH, Ryan AH, Lear JD, Degrado WF, Shandler SJ. Computational design of a self-assembling ß-peptide oligomer. Org Lett. 2010 Nov 19; 12(22):5142-5.
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  90. Donald JE, Zhu H, Litvinov RI, DeGrado WF, Bennett JS. Identification of interacting hot spots in the beta3 integrin stalk using comprehensive interface design. J Biol Chem. 2010 Dec 3; 285(49):38658-65.
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  91. Grigoryan G, Degrado WF. Probing designability via a generalized model of helical bundle geometry. J Mol Biol. 2011 Jan 28; 405(4):1079-100.
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  92. Lau WL, Degrado WF, Roder H. The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil. Biophys J. 2010 Oct 6; 99(7):2299-308.
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  93. Leiding T, Wang J, Martinsson J, DeGrado WF, Arsköld SP. Proton and cation transport activity of the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A. 2010 Aug 31; 107(35):15409-14.
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  94. Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15075-80.
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  95. Su Y, DeGrado WF, Hong M. Orientation, dynamics, and lipid interaction of an antimicrobial arylamide investigated by 19F and 31P solid-state NMR spectroscopy. J Am Chem Soc. 2010 Jul 7; 132(26):9197-205.
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  96. Zhu H, Metcalf DG, Streu CN, Billings PC, Degrado WF, Bennett JS. Specificity for homooligomer versus heterooligomer formation in integrin transmembrane helices. J Mol Biol. 2010 Sep 3; 401(5):882-91.
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  97. Lucumi E, Darling C, Jo H, Napper AD, Chandramohanadas R, Fisher N, Shone AE, Jing H, Ward SA, Biagini GA, DeGrado WF, Diamond SL, Greenbaum DC. Discovery of potent small-molecule inhibitors of multidrug-resistant Plasmodium falciparum using a novel miniaturized high-throughput luciferase-based assay. Antimicrob Agents Chemother. 2010 Sep; 54(9):3597-604.
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  98. Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF. Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc. 2010 Jun 2; 132(21):7312-20.
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  99. Montalvo G, Waegele MM, Shandler S, Gai F, DeGrado WF. Infrared signature and folding dynamics of a helical beta-peptide. J Am Chem Soc. 2010 Apr 28; 132(16):5616-8.
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  100. Goldberg SD, Clinthorne GD, Goulian M, DeGrado WF. Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ. Proc Natl Acad Sci U S A. 2010 May 4; 107(18):8141-6.
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  101. Fry HC, Lehmann A, Saven JG, DeGrado WF, Therien MJ. Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J Am Chem Soc. 2010 Mar 24; 132(11):3997-4005.
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  102. Cady SD, Schmidt-Rohr K, Wang J, Soto CS, Degrado WF, Hong M. Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature. 2010 Feb 4; 463(7281):689-92.
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  103. Balannik V, Carnevale V, Fiorin G, Levine BG, Lamb RA, Klein ML, Degrado WF, Pinto LH. Functional studies and modeling of pore-lining residue mutants of the influenza a virus M2 ion channel. Biochemistry. 2010 Feb 2; 49(4):696-708.
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  104. Tew GN, Scott RW, Klein ML, Degrado WF. De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications. Acc Chem Res. 2010 Jan 19; 43(1):30-9.
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  105. Balannik V, Wang J, Ohigashi Y, Jing X, Magavern E, Lamb RA, Degrado WF, Pinto LH. Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Biochemistry. 2009 Dec 22; 48(50):11872-82.
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  106. Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. Consensus motif for integrin transmembrane helix association. Proc Natl Acad Sci U S A. 2010 Jan 12; 107(2):703-8.
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  107. Balannik V, Obrdlik P, Inayat S, Steensen C, Wang J, Rausch JM, DeGrado WF, Kelety B, Pinto LH. Solid-supported membrane technology for the investigation of the influenza A virus M2 channel activity. Pflugers Arch. 2010 Mar; 459(4):593-605.
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  108. Faiella M, Andreozzi C, de Rosales RT, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A. An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol. 2009 Dec; 5(12):882-4.
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  109. San Antonio JD, Zoeller JJ, Habursky K, Turner K, Pimtong W, Burrows M, Choi S, Basra S, Bennett JS, DeGrado WF, Iozzo RV. A key role for the integrin alpha2beta1 in experimental and developmental angiogenesis. Am J Pathol. 2009 Sep; 175(3):1338-47.
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  110. Zhang Y, Kulp DW, Lear JD, DeGrado WF. Experimental and computational evaluation of forces directing the association of transmembrane helices. J Am Chem Soc. 2009 Aug 19; 131(32):11341-3.
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  111. Kuhlman B, DeGrado WF. Engineering and design: editorial overview. Curr Opin Struct Biol. 2009 Aug; 19(4):440-1.
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  112. He F, Nair GR, Soto CS, Chang Y, Hsu L, Ronzone E, DeGrado WF, Binns AN. Molecular basis of ChvE function in sugar binding, sugar utilization, and virulence in Agrobacterium tumefaciens. J Bacteriol. 2009 Sep; 191(18):5802-13.
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  113. Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF, Pinto LH. Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2009 Jul 28; 106(30):12283-8.
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  114. Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M. Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17; 131(23):8066-76.
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  115. Goldberg SD, Derr P, DeGrado WF, Goulian M. Engineered single- and multi-cell chemotaxis pathways in E. coli. Mol Syst Biol. 2009; 5:283.
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  116. Metcalf DG, Kulp DW, Bennett JS, DeGrado WF. Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer. J Mol Biol. 2009 Oct 2; 392(4):1087-101.
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  117. Choi S, Isaacs A, Clements D, Liu D, Kim H, Scott RW, Winkler JD, DeGrado WF. De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers. Proc Natl Acad Sci U S A. 2009 Apr 28; 106(17):6968-73.
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  118. Tang J, Yin H, Qiu J, Tucker MJ, DeGrado WF, Gai F. Using two fluorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide. J Am Chem Soc. 2009 Mar 25; 131(11):3816-7.
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  119. Signarvic RS, Degrado WF. Metal-binding dependent disruption of membranes by designed helices. J Am Chem Soc. 2009 Mar 11; 131(9):3377-84.
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  120. Liu F, Dumont C, Zhu Y, DeGrado WF, Gai F, Gruebele M. A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D. J Chem Phys. 2009 Feb 14; 130(6):061101.
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  121. Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF, Klein ML. Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):1069-74.
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  122. Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS, DeGrado WF. Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism. Proc Natl Acad Sci U S A. 2009 Jan 20; 106(3):719-24.
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  123. Bell CB, Calhoun JR, Bobyr E, Wei PP, Hedman B, Hodgson KO, Degrado WF, Solomon EI. Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes. Biochemistry. 2009 Jan 13; 48(1):59-73.
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  124. Kuroda K, Caputo GA, DeGrado WF. The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives. Chemistry. 2009; 15(5):1123-33.
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  125. Bissonnette ML, Donald JE, DeGrado WF, Jardetzky TS, Lamb RA. Functional analysis of the transmembrane domain in paramyxovirus F protein-mediated membrane fusion. J Mol Biol. 2009 Feb 13; 386(1):14-36.
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  126. Scott RW, DeGrado WF, Tew GN. De novo designed synthetic mimics of antimicrobial peptides. Curr Opin Biotechnol. 2008 Dec; 19(6):620-7.
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  127. Basani RB, Zhu H, Thornton MA, Soto CS, Degrado WF, Kowalska MA, Bennett JS, Poncz M. Species differences in small molecule binding to alpha IIb beta 3 are the result of sequence differences in 2 loops of the alpha IIb beta propeller. Blood. 2009 Jan 22; 113(4):902-10.
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  128. Nguyen PA, Soto CS, Polishchuk A, Caputo GA, Tatko CD, Ma C, Ohigashi Y, Pinto LH, DeGrado WF, Howard KP. pH-induced conformational change of the influenza M2 protein C-terminal domain. Biochemistry. 2008 Sep 23; 47(38):9934-6.
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  129. McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc. 2008 Sep 10; 130(36):11921-7.
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  130. Caputo GA, Litvinov RI, Li W, Bennett JS, Degrado WF, Yin H. Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry. 2008 Aug 19; 47(33):8600-6.
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  131. Shu JY, Tan C, DeGrado WF, Xu T. New design of helix bundle peptide-polymer conjugates. Biomacromolecules. 2008 Aug; 9(8):2111-7.
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  132. Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH, DeGrado WF. The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the M2 proton channel from the influenza A virus. Structure. 2008 Jul; 16(7):1067-76.
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  133. Grigoryan G, Degrado WF. Modest membrane hydrogen bonds deliver rich results. Nat Chem Biol. 2008 Jul; 4(7):393-4.
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  134. Moore DT, Berger BW, DeGrado WF. Protein-protein interactions in the membrane: sequence, structural, and biological motifs. Structure. 2008 Jul; 16(7):991-1001.
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  135. Calhoun JR, Bell CB, Smith TJ, Thamann TJ, DeGrado WF, Solomon EI. Oxygen reactivity of the biferrous site in the de novo designed four helix bundle peptide DFsc: nature of the "intermediate" and reaction mechanism. J Am Chem Soc. 2008 Jul 23; 130(29):9188-9.
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  136. Goldberg SD, Soto CS, Waldburger CD, Degrado WF. Determination of the physiological dimer interface of the PhoQ sensor domain. J Mol Biol. 2008 Jun 13; 379(4):656-65.
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  137. Ma C, Soto CS, Ohigashi Y, Taylor A, Bournas V, Glawe B, Udo MK, Degrado WF, Lamb RA, Pinto LH. Identification of the pore-lining residues of the BM2 ion channel protein of influenza B virus. J Biol Chem. 2008 Jun 6; 283(23):15921-31.
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  138. Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ, DeGrado WF. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure. 2008 Feb; 16(2):210-5.
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  139. Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 2008 Jan 31; 451(7178):596-9.
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  140. Tang J, Signarvic RS, DeGrado WF, Gai F. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry. 2007 Dec 4; 46(48):13856-63.
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  141. Choi S, Vilaire G, Marcinkiewicz C, Winkler JD, Bennett JS, DeGrado WF. Small molecule inhibitors of integrin alpha2beta1. J Med Chem. 2007 Nov 1; 50(22):5457-62.
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  142. Balakrishnan G, Hu Y, Bender GM, Getahun Z, DeGrado WF, Spiro TG. Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy. J Am Chem Soc. 2007 Oct 24; 129(42):12801-8.
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  143. Mukherjee S, Chowdhury P, DeGrado WF, Gai F. Site-specific hydration status of an amphipathic peptide in AOT reverse micelles. Langmuir. 2007 Oct 23; 23(22):11174-9.
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  144. Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc. 2007 Sep 5; 129(35):10732-40.
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  145. Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. J Phys Chem A. 2007 Aug 2; 111(30):6977-90.
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  146. Goodman CM, Choi S, Shandler S, DeGrado WF. Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol. 2007 May; 3(5):252-62.
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  147. Metcalf DG, Law PB, DeGrado WF. Mutagenesis data in the automated prediction of transmembrane helix dimers. Proteins. 2007 May 1; 67(2):375-84.
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  148. Cady SD, Goodman C, Tatko CD, DeGrado WF, Hong M. Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle. J Am Chem Soc. 2007 May 2; 129(17):5719-29.
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  149. Lee MH, Adams CS, Boettiger D, Degrado WF, Shapiro IM, Composto RJ, Ducheyne P. Adhesion of MC3T3-E1 cells to RGD peptides of different flanking residues: detachment strength and correlation with long-term cellular function. J Biomed Mater Res A. 2007 Apr; 81(1):150-60.
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  150. Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF. Computational design of peptides that target transmembrane helices. Science. 2007 Mar 30; 315(5820):1817-22.
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  151. Wang PC, Vilaire G, DeGrado WF, Bennett JS. Interactions of ADP-stimulated human platelets with PEGylated polystyrene substrates prepared by surface amidation. Colloids Surf B Biointerfaces. 2007 Aug 1; 58(2):225-30.
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  152. White TC, Berny MA, Robinson DK, Yin H, DeGrado WF, Hanson SR, McCarty OJ. The leech product saratin is a potent inhibitor of platelet integrin alpha2beta1 and von Willebrand factor binding to collagen. FEBS J. 2007 Mar; 274(6):1481-91.
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  153. Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM. Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer. Proc Natl Acad Sci U S A. 2006 Nov 7; 103(45):16740-5.
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  154. Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol. 2007 Mar; 157(3):444-53.
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  155. Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, Degrado WF, Bennett JS. Activation of platelet alphaIIbbeta3 by an exogenous peptide corresponding to the transmembrane domain of alphaIIb. J Biol Chem. 2006 Dec 1; 281(48):36732-41.
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  156. Bunagan MR, Cristian L, DeGrado WF, Gai F. Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding. Biochemistry. 2006 Sep 12; 45(36):10981-6.
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  157. Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. J Mol Biol. 2007 Feb 16; 366(2):436-48.
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  158. Walters RF, DeGrado WF. Helix-packing motifs in membrane proteins. Proc Natl Acad Sci U S A. 2006 Sep 12; 103(37):13658-63.
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  159. Wade H, Stayrook SE, Degrado WF. The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis. Angew Chem Int Ed Engl. 2006 Jul 24; 45(30):4951-4.
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  160. Yin H, Gerlach LO, Miller MW, Moore DT, Liu D, Vilaire G, Bennett JS, DeGrado WF. Arylamide derivatives as allosteric inhibitors of the integrin alpha2beta1/type I collagen interaction. Bioorg Med Chem Lett. 2006 Jul 1; 16(13):3380-2.
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  161. North B, Cristian L, Fu Stowell X, Lear JD, Saven JG, Degrado WF. Characterization of a membrane protein folding motif, the Ser zipper, using designed peptides. J Mol Biol. 2006 Jun 16; 359(4):930-9.
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  162. Litvinov RI, Vilaire G, Li W, DeGrado WF, Weisel JW, Bennett JS. Activation of individual alphaIIbbeta3 integrin molecules by disruption of transmembrane domain interactions in the absence of clustering. Biochemistry. 2006 Apr 18; 45(15):4957-64.
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  163. Tatko CD, Nanda V, Lear JD, Degrado WF. Polar networks control oligomeric assembly in membranes. J Am Chem Soc. 2006 Apr 5; 128(13):4170-1.
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  164. Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML, DeGrado WF. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study. J Phys Chem B. 2006 Mar 2; 110(8):3517-26.
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  165. Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. J Am Chem Soc. 2006 Feb 15; 128(6):1778-9.
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  166. Nanda V, DeGrado WF. Computational design of heterochiral peptides against a helical target. J Am Chem Soc. 2006 Jan 25; 128(3):809-16.
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  167. Yin H, Frederick KK, Liu D, Wand AJ, Degrado WF. Arylamide derivatives as peptidomimetic inhibitors of calmodulin. Org Lett. 2006 Jan 19; 8(2):223-5.
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  168. Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF. Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography. J Am Chem Soc. 2005 Dec 14; 127(49):17266-76.
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  169. Wei PP, Skulan AJ, Wade H, DeGrado WF, Solomon EI. Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity. J Am Chem Soc. 2005 Nov 23; 127(46):16098-106.
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  170. Engel DE, DeGrado WF. Alpha-alpha linking motifs and interhelical orientations. Proteins. 2005 Nov 1; 61(2):325-37.
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  171. Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. The design and evaluation of heparin-binding foldamers. Angew Chem Int Ed Engl. 2005 Oct 21; 44(41):6685-9.
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  172. Summa CM, Levitt M, Degrado WF. An atomic environment potential for use in protein structure prediction. J Mol Biol. 2005 Sep 30; 352(4):986-1001.
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  173. Maglio O, Nastri F, Calhoun JR, Lahr S, Wade H, Pavone V, DeGrado WF, Lombardi A. Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops. J Biol Inorg Chem. 2005 Aug; 10(5):539-49.
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  174. Wang T, Lau WL, DeGrado WF, Gai F. T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1. Biophys J. 2005 Dec; 89(6):4180-7.
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  175. Willcox PJ, Reinhart-King CA, Lahr SJ, DeGrado WF, Hammer DA. Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion. Biomaterials. 2005 Aug; 26(23):4757-66.
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  176. Kovalenko OV, Metcalf DG, DeGrado WF, Hemler ME. Structural organization and interactions of transmembrane domains in tetraspanin proteins. BMC Struct Biol. 2005; 5:11.
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  177. Nanda V, DeGrado WF. Automated use of mutagenesis data in structure prediction. Proteins. 2005 May 15; 59(3):454-66.
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  178. Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 2005 May 15; 59(3):496-509.
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  179. Slovic AM, Stayrook SE, North B, Degrado WF. X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils. J Mol Biol. 2005 May 6; 348(3):777-87.
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  180. Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF. De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc. 2005 Apr 27; 127(16):5804-5.
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  181. Cristian L, Nanda V, Lear JD, DeGrado WF. Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability. J Mol Biol. 2005 May 20; 348(5):1225-33.
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  182. Kuroda K, DeGrado WF. Amphiphilic polymethacrylate derivatives as antimicrobial agents. J Am Chem Soc. 2005 Mar 30; 127(12):4128-9.
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  183. Duong-Ly KC, Nanda V, Degrado WF, Howard KP. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci. 2005 Apr; 14(4):856-61.
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  184. Slovic AM, Lear JD, DeGrado WF. De novo design of a pentameric coiled-coil: decoding the motif for tetramer versus pentamer formation in water-soluble phospholamban. J Pept Res. 2005 Mar; 65(3):312-21.
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  185. Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO. Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Sci. 2005 Apr; 14(4):1019-24.
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  186. Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc. 2005 Feb 9; 127(5):1346-7.
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  187. Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS. A push-pull mechanism for regulating integrin function. Proc Natl Acad Sci U S A. 2005 Feb 1; 102(5):1424-9.
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  188. Stouffer AL, Nanda V, Lear JD, DeGrado WF. Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. J Mol Biol. 2005 Mar 18; 347(1):169-79.
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  189. Lahr SJ, Engel DE, Stayrook SE, Maglio O, North B, Geremia S, Lombardi A, DeGrado WF. Analysis and design of turns in alpha-helical hairpins. J Mol Biol. 2005 Mar 11; 346(5):1441-54.
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  190. Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF. Artificial diiron proteins: from structure to function. Biopolymers. 2005; 80(2-3):264-78.
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  191. Ghirlanda G, Hilcove SA, Pidikiti R, Johansson JS, Lear JD, Degrado WF, Eckenhoff RG. Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide. FEBS Lett. 2004 Dec 3; 578(1-2):140-4.
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  192. Nanda V, Degrado WF. Simulated evolution of emergent chiral structures in polyalanine. J Am Chem Soc. 2004 Nov 10; 126(44):14459-67.
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  193. Doerksen RJ, Chen B, Liu D, Tew GN, Degrado WF, Klein ML. Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers. Chemistry. 2004 Oct 11; 10(20):5008-16.
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  194. Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J. 2004 Nov; 87(5):3421-9.
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  195. Kaplan J, DeGrado WF. De novo design of catalytic proteins. Proc Natl Acad Sci U S A. 2004 Aug 10; 101(32):11566-70.
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  196. Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol. 2004 Aug; 14(4):465-79.
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  197. Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ, DeGrado WF. De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1. J Am Chem Soc. 2004 Jul 7; 126(26):8141-7.
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  198. Li R, Bennett JS, Degrado WF. Structural basis for integrin alphaIIbbeta3 clustering. Biochem Soc Trans. 2004 Jun; 32(Pt3):412-5.
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  199. Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F. A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides. J Am Chem Soc. 2004 Apr 28; 126(16):5078-9.
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  200. Engel DE, DeGrado WF. Amino acid propensities are position-dependent throughout the length of alpha-helices. J Mol Biol. 2004 Apr 9; 337(5):1195-205.
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  201. Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes. J Biol Chem. 2004 Jun 18; 279(25):26666-73.
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  202. Liu D, Choi S, Chen B, Doerksen RJ, Clements DJ, Winkler JD, Klein ML, DeGrado WF. Nontoxic membrane-active antimicrobial arylamide oligomers. Angew Chem Int Ed Engl. 2004 Feb 20; 43(9):1158-62.
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  203. Slovic AM, Kono H, Lear JD, Saven JG, DeGrado WF. Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci U S A. 2004 Feb 17; 101(7):1828-33.
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  204. Lau WL, Ege DS, Lear JD, Hammer DA, DeGrado WF. Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization. Biophys J. 2004 Jan; 86(1 Pt 1):272-84.
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  205. Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG. Computational design and characterization of a monomeric helical dinuclear metalloprotein. J Mol Biol. 2003 Dec 12; 334(5):1101-15.
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  206. Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F. Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15486-91.
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  207. Cristian L, Lear JD, DeGrado WF. Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers. Proc Natl Acad Sci U S A. 2003 Dec 9; 100(25):14772-7.
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  208. Signarvic RS, DeGrado WF. De novo design of a molecular switch: phosphorylation-dependent association of designed peptides. J Mol Biol. 2003 Nov 14; 334(1):1-12.
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  209. Cristian L, Lear JD, DeGrado WF. Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange. Protein Sci. 2003 Aug; 12(8):1732-40.
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  210. Lear JD, Gratkowski H, Adamian L, Liang J, DeGrado WF. Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry. 2003 Jun 3; 42(21):6400-7.
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  211. DeGrado WF. Computational biology: Biosensor design. Nature. 2003 May 8; 423(6936):132-3.
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  212. Li R, Mitra N, Gratkowski H, Vilaire G, Litvinov R, Nagasami C, Weisel JW, Lear JD, DeGrado WF, Bennett JS. Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations. Science. 2003 May 2; 300(5620):795-8.
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  213. DeGrado WF, Gratkowski H, Lear JD. How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci. 2003 Apr; 12(4):647-65.
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  214. Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF. Preorganization of molecular binding sites in designed diiron proteins. Proc Natl Acad Sci U S A. 2003 Apr 1; 100(7):3772-7.
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  215. Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF. The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Sci. 2003 Mar; 12(3):520-31.
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  216. Slovic AM, Summa CM, Lear JD, DeGrado WF. Computational design of a water-soluble analog of phospholamban. Protein Sci. 2003 Feb; 12(2):337-48.
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  217. DeGrado WF, Di Costanzo L, Geremia S, Lombardi A, Pavone V, Randaccio L. Sliding helix and change of coordination geometry in a model di-MnII protein. Angew Chem Int Ed Engl. 2003 Jan 27; 42(4):417-20.
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  218. Getahun Z, Huang CY, Wang T, De León B, DeGrado WF, Gai F. Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc. 2003 Jan 15; 125(2):405-11.
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  219. Papoian GA, DeGrado WF, Klein ML. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor. J Am Chem Soc. 2003 Jan 15; 125(2):560-9.
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  220. Li R, Hoess RH, Bennett JS, DeGrado WF. Use of phage display to probe the evolution of binding specificity and affinity in integrins. Protein Eng. 2003 Jan; 16(1):65-72.
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  221. Li R, Babu CR, Valentine K, Lear JD, Wand AJ, Bennett JS, DeGrado WF. Characterization of the monomeric form of the transmembrane and cytoplasmic domains of the integrin beta 3 subunit by NMR spectroscopy. Biochemistry. 2002 Dec 31; 41(52):15618-24.
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  222. Huang CY, He S, DeGrado WF, McCafferty DG, Gai F. Light-induced helix formation. J Am Chem Soc. 2002 Oct 30; 124(43):12674-5.
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  223. Cheng RP, DeGrado WF. Long-range interactions stabilize the fold of a non-natural oligomer. J Am Chem Soc. 2002 Oct 2; 124(39):11564-5.
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  224. Gratkowski H, Dai QH, Wand AJ, DeGrado WF, Lear JD. Cooperativity and specificity of association of a designed transmembrane peptide. Biophys J. 2002 Sep; 83(3):1613-9.
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  225. Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol. 2002 Aug 30; 321(5):923-38.
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  226. Howard KP, Lear JD, DeGrado WF. Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8568-72.
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  227. Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF. A hierarchic approach to the design of hexameric helical barrels. J Mol Biol. 2002 May 24; 319(1):243-53.
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  228. Tew GN, Liu D, Chen B, Doerksen RJ, Kaplan J, Carroll PJ, Klein ML, DeGrado WF. De novo design of biomimetic antimicrobial polymers. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5110-4.
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  229. Marsh EN, DeGrado WF. Noncovalent self-assembly of a heterotetrameric diiron protein. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5150-4.
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  230. Huang CY, Getahun Z, Zhu Y, Klemke JW, DeGrado WF, Gai F. Helix formation via conformation diffusion search. Proc Natl Acad Sci U S A. 2002 Mar 5; 99(5):2788-93.
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  231. Di Costanzo L, Wade H, Geremia S, Randaccio L, Pavone V, DeGrado WF, Lombardi A. Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center. J Am Chem Soc. 2001 Dec 26; 123(51):12749-57.
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  232. Cheng RP, Suich DJ, Cheng H, Roder H, DeGrado WF. Template-constrained somatostatin analogues: a biphenyl linker induces a type-V' turn. J Am Chem Soc. 2001 Dec 19; 123(50):12710-1.
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  233. Huang CY, Getahun Z, Wang T, DeGrado WF, Gai F. Time-resolved infrared study of the helix-coil transition using (13)C-labeled helical peptides. J Am Chem Soc. 2001 Dec 5; 123(48):12111-2.
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  234. Li R, Babu CR, Lear JD, Wand AJ, Bennett JS, DeGrado WF. Oligomerization of the integrin alphaIIbbeta3: roles of the transmembrane and cytoplasmic domains. Proc Natl Acad Sci U S A. 2001 Oct 23; 98(22):12462-7.
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  235. Cheng RP, Gellman SH, DeGrado WF. beta-Peptides: from structure to function. Chem Rev. 2001 Oct; 101(10):3219-32.
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  236. Huang CY, Klemke JW, Getahun Z, DeGrado WF, Gai F. Temperature-dependent helix-coil transition of an alanine based peptide. J Am Chem Soc. 2001 Sep 26; 123(38):9235-8.
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  237. North B, Summa CM, Ghirlanda G, DeGrado WF. D(n)-symmetrical tertiary templates for the design of tubular proteins. J Mol Biol. 2001 Aug 31; 311(5):1081-90.
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  238. Walsh ST, Lee AL, DeGrado WF, Wand AJ. Dynamics of a de novo designed three-helix bundle protein studied by 15N, 13C, and 2H NMR relaxation methods. Biochemistry. 2001 Aug 14; 40(32):9560-9.
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  239. Liu D, DeGrado WF. De novo design, synthesis, and characterization of antimicrobial beta-peptides. J Am Chem Soc. 2001 Aug 8; 123(31):7553-9.
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  240. Lear JD, Gratkowski H, DeGrado WF. De novo design, synthesis and characterization of membrane-active peptides. Biochem Soc Trans. 2001 Aug; 29(Pt 4):559-64.
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  241. Cheng RP, DeGrado WF. De novo design of a monomeric helical beta-peptide stabilized by electrostatic interactions. J Am Chem Soc. 2001 May 30; 123(21):5162-3.
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  242. Pasternak A, Kaplan J, Lear JD, Degrado WF. Proton and metal ion-dependent assembly of a model diiron protein. Protein Sci. 2001 May; 10(5):958-69.
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  243. Tang Y, Ghirlanda G, Vaidehi N, Kua J, Mainz DT, Goddard III WA, DeGrado WF, Tirrell DA. Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine. Biochemistry. 2001 Mar 6; 40(9):2790-6.
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  244. Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF, Eisenberg D. Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc Natl Acad Sci U S A. 2001 Feb 13; 98(4):1404-9.
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  245. Gratkowski H, Lear JD, DeGrado WF. Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci U S A. 2001 Jan 30; 98(3):880-5.
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  246. Walsh ST, Sukharev VI, Betz SF, Vekshin NL, DeGrado WF. Hydrophobic core malleability of a de novo designed three-helix bundle protein. J Mol Biol. 2001 Jan 12; 305(2):361-73.
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  247. Dalby PA, Hoess RH, DeGrado WF. Evolution of binding affinity in a WW domain probed by phage display. Protein Sci. 2000 Dec; 9(12):2366-76.
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  248. Salom D, Hill BR, Lear JD, DeGrado WF. pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry. 2000 Nov 21; 39(46):14160-70.
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  249. Talaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF, Hochstrasser RM. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc Natl Acad Sci U S A. 2000 Nov 21; 97(24):13021-6.
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  250. O'Neil KT, Bach AC, DeGrado WF. Structural consequences of an amino acid deletion in the B1 domain of protein G. Proteins. 2000 Nov 15; 41(3):323-33.
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  251. Hill RB, Raleigh DP, Lombardi A, DeGrado WF. De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res. 2000 Nov; 33(11):745-54.
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  252. Suich DJ, Mousa SA, Singh G, Liapakis G, Reisine T, DeGrado WF. Template-constrained cyclic peptide analogues of somatostatin: subtype-selective binding to somatostatin receptors and antiangiogenic activity. Bioorg Med Chem. 2000 Sep; 8(9):2229-41.
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  253. Helluin O, Chan C, Vilaire G, Mousa S, DeGrado WF, Bennett JS. The activation state of alphavbeta 3 regulates platelet and lymphocyte adhesion to intact and thrombin-cleaved osteopontin. J Biol Chem. 2000 Jun 16; 275(24):18337-43.
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  254. Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V, DeGrado WF. Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci U S A. 2000 Jun 6; 97(12):6298-305.
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  255. Hill RB, DeGrado WF. A polar, solvent-exposed residue can be essential for native protein structure. Structure. 2000 May 15; 8(5):471-9.
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  256. Choma C, Gratkowski H, Lear JD, DeGrado WF. Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol. 2000 Feb; 7(2):161-6.
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  257. Kochendoerfer GG, Salom D, Lear JD, Wilk-Orescan R, Kent SB, DeGrado WF. Total chemical synthesis of the integral membrane protein influenza A virus M2: role of its C-terminal domain in tetramer assembly. Biochemistry. 1999 Sep 14; 38(37):11905-13.
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  258. DeGrado WF, Schneider JP, Hamuro Y. The twists and turns of beta-peptides. J Pept Res. 1999 Sep; 54(3):206-17.
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  259. Summa CM, Lombardi A, Lewis M, DeGrado WF. Tertiary templates for the design of diiron proteins. Curr Opin Struct Biol. 1999 Aug; 9(4):500-8.
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  260. Patterson WR, Anderson DH, DeGrado WF, Cascio D, Eisenberg D. Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1. Protein Sci. 1999 Jul; 8(7):1410-22.
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  261. Walsh ST, Cheng H, Bryson JW, Roder H, DeGrado WF. Solution structure and dynamics of a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A. 1999 May 11; 96(10):5486-91.
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  262. Rockwell AL, Rafalski M, Pitts WJ, Batt DG, Petraitis JJ, DeGrado WF, Mousa S, Jadhav PK. Rapid synthesis of RGD mimetics with isoxazoline scaffolds on solid phase: identification of alphavbeta3 antagonists lead compounds. Bioorg Med Chem Lett. 1999 Apr 5; 9(7):937-42.
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  263. Hamm P, Lim M, DeGrado WF, Hochstrasser RM. The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure. Proc Natl Acad Sci U S A. 1999 Mar 2; 96(5):2036-41.
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  264. Gandhi CS, Shuck K, Lear JD, Dieckmann GR, DeGrado WF, Lamb RA, Pinto LH. Cu(II) inhibition of the proton translocation machinery of the influenza A virus M2 protein. J Biol Chem. 1999 Feb 26; 274(9):5474-82.
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  265. Dieckmann GR, Lear JD, Zhong Q, Klein ML, DeGrado WF, Sharp KA. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophys J. 1999 Feb; 76(2):618-30.
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  266. DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A. De novo design and structural characterization of proteins and metalloproteins. Annu Rev Biochem. 1999; 68:779-819.
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  267. Xue CB, Roderick J, Mousa S, Olson RE, DeGrado WF. Synthesis and antiplatelet effects of an isoxazole series of glycoprotein IIb/IIIa antagonists. Bioorg Med Chem Lett. 1998 Dec 15; 8(24):3499-504.
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  268. Ghirlanda G, Lear JD, Lombardi A, DeGrado WF. From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin. J Mol Biol. 1998 Aug 14; 281(2):379-91.
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  269. Dieckmann GR, McRorie DK, Lear JD, Sharp KA, DeGrado WF, Pecoraro VL. The role of protonation and metal chelation preferences in defining the properties of mercury-binding coiled coils. J Mol Biol. 1998 Jul 31; 280(5):897-912.
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  270. Bryson JW, Desjarlais JR, Handel TM, DeGrado WF. From coiled coils to small globular proteins: design of a native-like three-helix bundle. Protein Sci. 1998 Jun; 7(6):1404-14.
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  271. Cherney RJ, Wang L, Meyer DT, Xue CB, Wasserman ZR, Hardman KD, Welch PK, Covington MB, Copeland RA, Arner EC, DeGrado WF, Decicco CP. Macrocyclic amino carboxylates as selective MMP-8 inhibitors. J Med Chem. 1998 May 21; 41(11):1749-51.
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  272. Xue CB, He X, Roderick J, DeGrado WF, Cherney RJ, Hardman KD, Nelson DJ, Copeland RA, Jaffee BD, Decicco CP. Design and synthesis of cyclic inhibitors of matrix metalloproteinases and TNF-alpha production. J Med Chem. 1998 May 21; 41(11):1745-8.
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  273. Schneider JP, Lombardi A, DeGrado WF. Analysis and design of three-stranded coiled coils and three-helix bundles. Fold Des. 1998; 3(2):R29-40.
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  274. Forrest LR, DeGrado WF, Dieckmann GR, Sansom MS. Two models of the influenza A M2 channel domain: verification by comparison. Fold Des. 1998; 3(6):443-8.
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  275. Pinto LH, Dieckmann GR, Gandhi CS, Papworth CG, Braman J, Shaughnessy MA, Lear JD, Lamb RA, DeGrado WF. A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity. Proc Natl Acad Sci U S A. 1997 Oct 14; 94(21):11301-6.
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  276. DeGrado WF. Proteins from scratch. Science. 1997 Oct 3; 278(5335):80-1.
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  277. Dieckmann GR, DeGrado WF. Modeling transmembrane helical oligomers. Curr Opin Struct Biol. 1997 Aug; 7(4):486-94.
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  278. Xue CB, Roderick J, Jackson S, Rafalski M, Rockwell A, Mousa S, Olson RE, DeGrado WF. Design, synthesis, and in vitro activities of benzamide-core glycoprotein IIb/IIIa antagonists: 2,3-diaminopropionic acid derivatives as surrogates of aspartic acid. Bioorg Med Chem. 1997 Apr; 5(4):693-705.
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  279. Bennett JS, Chan C, Vilaire G, Mousa SA, DeGrado WF. Agonist-activated alphavbeta3 on platelets and lymphocytes binds to the matrix protein osteopontin. J Biol Chem. 1997 Mar 28; 272(13):8137-40.
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  280. Betz SF, Liebman PA, DeGrado WF. De novo design of native proteins: characterization of proteins intended to fold into antiparallel, rop-like, four-helix bundles. Biochemistry. 1997 Mar 4; 36(9):2450-8.
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  281. Ogihara NL, Weiss MS, Degrado WF, Eisenberg D. The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies. Protein Sci. 1997 Jan; 6(1):80-8.
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  282. Boice JA, Dieckmann GR, DeGrado WF, Fairman R. Thermodynamic analysis of a designed three-stranded coiled coil. Biochemistry. 1996 Nov 19; 35(46):14480-5.
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  283. Mousa SA, Forsythe M, Lorelli W, Bozarth J, Xue CB, Wityak J, Sielecki TM, Olson RE, DeGrado W, Kapil R, Hussain M, Wexler R, Thoolen MJ, Reilly TM. Novel nonpeptide antiplatelet glycoprotein IIb/IIIa receptor antagonist, DMP754: receptor binding affinity and specificity. Coron Artery Dis. 1996 Oct; 7(10):767-74.
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  284. Betz SF, Bryson JW, Passador MC, Brown RJ, O'Neil KT, DeGrado WF. Expression of de novo designed alpha-helical bundles. Acta Chem Scand. 1996 Aug; 50(8):688-96.
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  285. DeGrado WF, Sosnick TR. Protein minimization: downsizing through mutation. Proc Natl Acad Sci U S A. 1996 Jun 11; 93(12):5680-1.
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  286. Betz SF, DeGrado WF. Controlling topology and native-like behavior of de novo-designed peptides: design and characterization of antiparallel four-stranded coiled coils. Biochemistry. 1996 May 28; 35(21):6955-62.
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  287. Zhou HX, Hoess RH, DeGrado WF. In vitro evolution of thermodynamically stable turns. Nat Struct Biol. 1996 May; 3(5):446-51.
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  288. Sosnick TR, Jackson S, Wilk RR, Englander SW, DeGrado WF. The role of helix formation in the folding of a fully alpha-helical coiled coil. Proteins. 1996 Apr; 24(4):427-32.
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  289. Mousa SA, DeGrado WF, Mu DX, Kapil RP, Lucchesi BR, Reilly TM. Oral antiplatelet, antithrombotic efficacy of DMP 728, a novel platelet GPIIb/IIIa antagonist. Circulation. 1996 Feb 1; 93(3):537-43.
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  290. Lombardi A, Bryson JW, DeGrado WF. De novo design of heterotrimeric coiled coils. Biopolymers. 1996; 40(5):495-504.
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  291. Betz SF, Raleigh DP, DeGrado WF, Lovejoy B, Anderson D, Ogihara N, Eisenberg D. Crystallization of a designed peptide from a molten globule ensemble. Fold Des. 1996; 1(1):57-64.
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  292. Bryson JW, Betz SF, Lu HS, Suich DJ, Zhou HX, O'Neil KT, DeGrado WF. Protein design: a hierarchic approach. Science. 1995 Nov 10; 270(5238):935-41.
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  293. Betz SF, Bryson JW, DeGrado WF. Native-like and structurally characterized designed alpha-helical bundles. Curr Opin Struct Biol. 1995 Aug; 5(4):457-63.
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  294. Betz S, Fairman R, O'Neil K, Lear J, Degrado W. Design of two-stranded and three-stranded coiled-coil peptides. Philos Trans R Soc Lond B Biol Sci. 1995 Apr 29; 348(1323):81-8.
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  295. O'Neil KT, Hoess RH, Raleigh DP, DeGrado WF. Thermodynamic genetics of the folding of the B1 immunoglobulin-binding domain from streptococcal protein G. Proteins. 1995 Jan; 21(1):11-21.
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  296. Regan L, Rockwell A, Wasserman Z, DeGrado W. Disulfide crosslinks to probe the structure and flexibility of a designed four-helix bundle protein. Protein Sci. 1994 Dec; 3(12):2419-27.
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  297. Farid RS, Robertson DE, Moser CC, Pilloud D, DeGrado WF, Dutton PL. Design and synthesis of simplified energy-converting proteins. Biochem Soc Trans. 1994 Aug; 22(3):689-93.
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  298. Kienker PK, DeGrado WF, Lear JD. A helical-dipole model describes the single-channel current rectification of an uncharged peptide ion channel. Proc Natl Acad Sci U S A. 1994 May 24; 91(11):4859-63.
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  299. Robertson DE, Farid RS, Moser CC, Urbauer JL, Mulholland SE, Pidikiti R, Lear JD, Wand AJ, DeGrado WF, Dutton PL. Design and synthesis of multi-haem proteins. Nature. 1994 Mar 31; 368(6470):425-32.
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  300. O'Neil KT, DeGrado WF, Mousa SA, Ramachandran N, Hoess RH. Identification of recognition sequences of adhesion molecules using phage display technology. Methods Enzymol. 1994; 245:370-86.
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  301. Fairman R, Beran-Steed RK, Anthony-Cahill SJ, Lear JD, Stafford WF, DeGrado WF, Benfield PA, Brenner SL. Multiple oligomeric states regulate the DNA binding of helix-loop-helix peptides. Proc Natl Acad Sci U S A. 1993 Nov 15; 90(22):10429-33.
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  302. DeGrado WF. Peptide engineering. Catalytic molten globules. Nature. 1993 Oct 7; 365(6446):488-9.
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  303. Handel TM, Williams SA, DeGrado WF. Metal ion-dependent modulation of the dynamics of a designed protein. Science. 1993 Aug 13; 261(5123):879-85.
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  304. Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D. Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science. 1993 Feb 26; 259(5099):1288-93.
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  305. O'Neil KT, Hoess RH, Jackson SA, Ramachandran NS, Mousa SA, DeGrado WF. Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library. Proteins. 1992 Dec; 14(4):509-15.
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  306. Rao U, Teeter MM, Erickson-Viitanen S, DeGrado WF. Calmodulin binding to alpha 1-purothionin: solution binding and modeling of the complex. Proteins. 1992 Oct; 14(2):127-38.
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  307. Lovejoy B, Akerfeldt KS, DeGrado WF, Eisenberg D. Crystallization of proton channel peptides. Protein Sci. 1992 Aug; 1(8):1073-7.
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  308. Chung LA, Lear JD, DeGrado WF. Fluorescence studies of the secondary structure and orientation of a model ion channel peptide in phospholipid vesicles. Biochemistry. 1992 Jul 21; 31(28):6608-16.
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  309. Lovejoy B, Le TC, Lüthy R, Cascio D, O'Neil KT, DeGrado WF, Eisenberg D. X-ray grade crystals of a designed alpha-helical coiled coil. Protein Sci. 1992 Jul; 1(7):956-7.
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  310. Epand RM, Cheetham JJ, Epand RF, Yeagle PL, Richardson CD, Rockwell A, Degrado WF. Peptide models for the membrane destabilizing actions of viral fusion proteins. Biopolymers. 1992 Apr; 32(4):309-14.
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  311. Anthony-Cahill SJ, Benfield PA, Fairman R, Wasserman ZR, Brenner SL, Stafford WF, Altenbach C, Hubbell WL, DeGrado WF. Molecular characterization of helix-loop-helix peptides. Science. 1992 Feb 21; 255(5047):979-83.
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  312. Rafalski M, Ortiz A, Rockwell A, van Ginkel LC, Lear JD, DeGrado WF, Wilschut J. Membrane fusion activity of the influenza virus hemagglutinin: interaction of HA2 N-terminal peptides with phospholipid vesicles. Biochemistry. 1991 Oct 22; 30(42):10211-20.
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  313. O'Neil KT, Shuman JD, Ampe C, DeGrado WF. DNA-induced increase in the alpha-helical content of C/EBP and GCN4. Biochemistry. 1991 Sep 17; 30(37):9030-4.
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  314. O'Neil KT, DeGrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science. 1990 Nov 2; 250(4981):646-51.
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  315. Rafalski M, Lear JD, DeGrado WF. Phospholipid interactions of synthetic peptides representing the N-terminus of HIV gp41. Biochemistry. 1990 Aug 28; 29(34):7917-22.
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  316. O'Neil KT, Hoess RH, DeGrado WF. Design of DNA-binding peptides based on the leucine zipper motif. Science. 1990 Aug 17; 249(4970):774-8.
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  317. Hill CP, Anderson DH, Wesson L, DeGrado WF, Eisenberg D. Crystal structure of alpha 1: implications for protein design. Science. 1990 Aug 3; 249(4968):543-6.
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  318. O'Neil KT, DeGrado WF. How calmodulin binds its targets: sequence independent recognition of amphiphilic alpha-helices. Trends Biochem Sci. 1990 Feb; 15(2):59-64.
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  319. DeGrado WF, Lear JD. Conformationally constrained alpha-helical peptide models for protein ion channels. Biopolymers. 1990 Jan; 29(1):205-13.
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  320. O'Neil KT, Erickson-Viitanen S, DeGrado WF. Photolabeling of calmodulin with basic, amphiphilic alpha-helical peptides containing p-benzoylphenylalanine. J Biol Chem. 1989 Aug 25; 264(24):14571-8.
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  321. Degrado WF, May SW. Emil Thomas Kaiser 1938-1988. J Mol Recognit. 1989 Apr; 1(4):i-ii.
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  322. DeGrado WF, Wasserman ZR, Lear JD. Protein design, a minimalist approach. Science. 1989 Feb 3; 243(4891):622-8.
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  323. Degrado WF. Contributions of chemistry: biotechnology and materials science. Science. 1989 Jan 6; 243(4887):102-3.
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  324. O'Neil KT, DeGrado WF. The interaction of calmodulin with fluorescent and photoreactive model peptides: evidence for a short interdomain separation. Proteins. 1989; 6(3):284-93.
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  325. Regan L, DeGrado WF. Characterization of a helical protein designed from first principles. Science. 1988 Aug 19; 241(4868):976-8.
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  326. Lear JD, Wasserman ZR, DeGrado WF. Synthetic amphiphilic peptide models for protein ion channels. Science. 1988 May 27; 240(4856):1177-81.
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  327. Degrado WF. Design of peptides and proteins. Adv Protein Chem. 1988; 39:51-124.
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  328. O'Neil KT, Wolfe HR, Erickson-Viitanen S, DeGrado WF. Fluorescence properties of calmodulin-binding peptides reflect alpha-helical periodicity. Science. 1987 Jun 12; 236(4807):1454-6.
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  329. Lear JD, DeGrado WF. Membrane binding and conformational properties of peptides representing the NH2 terminus of influenza HA-2. J Biol Chem. 1987 May 15; 262(14):6500-5.
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  330. Erickson-Viitanen S, DeGrado WF. Recognition and characterization of calmodulin-binding sequences in peptides and proteins. Methods Enzymol. 1987; 139:455-78.
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  331. DeGrado WF, Regan L, Ho SP. The design of a four-helix bundle protein. Cold Spring Harb Symp Quant Biol. 1987; 52:521-6.
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  332. DeGrado WF, Erickson-Viitanen S, Wolfe HR, O'Neil KT. Predicted calmodulin-binding sequence in the gamma subunit of phosphorylase b kinase. Proteins. 1987; 2(1):20-33.
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  333. Eisenberg D, Wilcox W, Eshita SM, Pryciak PM, Ho SP, DeGrado WF. The design, synthesis, and crystallization of an alpha-helical peptide. Proteins. 1986 Sep; 1(1):16-22.
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  334. Kauer JC, Erickson-Viitanen S, Wolfe HR, DeGrado WF. p-Benzoyl-L-phenylalanine, a new photoreactive amino acid. Photolabeling of calmodulin with a synthetic calmodulin-binding peptide. J Biol Chem. 1986 Aug 15; 261(23):10695-700.
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  335. Cheng YS, Becker-Manley MF, Nguyen TD, DeGrado WF, Jonak GJ. Nonidentical induction of the guanylate binding protein and the 56K protein by type I and type II interferons. J Interferon Res. 1986 Aug; 6(4):417-27.
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  336. O'Neil KT, DeGrado WF. A predicted structure of calmodulin suggests an electrostatic basis for its function. Proc Natl Acad Sci U S A. 1985 Aug; 82(15):4954-8.
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  337. Briggs MS, Gierasch LM, Zlotnick A, Lear JD, DeGrado WF. In vivo function and membrane binding properties are correlated for Escherichia coli lamB signal peptides. Science. 1985 May 31; 228(4703):1096-9.
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  338. Cox JA, Comte M, Fitton JE, DeGrado WF. The interaction of calmodulin with amphiphilic peptides. J Biol Chem. 1985 Feb 25; 260(4):2527-34.
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  339. DeGrado WF, Prendergast FG, Wolfe HR, Cox JA. The design, synthesis, and characterization of tight-binding inhibitors of calmodulin. J Cell Biochem. 1985; 29(2):83-93.
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  340. Chow TP, DeGrado WF, Knight E. Antibodies to synthetic peptides of human interferon-beta. Use in biosynthetic studies. J Biol Chem. 1984 Oct 10; 259(19):12220-5.
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  341. Persson H, Hennighausen L, Taub R, DeGrado W, Leder P. Antibodies to human c-myc oncogene product: evidence of an evolutionarily conserved protein induced during cell proliferation. Science. 1984 Aug 17; 225(4663):687-93.
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  342. Sigal IS, DeGrado WF, Thomas BJ, Petteway SR. Purification and properties of thiol beta-lactamase. A mutant of pBR322 beta-lactamase in which the active site serine has been replaced with cysteine. J Biol Chem. 1984 Apr 25; 259(8):5327-32.
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  343. Robb RJ, Kutny RM, Panico M, Morris H, DeGrado WF, Chowdhry V. Posttranslational modification of human T-cell growth factor. Biochem Biophys Res Commun. 1983 Nov 15; 116(3):1049-55.
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  344. DeGrado WF, Wasserman ZR, Chowdhry V. Sequence and structural homologies among type I and type II interferons. Nature. 1982 Nov 25; 300(5890):379-81.
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  345. DeGrado WF, Musso GF, Lieber M, Kaiser ET, Kézdy FJ. Kinetics and mechanism of hemolysis induced by melittin and by a synthetic melittin analogue. Biophys J. 1982 Jan; 37(1):329-38.
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