Because James Wells is a common name, his publications are also manually curated in PubMed:
2025
Zhao F, Wu Y, Schaefer K, Zhang Y, Miao K, Yao Z, Ganjave SD, Kumru KS, Peters-Clarke TM, Inague A, Olzmann JA, Leung KK, Wells JA. Low-density lipoprotein receptor-targeting chimeras for membrane protein degradation and enhanced drug delivery. bioRxiv, 2025 Jun 9. DOI: 10.1101/2025.06.06.658366 (Preprint)
Pluvinage JV, Ngo T, Fouassier C, McDonagh M, Holmes BB, Bartley CM, Kondapavulur S, Hurabielle C, Bodansky A, Pai V, Hinman S, Aslanpour A, Alvarenga BD, Zorn KC, Zamecnik C, McCann A, Asencor AI, Huynh T, Browne W, Tubati A, Haney MS, Douglas VC, Louine M, Cree BAC, Hauser SL, Seeley W, Baranzini SE, Wells JA, Spudich S, Farhadian S, Ramachandran PS, Gillum L, Hales CM, Zikherman J, Anderson MS, Yazdany J, Smith B, Nath A, Suh G, Flanagan EP, Green AJ, Green R, Gelfand JM, DeRisi JL, Pleasure SJ, Wilson MR. Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency. Sci Transl Med. 2024 Jun 26;16(753):eadl3758. Epub 2024 Jun 26. PMID: 38924428; PMCID: PMC11520464. DOI: 10.1126/scitranslmed.adl3758
Lui I, Schaefer K, Kirkemo LL, Zhou J, Perera RM, Leung KK, Wells JA. Hypoxia Induces Extensive Protein and Proteolytic Remodeling of the Cell Surface in Pancreatic Adenocarcinoma (PDAC) Cell Lines. J Proteome Res. 2025 Jun 6;24(6):2791-2800. Epub 2025 May 1. PMID: 40312771; PMCID: PMC12161487. DOI: 10.1021/acs.jproteome.4c01037
Teter OM, McQuade A, Hagan V, Liang W, Dräger NM, Sattler SM, Holmes BB, Castillo VC, Papakis V, Leng K, Boggess S, Nowakowski TJ, Wells J, Kampmann M. CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning. bioRxiv [Preprint]. 2024 Nov 17:2024.06.01.596962. doi: 10.1101/2024.06.01.596962. Update in: Mol Psychiatry. 2025 Apr 6. PMID: 39605704; PMCID: PMC11601228. DOI: 10.1038/s41380-025-02997-z
Leung KK, Schaefer K, Lin Z, Yao Z, Wells JA. Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome. Chem Rev. 2025 Apr 23;125(8):4069-4110. Epub 2025 Apr 3. PMID: 40178992; PMCID: PMC12022999. DOI: 10.1021/acs.chemrev.4c00554
Ngo W, Peukes J, Baldwin A, Xue ZW, Hwang S, Stickels RR, Lin Z, Satpathy AT, Wells JA, Schekman R, Nogales E, Doudna JA. Mechanism-guided engineering of a minimal biological particle for genome editing. Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2413519121. Epub 2024 Dec 30. PMID: 39793042; PMCID: PMC11725915. DOI: 10.1073/pnas.2413519121
2024
Lin Z, Ngo W, Chou YT, Wu H, Susa KJ, Jun YW, Bivona TG, Doudna JA, Wells JA. Spatiotemporal photocatalytic proximity labeling proteomics reveals ligand-activated extracellular and intracellular EGFR neighborhoods. bioRxiv. 2024:2024-12. DOI: https://doi.org/10.1101/2024.12.21.629933
Delaveris CS, Kong S, Glasgow J, Loudermilk RP, Kirkemo LL, Zhao F, Salangsang F, Phojanakong P, Camara Serrano JA, Steri V, Wells JA. Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α. Cell Chem Biol. 2024 Sep 19;31(9):1729-1739.e9. Epub 2024 Aug 22. PMID: 39178841; PMCID: PMC11482644. DOI: 10.1016/j.chembiol.2024.07.018
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science. 2024 Jul 19;385(6706):eadl5763. doi: 10.1126/science.adl5763. Epub 2024 Jul 19. PMID: 39024454. DOI: 10.1126/science.adl5763
Zhou J, Le CQ, Zhang Y, Wells JA. A general approach for selection of epitope-directed binders to proteins. Proc Natl Acad Sci U S A. 2024 May 7;121(19):e2317307121. doi:10.1073/pnas.2317307121. Epub 2024 Apr 29. PMID: 38683990; PMCID: PMC11087759. DOI: 10.1073/pnas.2317307121
Bartholow TG, Burroughs PWW, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells. ACS Cent Sci. 2023 Dec 26;10(1):199-208. doi: 10.1021/acscentsci.3c01473. PMID: 38292613; PMCID: PMC10823516. DOI: 10.1021/acscentsci.3c01473
Yang J, Wang L, Byrnes JR, Kirkemo LL, Driks H, Belair CD, Aguilar OA, Lanier LL, Wells JA, Fong L, Blelloch R. PVRL2 Suppresses Antitumor Immunity through PVRIG- and TIGIT-independent Pathways. Cancer Immunol Res. 2024 May 2;12(5):575-591. doi: 10.1158/2326-6066.CIR-23-0722. PMID: 38588410; PMCID: PMC11063765. DOI: 10.1158/2326-6066.CIR-23-0722
Xie X, Moon PJ, Crossley SWM, Bischoff AJ, He D, Li G, Dao N, Gonzalez-Valero A, Reeves AG, McKenna JM, Elledge SK, Wells JA, Toste FD, Chang CJ. Oxidative cyclization reagents reveal tryptophan cation-π interactions. Nature. 2024 Mar;627(8004):680-687. doi: 10.1038/s41586-024-07140-6. Epub 2024 Mar 6. Erratum in: Nature. 2025 Jan;637(8047):E24. PMID: 38448587; PMCID: PMC11198740. DOI: 10.1038/s41586-024-08558-8
McHenry MW, Shi P, Camara CM, Cohen DT, Rettenmaier TJ, Adhikary U, Gygi MA, Yang K, Gygi SP, Wales TE, Engen JR, Wells JA, Walensky LD. Covalent inhibition of pro-apoptotic BAX. Nat Chem Biol. 2024 Jan 17. PMID: 38233584. DOI: 10.1038/s41589-023-01537-6
Zhou, X., Kong, S., Maker, A., Remesh, S.G., Leung, K.K., Verba, K.A., Wells, J.A. Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4. Nat Chem Bio 20, 742–750 (2024). https://doi.org/10.1038/s41589-023-01535-8
Xie X, Moon PJ, Crossley SWM, Bischoff AJ, He D, Li G, Dao N, Gonzalez-Valero A, Reeves AG, McKenna JM, Elledge SK, Wells JA, Toste FD, Chang CJ. Oxidative cyclization reagents reveal tryptophan cation-π interactions. Nature. 2024 Mar;627(8004):680-687. doi: 10.1038/s41586-024-07140-6. Epub 2024 Mar 6. PMID: 38448587; PMCID: PMC11198740. DOI: 10.1038/s41586-024-07140-6
2023
Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH Jr, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Pawar KI, Pourmal S, Smith AM, Zhou F; QCRG Structural Biology Consortium; DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. bioRxiv [Preprint]. 2022 Aug 10:2022.08.09.503400. Update in: Structure. 2023 Mar 2;31(3):253-264.e6. PMID: 35982665; PMCID: PMC9387132. DOI: 10.1101/2022.08.09.503400
Harvey EP, Hauseman ZJ, Cohen DT, Rettenmaier TJ, Lee S, Huhn AJ, Wales TE, Seo HS, Luccarelli J, Newman CE, Guerra RM, Bird GH, Dhe-Paganon S, Engen JR, Wells JA, Walensky LD. Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering. Cell Chem Biol. 2020 Jun 18;27(6):647-656.e6. Epub 2020 May 14. PMID: 32413285; PMCID: PMC7405809. DOI: 10.1016/j.chembiol.2020.04.004
Wells JA, Kumru K. Extracellular targeted protein degradation: an emerging modality for drug discovery. Nat Rev Drug Discov. 2024 Feb;23(2):126-140. Epub 2023 Dec 7. PMID: 38062152. DOI: 10.1038/s41573-023-00833-z
Zhou J, Le CQ, Zhang Y, Wells JA. A general approach for selection of epitope-directed binders to proteins. bioRxiv DOI: https://doi.org/10.1101/2022.10.24.513434.
Bartholow TG, Burroughs P, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Site-specific proximity labeling at single residue resolution for identification of protein partners in vitro and on cells. bioRxiv [Preprint]. 2023 Jul 27:2023.07.27.550738. PMID: 37546992; PMCID: PMC10402114. DOI: 10.1101/2023.07.27.550738
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. bioRxiv [Preprint]. 2023 Oct 29:2023.10.28.564055. PMID: 37961561; PMCID: PMC10634877. DOI: 10.1101/2023.10.28.564055 (In Press)
Chopra S, Trepka K, Sakhamuri S, Carretero-González A, Zhu J, Egusa E, Zhou J, Leung K, Zhao N, Hooshdaran N, Feng FY, Wells JA, Chou J, Evans MJ. Theranostic Targeting of CUB Domain-Containing Protein 1 (CDCP1) in Multiple Subtypes of Bladder Cancer. Clin Cancer Res. 2023 Apr 3;29(7):1232-1242. PMID: 36648492; PMCID: PMC10073270. 0.1158/1078-0432.CCR-22-1973
Rettko NJ, Kirkemo LL, Wells JA. Secreted HLA-Fc fusion profiles immunopeptidome in hypoxic PDAC and cellular senescence. PNAS Nexus. 2023 Dec 14;2(12):pgad400. doi: 10.1093/pnasnexus/pgad400. PMID: 38099269; PMCID: PMC10720946. DOI: 10.1093/pnasnexus/pgad400
Solomon PE, Bracken CJ, Carozza JA, Wang H, Young EP, Wellner A, Liu CC, Sweet-Cordero EA, Li L, Wells JA. Discovery of VH domains that allosterically inhibit ENPP1. Nat Chem Biol. 2023 Jul 3. Epub ahead of print. PMID: 37400538. DOI: 10.1038/s41589-023-01368-5
Zhou X, Kong S, Maker A, Remesh S, Leung KK, Verba. KA, Wells, JA; Identifying regulatory mechanisms of protein arginine deiminase 4 through recombinant antibody discovery. Nat Chem Biol (In Press)
2022
Jiang Z, Kuo YH, Zhong M, Zhang J, Zhou XX, Xing L, Wells JA, Wang Y, Arkin MR. Adaptor-Specific Antibody Fragment Inhibitors for the Intracellular Modulation of p97 (VCP) Protein-Protein Interactions. J Am Chem Soc. 2022 Jul 27;144(29):13218-13225. . Epub 2022 Jul 12. PMID: 35819848; PMCID: PMC9335864. 10.1021/jacs.2c03665
Pance K, Gramespacher JA, Byrnes JR, Salangsang F, Serrano JC, Cotton AD, Steri V, Wells JA. Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins. Nat Biotechnol. 2022 Sep 22. Epub ahead of print. PMID: 36138170. 10.1038/s41587-022-01456-2
Kaitlin Schaefer, Irene Lui, James R. Byrnes, Emily Kang, Jie Zhou, Amy M. Weeks, and James A. Wells. ACS Central Science 2022 8 (10), 1447-1456 https://doi.org/10.1021/acscentsci.2c00899
Solomo PE, Kirkemo LL, Wilson GM, Leung KK, Almond MH, Sayles LC, Sweet-Cordero EA, Rosenberg OS, Coon JJ, Wells JA. Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation. Mol Cell Proteomics. 2022 Jul;21(7):100247. Epub 2022 May 18. 10.1016/j.mcpro.2022.100247
Zhao N, Chopra S, Trepka K, Wang YH, Sakhamuri S, Hooshdaran N, Kim H, Zhou J, Lim SA, Leung KK, Egusa EA, Zhu J, Zhang L, Foye A, Sriram R, Chan E, Seo Y, Feng FY, Small EJ, Chou J, Wells JA, Aggarwal R, Evans MJ. CUB Domain-Containing Protein 1 (CDCP1) Is a Target for Radioligand Therapy in Castration-Resistant Prostate Cancer, including PSMA Null Disease. Clin Cancer Res. 2022 Jul 15;28(14):3066-3075. PMID: 35604681; PMCID: PMC9288514. 10.1158/1078-0432.CCR-21-3858
Ferguson ID, Patiño-Escobar B, Tuomivaara ST, Lin YT, Nix MA, Leung KK, Kasap C, Ramos E, Nieves Vasquez W, Talbot A, Hale M, Naik A, Kishishita A, Choudhry P, Lopez-Girona A, Miao W, Wong SW, Wolf JL, Martin TG 3rd, Shah N, Vandenberg S, Prakash S, Besse L, Driessen C, Posey AD Jr, Mullins RD, Eyquem J, Wells JA, Wiita AP. The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance. Nat Commun. 2022 Jul 15;13(1):4121. PMID: 35840578; PMCID: PMC9287322. 10.1038/s41467-022-31810-6
Cotton AD, Wells JA, Seiple IB. Biotin as a Reactive Handle to Selectively Label Proteins and DNA with Small Molecules. ACS Chem Biol. 2021 Aug 19.Epub ahead of print. PMID: 34410115. 10.1021/acschembio.1c00252
Gramespacher JA, Cotton AD, Burroughs PWW, Seiple IB, Wells JA. Roadmap for Optimizing and Broadening Antibody-Based PROTACs for Degradation of Cell Surface Proteins. ACS Chem Biol. 2022 May 20;17(5):1259-1268. Epub 2022 Apr 28. PMID: 35481357. 10.1021/acschembio.2c00185
Li Z, Ferguson L, Deol KK, Roberts MA, Magtanong L, Hendricks JM, Mousa GA, Kilinc S, Schaefer K, Wells JA, Bassik MC, Goga A, Dixon SJ, Ingolia NT, Olzmann JA. Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability. Nat Chem Biol. 2022 May 30. Epub ahead of print. PMID: 35637349 DOI: 10.1038/s41589-022-01033-3
Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA. Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest. 2022 Feb 15;132(4):e154604. DOI: 10.1172/JCI154604 Commentary: DOI: 10.1172/JCI157168
Glasgow JE, Byrnes JR, Barbee SD, Moreau JM, Rosenblum MD, Wells JA. Identifying and antagonizing the interactions between layilin and glycosylated collagens. Cell Chem Biol. 2022 Jan 31:S2451-9456(22)00003-4. DOI: 10.1016/j.chembiol.2022.01.003
Kirkemo LL, Elledge SK, Yang J, Byrnes JR, Glasgow JE, Blelloch R, Wells JA. Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells. Elife. 2022 Mar 8;11:e73982. doi: 10.7554/eLife.73982. PMID: 35257663; PMCID: PMC8983049. DOI: 10.7554/eLife.73982
Rettko NJ, Campisi J, Wells JA. Engineering Antibodies Targeting p16 MHC-Peptide Complexes. ACS Chem Biol. 2022 Feb 25. DOI: 10.1021/acschembio.1c00808
Martinko AJ, Simonds EF, Prasad S, Ponce A, Bracken CJ, Wei J, Wang YH, Chow TL, Huang Z, Evans MJ, Wells JA, Hill ZB. Switchable assembly and function of antibody complexes in vivo using a small molecule. Proc Natl Acad Sci U S A. 2022 Mar 1;119(9):e2117402119. DOI: 10.1073/pnas.2117402119
Byrnes JR, Weeks AM, Shifrut E, Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells JA. Hypoxia is a dominant remodeler of the effector T cell surface proteome relative to activation and regulatory T cell suppression. Mol Cell Proteomics. 2022 Feb 22:100217. DOI: 10.1016/j.mcpro.2022.100217
Stopfer LE, Rettko NJ, Leddy O, Mesfin JM, Brown E, Winski S, Bryson B, Wells JA, White FM. MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas. Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2208900119. doi: 10.1073/pnas.2208900119. Epub 2022 Dec 1. PMID: 36454758; PMCID: PMC9894220. DOI: 10.1073/pnas.2208900119
2021
Ma Y, Chen K, Xia F, Atwal R, Wang H, Ahmed SU, Cardarelli L, Lui I, Duong B, Wang Z, Wells JA, Sidhu SS, Kelley SO. Phage-Based Profiling of Rare Single Cells Using Nanoparticle-Directed Capture. ACS Nano. 2021 Dec 28;15(12):19202-19210. Epub 2021 Nov 23. PMID: 34813293. 10.1021/acsnano.1c03935
Kang E, Kadoch C, Rubenstein JL, Lanier LL, Wells JA. A functional mammalian display screen identifies rare antibodies that stimulate NK cell-mediated cytotoxicity. Proc Natl Acad Sci U S A. 2021 Aug 3;118(31):e2104099118. PMID: 34330834; PMCID: PMC8346823. doi: 10.1073/pnas.2104099118. 10.1073/pnas.2104099118
Lim S.A., Zhou J, Martinko A. J, Wang Y-H, Filippova E.V., Steri V, Wang D, Remesh S.G., Liu J, Hann B, Kossiakoff A.A., Evans M.J., Leung K.K., Wells A. J. Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer. bioRxiv 2021.06.14.448427; doi: https://doi.org/10.1101/2021.06.14.448427
Byrnes J.R., Weeks A. M., Shifrut E. M., Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells J.A. Hypoxia is a dominant remodeler of the CD8+ T cell surface proteome relative to activation and regulatory T cell-mediated suppression bioRxiv 2021.06.07.447379; doi: https://doi.org/10.1101/2021.06.07.447379
Ferguson ID, Patino Escobar B, Tuomivaara ST, Lin Y-HT, Nix MA, Leung KK, Hale M, Choudhry P, Lopez-Girona A, Ramos E, Wong SW, Wolf JL, Martin TG, Shah N, Vandenberg S, Prakash S, Besse L, Driessen C, Wells JA, Wiita AP. Defining the cell surface proteomic landscape of multiple myeloma reveals immunotherapeutic strategies and biomarkers of drug resistance. BioRxiv. Originally posted January 19, 2021
Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer NS, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. Nat Biotechnol. 2021 Mar 25 10.1038/s41587-021-00878-8
Glasgow J, Glasgow A, Kortemme T, Wells JA. Reply to Liu et al.: Specific mutations matter in specificity and catalysis in ACE2. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15) 10.1073/pnas.2024450118
Lim, S. A., Gramespacher, J. A., Pance, K., Rettko, N. J., Solomon, P., Jin, J., Lui, I., Elledge, S. K., Liu, J., Bracken, C. J., Simmons, G., Zhou, X. X., Leung, K. K., & Wells, J. A. (2020). Bi-specific VH/Fab antibodies targeting neutralizing and non-neutralizing Spike epitopes demonstrate enhanced potency against SARS-CoV-2. mAbs,13(1). 10.1080/19420862.2021.1893426
Chen, W., Mou, K. Y., Solomon, P., Aggarwal, R., Leung, K. K., & Wells, J. A. (2021). Large remodeling of the Myc-induced cell surface proteome in B cells and prostate cells creates new opportunities for immunotherapy. Proceedings of the National Academy of Sciences of the United States of America, 118(4), 1–11. 10.1073/pnas.2018861118
Cotton, A. D., Nguyen, D. P., Gramespacher, J. A., Seiple, I. B., & Wells, J. A. (2021). Development of Antibody-Based PROTACs for the Degradation of the Cell-Surface Immune Checkpoint Protein PD-L1. Am Chem Soc. 2021 Jan 20;143(2):593-598. PMCID# PMC8154509 10.1021/jacs.0c10008
Weeks AM, Byrnes JR, Lui I, Wells JA. Mapping proteolytic neo-N termini at the surface of living cells. Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):e2018809118. PMID: 33536314; PMCID: PMC7923363. 10.1073/pnas.2018809118
2020
Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. Cell Rep Med. 2020 Oct 20;1(7):100123. doi: 10.1016/j.xcrm.2020.100123. Epub 2020 Sep 24. PMID: 32995758; PMCID: PMC7513813. DOI: 10.1016/j.xcrm.2020.100123
Weeks, A. M., & Wells, J. A. (2020). N-Terminal Modification of Proteins with Subtiligase Specificity Variants. Current Protocols in Chemical Biology, 12(1), 1–23. https://doi.org/10.1002/cpch.79
Weeks, A. M., & Wells, J. A. (2020). Subtiligase-Catalyzed Peptide Ligation. Chemical Reviews, 120(6), 3127–3160. https://doi.org/10.1021/acs.chemrev.9b00372
Lim, D. C., Joukov, V., Rettenmaier, T. J., Kumagai, A., Dunphy, W. G., Wells, J. A., & Yaffe, M. B. (2020). Redox priming promotes Aurora A activation during mitosis. Science Signaling, 13(641) 10.1126/scisignal.abb6707
Harvey EP, Hauseman ZJ, Cohen DT, Rettenmaier TJ, Lee S, Huhn AJ, Wales TE, Seo HS, Luccarelli J, Newman CE, Guerra RM, Bird GH, Dhe-Paganon S, Engen JR, Wells JA, Walensky LD. (2020). Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering. Cell Chem Biol, 27(6), 647–656. https://doi.org/10.1016/j.chembiol.2020.04.004
Glasgow, A., Glasgow, J., Limonta, D., Solomon, P., Lui, I., Zhang, Y., Nix, M. A., Rettko, N. J., Zha, S., Yamin, R., Kao, K., Rosenberg, O. S., Ravetch, J. V, Wiita, A. P., Leung, K. K., Lim, S. A., Zhou, X. X., Hobman, T. C., Kortemme, T., & Wells, J. A. (2020). Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proceedings of the National Academy of Sciences, 202016093. https://doi.org/10.1073/pnas.2016093117
Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K; QCRG Structural Biology Consortium, Zhou XX, Leung KK, Wells JA. Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2. Nat Chem Biol. 2020 Oct 20. Epub ahead of print. PMID: 33082574. 10.1038/s41589-020-00679-1
Yueh, C., Rettenmaier, J., Xia, B., Hall, D. R., Alekseenko, A., Porter, K. A., Barkovich, K., Keseru, G., Whitty, A., Wells, J. A., Vajda, S., & Kozakov, D. (2019). Kinase atlas: Druggability analysis of potential allosteric sites in kinases. Journal of Medicinal Chemistry, 62(14), 6512–6524. https://doi.org/10.1021/acs.jmedchem.9b00089
Byrnes, J. R., Zhou, X. X., Lui, I., Elledge, S. K., Glasgow, J. E., Lim, S. A., Loudermilk, R. P., Chiu, C. Y., Wang, T. T., Wilson, M. R., Leung, K. K., & Wells, J. A. (2020). Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding. MSphere, 5(5), 111. https://msphere.asm.org/content/5/5/e00802-20
Zhou, X. X., Bracken, C. J., Zhang, K., Zhou, J., Mou, Y., Wang, L., Cheng, Y., Leung, K. K., & Wells, J. A. (2020). Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. Journal of the American Chemical Society, epub ahead of print https://doi.org/10.1021/jacs.0c08458
Moroz, A., Wang, Y., Sharib, J. M., Wei, J., Zhao, N., Huang, Y., Chen, Z., Martinko, A. J., Zhuo, J., Lim, S. A., Zhang, L. H., Seo, Y., Carlin, S., Leung, K. K., Collisson, E. A., Kirkwood, K. S., Wells, J. A., & Evans, M. J. (2020). Theranostic Targeting of CUB Domain Containing Protein 1 (CDCP1) in Pancreatic Cancer. Clinical Cancer Research, 26(14), 3608–3615. https://doi.org/10.1158/1078-0432.CCR-20-0268
Zhou J, Li S, Leung KK, O'Donovan B, Zou JY, DeRisi JL, Wells JA. Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25464-25475.Epub 2020 Sep 24. 10.1073/pnas.2009279117
Mahuron, K. M., Moreau, J. M., Glasgow, J. E., Boda, D. P., Pauli, M. L., Gouirand, V., Panjabi, L., Grewal, R., Luber, J. M., Mathur, A. N., Feldman, R. M., Shifrut, E., Mehta, P., Lowe, M. M., Alvarado, M. D., Marson, A., Singer, M., Wells, J., Jupp, R., Daud, A., Rosenblum, M. D. (2020). Layilin augments integrin activation to promote antitumor immunity. Journal of Experimental Medicine, 217(9). https://doi.org/10.1084/jem.20192080
Lim, S. A. & Wells, J. A. (2020) Split enzymes: Design principles and strategy. Methods Enzymol. 1–22. https://doi.org/10.1016/bs.mie.2020.04.036
Weeks, A.M., Byrnes, J.R., Lui, I., and Wells, J.A. (2020). Mapping proteolytic neo-N termini at the surface of living cells. Deposited in bioRxiv https://doi.org/10.1101/2020.02.23.961904
Elledge, S.K., Tran, H.L., Christian, A.H., Steri, V., Hann, B., Toste, F.D., Chang, C.J., and Wells, J.A. (2020). Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation. Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):5733-5740
Leung, K. K., Wilson, G. M., Kirkemo, L. L., Riley, N. M., Coon, J. J., & Wells, J. A. (2020). Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proceedings of the National Academy of Sciences of the United States of America, 117 (14), 7764–7775. https://doi.org/10.1073/pnas.1917947117
Wei, J., Leung, K., Truillet, C., Ruggero, D., Wells, J. A., & Evans, M. J. (2020). Profiling the Surfaceome Identifies Therapeutic Targets for Cells with Hyperactive mTORC1 Signaling. Molecular & Cellular Proteomics : MCP, 19 (2), 294–307. https://doi.org/10.1074/mcp.RA119.001785
2019
Yueh, C., Rettenmaier, J., Xia, B., Hall, D. R., Barkovich, K., Whitty, A., Wells, J. A., Vajda, S., & Kozakov, D. (2020). in Kinases: Druggability Analysis of Potential Allosteric Sites in Kinases. J Med Chem, 62(14), 6512–6524 10.1021/acs.jmedchem.9b00089
Leung KK, Nguyen A, Shi T, Tang L, Ni X, Escoubet L, MacBeth KJ, DiMartino J, Wells JA. Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome. Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):695-700. doi: 10.1073/pnas.1813666116. Epub 2018 Dec 24. PubMed PMID: 30584089; PubMed Central PMCID: PMC6329958. 10.1073/pnas.1813666116
Hertz NT, Adams EL, Weber RA, Shen RJ, O'Rourke MK, Simon DJ, Zebroski H, Olsen O, Morgan CW, Mileur TR, Hitchcock AM, Sinnott Armstrong NA, Wainberg M, Bassik MC, Molina H, Wells JA, Tessier-Lavigne M (2019). Neuronally Enriched RUFY3 Is Required for Caspase-Mediated Axon Degeneration. Neuron 103(3):412-422.e4
2018
Hill, M. E., Kumar, A., Wells, J. A., Hobman, T. C., Julien, O., & Hardy, J. A. (2018). The Unique Cofactor Region of Zika Virus NS2B-NS3 Protease Facilitates Cleavage of Key Host Proteins. ACS Chemical Biology, 13(9), 2398–2405. 10.1021/acschembio.8b00508
Maureen E. Hill, Anil Kumar, James A. Wells, Tom C. Hobman, Olivier Julien, and Jeanne A. Hardy (2018). The unique cofactor region of Zika virus NS2B-NS3 protease facilitates cleavage of key host proteins. ACS Chem. Biol. 13 (9), pp 2398–2405
Mou Y, Zhou X, Leung K, Martinko AJ, Yu J-Y, Chen W, and Wells JA. (2018) Engineering improved anti-phosphotyrosine antibodies based on immuno-convergent binding motif. J. Am. Chem. Soc. 140(48): 16615-16624
Henderson AR, Henley MJ, Foster NJ, Peiffer AL, Beyersdorf MS, Stanford KD, Sturlis SM, Linhares BM, Hill ZB, Wells JA, Cierpicki T, Brooks III CL, Fierke CA, Mapp AK. (2018) Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators. PNAS 115 (36) 8960-8965
Keedy D.A., Hill Z.B., Biel J.T., Kang E., Rettenmaier T.J., Brandao-Neto J., Pearce N.M., von Delft F., Wells J.A., Fraser J.S. (2018) "An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering." eLife 2018;7:e36307 
Pollock S.B., Hu A., Mou Y.M., Martinko A.J., Julien O., Hornsby M., Ploder L, Adams J.J., Geng H., Muschen M., Sidhu S., Moffat J, Wells J.A. (2018) Highly multiplexed and quantitative cell surface protein profiling using genetically barcoded antibodies. Proc. Natl. Acad. Sci. U.S.A. 115(11):2836-2841
Kroemer G., et al., Wells J.A., Wood W., Yuan J., Zakeri Z., Zhivotovsky B., Zitvogel L., Melino G. and Kroemer G. (2018) "Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018." Cell Death Differ. 25:486-541
Martinko A.J., Truillet C., Julien O., Diaz J.E., Horlbeck, M.A., Whiteley G., Blonder J., Weissman J.S., Bandyopadhyay S., Evans M.J., Wells J.A. (2018) "Targeting RAS Driven Human Cancer Cells with Antibodies to Upregulated and Essential Cell-Surface Proteins." eLife. 2018;7:e31098
eLife Press Release
UCSF News Center
Hill Z.B., Martinko A.J., Nguyen D.P., Wells J.A. (2018) "Human Antibody-Based Chemically Induced Dimerizers for Cell Therapeutic Applications." Nat. Chem. Biol. 14:112-117
F1000 recommendation
Weeks A.M. and Wells J.A. (2017) "Engineering peptide ligase specificity by proteomic identification of ligation sites." Nat. Chem. Biol. 14:50-57
Nat. Chem. Biol. News and Views
F1000 recommendation
2017
Srinivasan SR, Cesa LC, Li X, Julien O, Zhuang M, Shao H, Chung J, Maillard I, Wells JA, Duckett CS, Gestwicki JE. (2017) "Heat Shock Protein 70 (Hsp70) Suppresses RIP1-Dependent Apoptotic and Necroptotic Cascades." Molecular Cancer Research: MCR. 2018; 16(1):58-68.
Smart A.D., Pache R.A., Thomsen N., Kortemme T., Davis G.W., Wells J.A. (2017) "Engineering a Light-Activated Caspase-3 for Precise Ablation of Neurons in Vivo." Proc. Natl. Acad. Sci. U.S.A. 114:E8174-E8183
ACS Chem. Bio. Spotlight (PDF)
Diaz J.E., Morgan C.W., Minogue C.E., Hebert A.S., Coon J.J., Wells J.A. (2017) "A Split-Abl Kinase for Direct Activation in Cells." Cell Chem. Bio. 24:1-9
Liu T.Y., Huang H.H., Wheeler D., Xu Y., Wells J.A., Song Y.S., Wiita A.P. (2017) "Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics." Cell Syst. 4:636-644
Julien O. and Wells J.A. (2017) "Caspases and their substrates" Cell Death Differ. 24:1380-1389
Lin S., Yang X., Jia S., Weeks A.M., Hornsby M., Lee P.S., Nichiporuk R.V., Iavarone A.T., Wells J.A., Toste F.D., Chang C.J. (2017) "Redox-based reagents for chemoselective methionine bioconjugation." Science 355:597-602
Tran H.L., Lexa K.W., Julien O., Young T.S., Walsh C.T., Jacobson M.P., and Wells J.A. (2017) "SAR and molecular mechanics reveal the importance of ring entropy in the biosynthesis and activity of a natural product" J. Am. Chem. Soc. 139:2541-2544
Calvo S.E., Julien O., Clauser K.R., Shen H., Kamer K.J., Wells J.A. Mootha V.K. (2017) "Comparative analysis of mitochondrial N-termini from mouse, human, and yeast" Mol. Cell. Proteomics. 16:512-523
2016
Spangler B., Fontaine S.D., Shi Y., Sambucetti L.C., Mattis A.N., Hann B., Wells J.A., and Renslo A.R. (2016) "A Novel Tumor-Activated Prodrug Strategy Targeting Ferrous Iron is Effective in Multiple Preclinical Cancer Models" J. Med. Chem (in press)
Ye X., Chan K.C., Waters A.M., Bess M., Harned A., Wei B.R., Loncarek J., Luke B.T., Orsburn B.C., Hollinger B.D., Stephens R.M., Bagni R., Martinko A., Wells J.A., Nissley D.V., McCormick F., Whiteley G. and Blonder J. (2016) "Comparative proteomics of a model MCF10A‐KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface" Oncotargets (in press)
Henager SH., Chu N., Chen Z., Bolduc D., Dempsey D.R., Hwang Y., Wells J.A., Cole P.A. (2016) "Enzyme-catalyzed expressed protein ligation." Nat. Methods 13:925-927
Hill Z.B., Pollock S.B., Zhuang Z., Wells J.A. (2016) "Direct proximity tagging of small molecule protein targets using an engineered NEDD8 ligase" J. Am. Chem. Soc. 138:13123-13126
Wang W., Nguyen L.T., Burlak C., Chegini F., Guo F., Chataway T., Ju S., Fisher O., Miller D.W., Datta D., Wu F., Wu C., Landeru A., Wells J.A., Cookson M.R., Boxer M.B., Thomas C.J, Gai W.P., Ringe D., Petsko G.A., and Hoang Q.Q. (2016) "Caspase-1 causes truncation and aggregation of the Parkinson's disease-associated protein α-synuclein." Proc. Natl. Acad. Sci. U.S.A. 113:9587-9592
Spangler B., Morgan C.W., Vander Wal M.N., Chang C.J., Hann B., Wells J.A., and Renslo A.R. (2016) "A reactivity-based probe of the intracellular labile ferrous iron pool." Nat. Chem. Biol. 12:680-685
Seaman J.E., Julien O., Lee P.S., Rettenmaier T.J., Thomsen N.D., Wells J.A. (2016) "Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues" Cell Death Differ. 23:1717-1726
F1000 recommendation
Nguyen D.P., Miyaoka Y., Gilbert L.A., Mayerl S.J., Lee B.H., Weissman J.S., Conklin B.R., and Wells J.A. (2016) "Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity." Nat. Commun. 7:12009.
Hill, M.E., MacPherson D.J., Wu P. Julien O., Wells J.A., and Hardy J.A. (2016) "Reprogramming Caspase‑7 Specificity by Regio-Specific Mutations and Selection Provides Alternate Solutions for Substrate Recognition." ACS Chem. Biol. 11:1603-1612
Julien O., Zhuang M., Wiita A.P., O’Donoghue A.J., Knudsen G.M., Craik C.S., and Wells J.A. (2016) "Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles." Proc. Natl. Acad. Sci. U.S.A. 113:E2001-2010
Cimermancic P., Weinkam P., Rettenmaier T.J., Bichmann L., Keedy D.A., Woldeyes R.A., Schneidmann D., Demerdash O.N., Mitchell J.C., Wells J.A., Fraser J.S., Sali A. (2016) "CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites." J. Mol. Biol. 428:709-719
2015
Rettenmaier J.T., Fan H., Karpiak J., Doak A., Sali A., Shoichet B., and Wells J.A. (2015) "Allosteric small-molecule modulators of the protein kinase PDK1 discovered by virtual screening" J. Med. Chem. 58:8285-8291
Hornsby M., Paduch M., Miersch S., Sääf A., Matsuguchi T., Lee B., Wypisniak K., Doak A., King D., Usatyuk S., Perry K., Lu V., Thomas W., Luke J., Goodman J., Hoey R.J., Lai D., Griffin C., Li Z., Vizeacoumar F.J., Dong D., Campbell E., Anderson S., Zhong N., Gräslund S., Koide S., Moffat J., Sidhu S., Kossiakoff A., and Wells J.A. (2015) "A High Through-put Platform for Recombinant Antibodies to Folded Proteins." Mol. Cell. Proteomics. 10:2833-2847
Morgan C.W., Diaz J.E., Zeitlin S.G., Gray D.C., and Wells J.A. (2014) "Engineered cellular gene-replacement platform for selective and inducible proteolytic profiling." Proc. Natl. Acad. Sci. U.S.A. 112:8344-8349
Miersch S., Li Z., Hanna R., McLaughlin M.E., Hornsby M., Matsuguchi T., Paduch M., Sääf A., Wells J.A., Koide S., Kossiakoff A., and Sidhu S.S. (2015) "Scalable high throughput selection from phage-displayed synthetic antibody libraries." J Vis Exp. 95:51492
Koerber J.T., Hornsby M.J., and Wells J.A. (2015) "An Improved Single-chain Fab Platform for Efficient Display and Recombinant Expression." J. Mol. Biol. 427:576-586
2014
Rettenmaier T.J., Sadowsky J.D., Thomsen N.D., Chen S.C., Doak A.K., Arkin M.R., and Wells J.A. (2014) "A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1." Proc. Natl. Acad. Sci. U.S.A. 111:18590-18595
Ordureau A., Sarraf S.A., Duda D.M., Heo J.M., Jedrykowski M.P., Sviderskiy V.O., Olszewski J.L., Koerber J.T., Xie T., Beausoleil S.A., Wells J.A., Gygi S.P., Schulman B.A., Harper J.W. (2014) "Quantitative Proteomics Reveal a Feedforward Mechanism for Mitochondrial PARKIN Translocation and Ubiquitin Chain Synthesis." Mol. Cell. 56:360-375
Julien O., Kampmann M., Bassik M.C., Zorn J.A., Venditto V.J., Shimbo K., Agard N.J., Shimada K., Rheingold A.L., Stockwell B.R., Weissman J.S., and Wells J.A. (2014) "Unraveling the mechanism of cell death induced by chemical fibrils." Nat. Chem. Biol. 10:969-976
Arkin M.R., Tang Y., Wells J.A. (2014) "Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality." Chem. Biol. 21:1102-1114.
Wiita A.P., Seaman J.E., Wells J.A. (2014) "Global analysis of cellular proteolysis by selective enzymatic labeling of protein N-termini." Methods Enzymol. 2014;544:327-358
Morgan C.W., Julien O., Unger E.K., Shah N.M., Wells J.A. (2014) "Turning on caspases with genetics and small molecules." Methods Enzymol. 2014;544:179-213
Wells J.A. and Kossiakoff A.A. (2014) "Cell biology. New tricks for an old dimer." Science. 2014 344:703-704
Wiita A.P., Hsu G.W., Lu C.M., Esensten J.H., Wells J.A. (2014) "Circulating Proteolytic Signatures of Chemotherapy-induced Cell Death in Humans Discovered by N-terminal Labeling." Proc. Natl. Acad. Sci. 111:7594-7599
Lodge J.M, Rettenmaier J.T., Wells J.A., Pomerantz W.C., and Mapp A.K. (2014) "FP tethering: a screening technique to rapidly identify compounds that disrupt protein–protein interactions"
Med. Chem. Commun. 5:370-375
2013
Ostrem J.M., Peters U., Sos M.L., Wells J.A., Shokat K.M. (2013) "K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions." Nature. 503:548-551
Wiita A.P., Ziv E., Wiita P.J., Urisman A., Julien O., Burlingame A.L., Weissman J.S., and Wells J.A. (2013) "Global cellular response to chemotherapy-induced apoptosis." eLife. 2:e01236
Koerber J.T, Thomsen N.D., Hannigan B.T., Degrado W.F., Wells J.A. (2013) "Nature-inspired design of motif-specific antibody scaffolds." Nat. Biotechnol. 31:916-921
Carter P.J., Hazuda D., Wells J.A. (2013) "Next generation therapeutics." Curr Opin Chem Biol. 17. 317-319
Yang C.F., Chiang M.C., Gray D.C., Prabhakaran M., Alvarado M., Juntti S.A., Unger E.K., Wells J.A., Shah N.M. (2013) "Sexually dimorphic neurons in the ventromedial hypothalamus govern mating in both sexes and aggression in males." Cell. 153:896-909
Thomsen N.D., Koerber J.T., Wells J.A. (2013) "Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation." Proc. Natl. Acad. Sci. 110. 8477-8482
Datta D., McClendon C.L., Jacobson M.P., Wells J.A. (2013) "Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3." J. Biol. Chem. 288. 9971-9981
Wang N., Majmudar C.Y., Pomerantz W.C., Gagnon J.K., Sadowsky J.D., Meagher J.L., Johnson T.K., Stuckey J.A., Brooks C.L. 3rd, Wells J.A., Mapp A.K. (2013) "Ordering a Dynamic Protein Via a Small-Molecule Stabilizer." J. Am. Chem. Soc. 135, 3363-2266
Crawford E.D., Seaman J.E., Agard N., Hsu G.W., Julien O., Mahrus S., Nguyen H., Shimbo K., Yoshihara H., Zhuang M., Chalkley R.J., Wells J.A. (2013) "The DegraBase: a database of proteolysis in healthy and apoptotic human cells." Mol. Cell. Proteomics 12, 813-824
Zhuang M., Guan S., Wang H., Burlingame A.L., Wells J.A. (2013) "Substrates of IAP Ubiquitin Ligases Identified with a Designed Orthogonal E3 Ligase, the NEDDylator" Mol. Cell. 49, 273-282.
2012
Crawford E.D., Seaman J.E., Barber A.E., David D.C., Babbitt P.C., Burlingame A.L., Wells J.A. (2012) "Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis" Cell Death Differ. 19, 2040-2048.
Zorn J.A., Wolan D.W., Agard N.J., Wells J.A. (2012) "Fibrils Colocalize Caspase-3 with Procaspase-3 to Foster Maturation" J. Biol. Chem. 287, 33781-22795.
Shimbo K., Hsu G.W., Nguyen H., Mahrus S., Trinidad J.C., Burlingame A.L., and Wells J.A. (2012) "Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis" Proc Natl Acad Sci U S A. 109, 12432-12437.
Agard N.J., Mahrus S., Trinidad J.C., Lynn A., Burlingame A.L., Wells J.A. (2012) "Global kinetic analysis of proteolysis via quantitative targeted proteomics" Proc Natl Acad Sci U S A. 109, 1913-1918.
2011
Zorn J.A., Wille H., Wolan D.W., Wells J.A. (2011) "Self-Assembling Small Molecules Form Nanofibrils That Bind Procaspase-3 to Promote Activation" J Am Chem Soc. 133, 19630-19633.
Gao J. & Wells J.A. (2011) "Identification of Specific Tethered Inhibitors for Caspase-5" Chem Biol Drug Des. 79, 209-215.
Tang Y., Wells J.A. & Arkin M.R. (2011) "Structural and enzymatic insights into caspase-2 substrate recognition and catalysis" J Biol Chem. 286, 34147-34154.
Crawford E.D. & Wells J.A. (2011) "Caspase substrates and cellular remodeling" Annu Rev Biochem. 80, 1055-87.
Sadowsky, J., Burlingame, M., Wolan, D., McClendon, C., Jacobson, M., & Wells, J.A. (2011) "Turning a protein kinase (PDK1) on or off from a single allosteric site via disulfide trapping" Proc. Natl. Acad. Sci. USA. 108, 6056-6061.
Perez-Paya, E., Orzaez, M, Mondragon, L, Wolan, D, Wells, JA, Messeguer, A, Vincent, MJ. (2011) "Molecules that modulate Apaf-1 activity" Med Res Rev. 31, 649-675.
2010
Gray, D.C., Mahrus, S. & Wells. J.A. (2010) "Activation of specific apoptotic caspases with an engineered small molecule activated protease" Cell 142, 637-646.
Barkan, D.T., Hostetter, D.R., Mahrus, S., Pieper, U., Wells, J.A., Craik, C.S. & Sali, A. (2010) "Prediction of protease substrates using sequence and structure features" Bioinformatics 26, 1714-22.
Agard, N.J, Maltby, D. & Wells, J.A. (2010) "Inflammatory stimuli regulate caspase substrate profiles" Mol. Cell. Proteomics 5, 880-893.
Zorn, JA, & Wells, JA. (2010) "Turning enzymes ON with small molecules" Nat Chem Biol 3, 179-188.
Wildes, D & Wells, J.A. (2010) "Sampling the N-terminal proteome of human blood" Proc. Natl. Acad. Sci. USA 107, 4561-4566.
2009
Wolan DW, Zorn JA, Gray DC, Wells JA. (2009) "Small-molecule activators of a proenzyme" Science 326, 853-858.
Agard, N. & Wells, J.A. (2009) "Methods for the proteomic identification of protease substrates" Curr Opin Chem Biol 13, 503-509.
Hardy, J. & Wells, J.A. (2009) "Dissecting an allosteric switch in caspase-7 using chemical and mutational probes" Journal of Biological Chemistry 284(38), 26063-26069. Journal of Biological Chemistry 284(38), 26063-26069.
Gao J, Sidhu SS, Wells JA. (2009) "Two-state selection of conformation-specific antibodies" Proc. Natl. Acad. Sci USA 106, 3071-3076.
2008
Yoshihara HA, Mahrus S, Wells JA. (2008) Bioorg Med Chem Lett. 18, 6000-6003. "Tags for labeling protein N-termini with subtiligase for proteomics"
Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. (2008) "Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini" Cell 134, 866-876.
Datta D, Scheer JM, Romanowski MJ, Wells JA. (2008) J Mol Biol. 381, 1157-1167. "An allosteric circuit in caspase-1"
2007
Wells JA, McClendon CL. (2007) Nature 450, 1001-1009. "Reaching for high-hanging fruit in drug discovery at protein-protein interfaces"
2006
Thanos, C.D., DeLano, W.L. and Wells, J.A. (2006) "Hot-spot mimicry of a cytokine receptor by a small molecule"
Scheer, J., Romanowski, M. and Wells, J.A. (2006) Proc. Natl. Acad. Sci. USA 103, 7595-7600. "A Common Allosteric Site and Mechanism in Caspases"
2005
Scheer, J., Wells, J.A. and Romanowski, M. (2005) Protein Expr. Purif. 148-153. "Malonate-assisted purification of human caspases"
Buck, E. and Wells, J.A. (2005) Proc. Natl. Acad. Sci. USA 102, 2719-2724. "Disulfide Trapping to Localize Small Molecule Agonists and Antagonists for the Complement 5a Receptor"
Buck, E., Bourne, H. and Wells, J.A. (2005) J. Biol. Chem 280, 4009-4012. "Site-specific Disulfide Capture of Agonist and Antagonist Peptides to the C5a Receptor"
2004
Hardy, J.A. and Wells, J.A. (2004) Curr Opin Struct Biol., 706-715. "Searching for new allosteric sites in enzymes."
Hardy, J.A., Lam, J., Nguyen, J.T., O’Brien, T and Wells, J.A. (2004) "Discovery of an Allosteric Site in Caspases." Proc. Natl. Acad. Sci. USA 101, 12461-12466.
Erlanson, D.A., Wells, J.A. and Braisted, A.B. (2004) "TETHERING: Fragment-based Drug Discovery." Annu. Rev. Biophys. Biomol Struct. 33, 199-233.
Stroud, R.M. and Wells, J.A. (2004) Science STKE, 2004, re7. "Mechanistic Diversity of Cytokine Signaling Across Cell Membranes"
Arkin, M.R. and Wells, J.A. (2004) Nature Rev. Drug Disc. 3, 301-317. "Small Molecule Inhibitors of Protein-Protein Interactions: Progressing Towards the Dream"
2003
Thanos, C.D., Randal, M., and Wells, J.A. (2003) J. Am. Chem. Soc., 125, 15280-15281. "Potent Small-molecule Binding to a Dynamic Hot-spot on IL-2"
Nguyen, J. and Wells, J.A. (2003) Machinery as a Mechanism to target Cancer Cells" Proc. Natl. Acad. Sci USA, 100, 7533-7538. "Direct Activation of the Apoptosis
Arkin, M.R., Randal, M., DeLano, W., Hyde, J., Loung, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., Wells, J.A., Braisted, A.C. (2003) "Binding of Small Molecules to an Adaptive Protein:Protein Interface" Proc. Natl. Acad. Sci USA 100, 1603-1608.
Selected Earlier Publications
Erlanson, D.A., Braisted, A.C., Raphael, D.R., Randal, M., Stroud, R.M., Gordon, E.M. and Wells, J.A. (2000) Proc. Natl. Acad. Sci. USA 97, 9367-9372. "Site-Directed Ligand Discovery"
DeLano, W.L., Ultsch, M.H., De Vos, A.M. and Wells, J.A. (2000) Science 287, 1279-1283. "Convergent Solutions to Binding at a Protein-Protein Interface"
Atwell, S. and Wells, J.A. (1999) Proc. Natl. Acad. Sci USA 96, 9497-9502. "Selection for Improved Subtiligases by Phage Display"
Ballinger, M.D. and Wells, J.A. (1998) Nature Struct. Biol. 5, 938-940. "Will Any Dimer Do?" News and Views
Clackson, T., Ultsch, M., Wells, J.A. and De Vos, A.A. (1998) J. Mol. Biol. 277, 1111-1128. "Structural and Functional Analysis of the 1:1 Growth Hormone:Receptor Complex Reveals the Molecular Basis for Receptor Affinity"
Wiesmann, C., Fuh, G., Christinger, H.W., Eigenbrot, C., Wells, J.A., De Vos, A.M. (1997) Cell 91, 695-704. "Crystal Structure at 1.7Å resolution of VEGF in Complex with Domain 2 of the Flt-1 Receptor"
Atwell, S., Ultsch, M., De Vos, A.M. and Wells, J.A. (1997) Science 278, 1124-1127 "Structural Plasticity in a Remodeled Protein-Protein Interface"
Ellman, J., Stoddard, B., and Wells, J.A. (1997) Proc. Natl. Acad. Sci. USA 94, 2779-2782. "Combinatorial Thinking in Chemistry and Biology"
Wells, J.A. (1996) Science 273, 449-450. "Hormone Mimicry." Review.
Li, B., Tom, J.Y.K., Oare, D., Yen, R., Fairbrother, W., Wells, J.A., and Cunningham, B.C. (1995) Science 270, 1657-1660. "Minimization of a Polypeptide Hormone"
Wells, J.A. (1995) Biotechnology 13, 647-651. "Structural and Functional Epitopes in the Growth Hormone Receptor Complex"
Clackson, T. and Wells, J.A. (1995) Science 267, 383-386. " A Hot Spot of Binding Energy in a Hormone-Receptor Interface"
Chang, T.K., Jackson, D.Y., Burnier, J.P. and Wells, J.A. (1994) Proc. Natl. Acad. Sci. USA 91, 12544-12548. "Subtiligase: a Tool for Semi-synthesis of Proteins"
Jackson, D.Y., Burnier, J., Quan, C., Stanley, M., Tom, J. and Wells, J.A. (1994) Science 266, 243-247. "A Designed Peptide Ligase for Total Synthesis of Ribonuclease A with Unnatural Catalytic Residues."
Matthews, D.J. and Wells, J.A. (1993) Science 260, 1113-1117. "Substrate Phage: Selection of Protease Substrates by Monovalent Phage Display."
Fuh, G. Cunningham, B.C., Fukunaga, R., Nagata, S., Goeddel, D.V., and Wells, J.A. (1992) Science, 256, 1677-1680. "Rational Design of Potent Antagonists to the Human Growth Hormone Receptor."
Cunningham, B.C., Ultsch, M., DeVos, A.M., Mulkerrin, M.G., Clauser, K.R., Wells, J.A. (1991) Science 254, 821-825. "Dimerization of the Extracellular Domain of the Human Growth Hormone Receptor by a Single Hormone Molecule."
Lowman, H.B., Bass, S., Simpson, N., Wells, J.A. (1991) Biochemistry 30, 10832-10838 "Engineering a Hormone for Improved Receptor binding Affinity by Monovalent Phage Display."
Cunningham, B.C., Mulkerrin, M.G., and Wells, J.A. (1991) Science 253, 545-548, "Dimerization of Human Growth Hormone by Zinc."
Cunningham, B.C., and Wells, J.A. (1991) Proc. Natl. Acad. Sci. USA 88, 3407-3411. "Rational design of receptor specific variants of human growth hormone."
Cunningham, B.C., Bass, S., Fuh, G., and Wells, J.A. (1990) Science 250, 1709-1712 "Zinc mediation of the binding of human growth hormone to the human prolactin receptor."
Cunningham, B.C., Henner, D.J. and Wells, J.A. (1990) Science 247, 1461-1465. "Engineering human prolactin to bind to the human growth hormone receptor."
Cunningham, B.C. and Wells, J.A., (1989) Science 244, 1081-1085. "High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis."
Cunningham, B.C., Jhurani, P., Ng, P. and Wells, J.A., (1989) Science 243, 1330-1336. "Receptor and antibody epitopes in human growth hormone identified by homolog-scanning mutagenesis."
Mitchinson, C. and Wells, J.A. (1989) Biochemistry 28, 4807-4815. "Protein engineering of disulfide bonds in subtilisin."
Wells, J.A. and Estell, D.A. (1988) Trends in Biochem. Sci. 13, 291-297. "Subtilisin - an enzyme designed to be engineered."
Carter, P. and Wells, J.A. (1988) Nature 332, 564-568. "Dissecting the catalytic triad of a serine protease."
Carter, P., and Wells, J.A. (1987) Science 24, 394-399. "Engineering substrate specificity by substrate-assisted catalysis."
Wells, J.A., Cunningham, B.C., Graycar, T.P., and Estell, D.A. (1987). Proc. Natl. Acad. Sci. USA 84, 5167-5171. "Recruitment of substrate specificity properties from one enzyme into a related one by protein engineering."
Wells, J.A., Powers, D.B., Bott, R.R., Graycar, T.P., and Estell, D.A. (1987) Proc. Natl. Acad. Sci. USA 84, 1219-1223. "Designing substrate specificity by protein engineering of electrostatic interactions."
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Wells, J.A., Powers, D.B., Bott, R.R., Katz, B.A., Ultsch, M.H., Kossiakoff, A.A., Power, S.D., Adams, R.M., Heyneker, H.H., Cunningham, B.C., Miller, J.V., Graycar, T.P., and Estell, D.A. (1987) in Protein Engineering (A.R. Liss) in press, "Protein engineering of subtilisin."
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Wells, J.A. and Yount, R.G. (1979) Proc. Natl. Acad. Sci. USA 76, 4966-4970. "Active site trapping of nucleotides by crosslinking two sulfhydryls in myosin sub-fragment 1."