UCSF

Mark J. S. Kelly Biosketch

The following is a biographical sketch intended for use by the National Institutes of Health (NIH).

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Who

Name

Mark J. S. Kelly

Position title

Associate Director UCSF NMR Lab and Adjunct Professor, Department of Pharmaceutical Chemistry

eRA Commons user name

MARKELLY

Education/training

Institution and location

Degree

Completion date

Field of study

King’s College, London

BSc

07/1986

Microbiology

Manchester Institute of Technology (UMIST)

MSc

07/1987

Biochemical Engineering

King’s College, London

PhD

10/1991

Microbiology

King’s College, London (Robert Poole)

Postdoctoral

02/1992

Molecular Biology

EMBL (Matti Saraste & Hartmut Oschkinat)

Postdoctoral

01/1996

Structural Biology

A. Personal statement

I have a broad background in microbiology, genetics, biochemistry and structural biology, with specific training and expertise in the application of Nuclear Magnetic Resonance spectroscopy (NMR) to studies of protein structure-function. As a postdoctoral fellow at the EMBL, Heidelberg, I developed NMR methodology, which facilitates rapid structure determination (global folds) and ligand binding studies for large protein complexes (50 kDa)1. During my time at Triad Therapeutics, I used NMR fragment screening and highly sensitive Inter-Ligand-nOe techniques to guide the development of nanomolar bi-ligand kinase inhibitors with high selectivity; these were also competitive with both ATP and substrate peptides. Techniques developed during these projects to refine and extend existing NMR methods to guide chemical linking of proximal binding fragments, led to publication of two patents2,3.

My main interest lies in the structural basis of protein function in cells. At UCSF, I and my lab have worked on a number structural and function studies together with other laboratories at UCSF. These have included applying NMR drug discovery methods to two NCI cancer targets (p97/VCP and Taspase-1) that were pursued within a CBC Specialized Applications Center at UCSF4. In another study, we used NMR to characterize the structural differences between two strains of the yeast prion protein Sup35, which propagate as a b-sheet rich prion form, whose structural properties depend on growth temperature (with Jonathan Weissman)5. Together with Diane Barber and Matt Jacobson, we showed how the protein Talin, thought to regulate cytoskeleton dynamics and cell migration in response to small changes in intracellular pH (pHi), functions as a pH sensor where protonation of His2418 allosterically regulates the actin binding site6. Together with Jack Taunton’s lab, we identified a previously unrecognized activation motif in a linker between the first two SH3 domains of the protein Nck, that directly engages the N-WASP GBD and competes with VCA binding activating the Arp2/3 complex7. In addition, we have studied metabolite patterns in animal models of stroke injury and investigated the outcomes following application of artificial hypothermia to ischemic neonatal brain slices (in collaboration with Dr. Lawrence Litt and Donna Ferriero)8. These studies represent a sample of studies pursued with several groups at UCSF over the last 12 years.

  1. Kelly M. J. S., Ball L. J., Richter G., Fischer M., Krieger C., Yu Y., Bermel W., Schmieder P., Karlsson G., Bacher A. and H. Oschkinat (2001). Structure and Function studies of the 47kDa 3,4-dihydroxy-2-butanone 4-phosphate synthase from Escherichia coli by NMR; an enzyme involved in riboflavin biosynthesis. Proceedings of the National Academy of Sciences of USA, 98:13025-13030. PMCID: PMC60818.
  2. WO 2004/083814 Kelly M. J. S., Villar H. O., Wang J., Lee M. S. and Y. Qin. (2004) Nuclear Magnetic Resonance Assembly of Chemical Entities Using Advanced Antenna Probes.
  3. US 7,653,490 Sem D. S., Pellecchia M., Dong Q., Kelly M. J. S. and M. S. Lee (2010) Nuclear Magnetic Resonance Assembly of Chemical Entities.
  4. Chimenti M.S., Bulfer S.L., Neitz R.J., Renslo A.R., Jacobson M.P., James T.L., Arkin M.R. and J. S. Kelly (2015). A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. Journal of Biomolecular Screening 20:788-800.
  5. Toyama B. H., Kelly M. J. S., Gross J. D. and J. S. Weissman (2007). The structural basis of yeast prion strain variants. Nature 449:233-7.
  6. Srivastava J., Barreiro G., Groscurth S., Gingras A. R., Goult B. T., Critchley D. R., Kelly M. J. S., Jacobson M. P. and D. L. Barber (2008). Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proceedings of the National Academy of Sciences of USA 105:14436-41. PMCID: PMC2532973.
  7. Okrut J., Prakash S., Wu Q., Kelly M. J. S. and J. Taunton (2015). Allosteric N-WASP activation by an inter-SH3 domain linker in Nck. Proceedings of the National Academy of Sciences of USA 112: E6436-45. PMCID: PMC4664294.
  8. Liu J, Sheldon R. A, Segal M .R., Kelly M. J. S., Pelton J. G., Ferriero D.M., James T.L., and L Litt (2013). 1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia-ischemia distinguished normothermic recovery from mild hypothermia recoveries. Pediatric Research 74:170-9. PMCID: PMC3734529.

B. Positions and honors

Positions and employment

1996–2002

Team Leader, Structural Biology, Institute of Molecular Pharmacology, Berlin, Germany

2002–2003

Group Leader, NMR Drug Discovery, Triad Therapeutics Inc., San Diego, CA

2003–2009

Ass. Adj. Professor, Pharmaceutical Chemistry, University of California, San Francisco, CA

2009–present

Adjunct Professor, Pharmaceutical Chemistry, University of California, San Francisco, CA

Honors

1987

SERC CASE Graduate Fellowship

1992

EMBO Long-Term Postdoctoral Fellowship

1994

Welcome Trust Traveling Fellowship

1995

EMBL Postdoctoral Fellowship

C. Contributions to science

  1. Structural studies of proteins involved in cellular signaling and disease

    With my early training in Microbiology, my main interest lies in the structural basis of protein function in cells. Early in my career during my graduate work and post-doc I used a number of spectroscopic and structural techniques to study the physiological roles and structure-function of cytochrome oxidases in the respiratory protection of the enzyme nitrogenase, and the function of a di-nuclear copper center in cytochrome c oxidasesa. Following a couple of years at a Biotech company, Triad Therapeutics, working on kinase targets (p38a), I moved to UCSF where I and my lab have worked on a number structure-function studies together with other laboratories at UCSF. Together with Jonathan Weissman’s lab, we used NMR to characterize the structural differences between two strains of the yeast prion protein Sup35, which propagate as a b-sheet rich prion form, whose structural properties depend on growth temperature (4°C or 37°C), and which, following infection of a host growing at the other temperature, show a hereditary behaviorb. Together with Diane Barber and Matt Jacobson’s labs, we showed how the protein Talin, thought to regulate cytoskeleton dynamics and cell migration in response to small changes in intracellular pH (pHi), functions as a pH sensor where protonation of His2418 allosterically regulates the actin binding sitec. Together with Jack Taunton’s lab, we identified a previously unrecognized activation motif in a linker between the first two SH3 domains of the protein Nck, that directly engages the N-WASP GBD and competes with VCA binding to the GTPase Binding Domain (GBD) releasing the inhibition of N-WASP and activating the Arp2/3 complex, thereby promoting actin filament assembly on cellular membranesd. These three studies represent a sample of several studies pursued at UCSF.

    1. Wilmanns M., Lappalainen P., Kelly M. J. S., Sauer-Eriksson E., and M Saraste (1995). Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered di-nuclear copper center. Proceedings of the National Academy of Sciences of USA 92:11955-11959. PMCID: PMC137846.
    2. Toyama B. H., Kelly M. J. S., Gross J. D. and J. S. Weissman (2007). The structural basis of yeast prion strain variants. Nature 449:233-7.
    3. Srivastava J., Barreiro G., Groscurth S., Gingras A. R., Goult B. T., Critchley D. R., Kelly M. J. S., Jacobson M. P. and D. L. Barber (2008). Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proceedings of the National Academy of Sciences of USA 105:14436-41. PMCID:
    4. Okrut J., Prakash S., Wu Q., Kelly M. J. S. and J. Taunton (2015). Allosteric N-WASP activation by an inter-SH3 domain linker in Nck. Proceedings of the National Academy of Sciences of USA 112: E6436-45. PMCID:
  2. New methods for NMR drug discovery to target large proteins and complex protein machines

    NMR offers both versatility and high-fidelity for de novo discovery of ligands and follow-up of binders due to low rates of false positives. During my time at Triad Therapeutics, I used NMR fragment screening and highly sensitive Inter-Ligand-nOe techniques to guide the development of nanomolar bi-ligand kinase inhibitors with high selectivity; these were also competitive with both ATP and substrate peptides. Techniques developed during these projects to refine and extend existing NMR methods to guide chemical linking of proximal binding fragments to generate new series of inhibitors, led to publication of two patentse,f.

    In addition to ‘ligand observe’ experiments, at Triad Therapeutics we applied methods developed during my post-doc using deuteration to selectively protonate the methyl groups of Met, Ile and Thr in kinase targets to provide probes to monitor ligand binding in these large targets. We exploited characteristics known for the behavior of isolated methyl groups in 2D [13C, 1H]-HMQC experiments that enable sensitive high-resolution spectra to be acquired for large proteins when utilizing these ‘methyl-protonated’ samples. A similar approach was refined and optimized by Lewis Kay’s group to develop an experiment termed ‘Methyl-TROSY’ that has enabled NMR studies of large protein complexes. At UCSF, I applied this technique to characterize ligand-binding to a large protein machine, the 324 kDa ND1 p97/VCP hexamerg, and recently to demonstrate the conformations of Ile residues in the binding site of an allosteric inhibitor are coupled to those in the ATP binding site in the p97/VCP D2 hexamer.

    1. WO 2004/083814 Kelly M. J. S., Villar H. O., Wang J., Lee M. S. and Y. Qin. (2004) Nuclear Magnetic Resonance Assembly of Chemical Entities Using Advanced Antenna Probes.
    2. US 7,653,490 Sem D. S., Pellecchia M., Dong Q., Kelly M. J. S. and M. S. Lee (2010) Nuclear Magnetic Resonance Assembly of Chemical Entities.
    3. Chimenti M.S., Bulfer S.L., Neitz R.J., Renslo A.R., Jacobson M.P., James T.L., Arkin M.R. and J. S. Kelly (2015). A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. Journal of Biomolecular Screening 20:788-800.
  3. New methods for structure determination of large proteins and complexes

    The application of the original 13C-/15N-isotope labelling methods introduced for NMR structure determination of medium sized proteins (10-20 kDa), ligand-binding and dynamics studies are limited to systems with M.W.<30 kDa. As a post-doc there was clearly potential for NMR to provide atomic-level descriptions of the mechanisms underlying important biological processes, such as dynamics and interactions with ligands and binding partners, as well as structural data (albeit at lower resolution - global folds) for larger systems. From earlier work, protein deuteration and amino acid-/site-selective labeling seemed to offer a means to overcome the fast relaxation and crowded spectra intrinsic to higher molecular weight systems. Working at the EMBL in Heidelberg, with access to the deuterated 13C-/15N-labelled growth media produced there for heterologous expression of proteins with different levels of deuteration, in collaboration with Ernest Laue and James Keeler’s groups at the University of Cambridge, we demonstrated the benefits of deuteration to increase sensitivity and resolution for multi-dimensional heteronuclear NMR experiments applied to larger systemsh. Two further studies showed deuteration in combination with amino acid-selective pronation permitted highly-sensitive well resolved NOESY experiments to be collected enabling global folds of larger systems to be determinedi,j. In a proof of principle study, we applied these methods to determine the structure of a 47 kDa homodimeric protein comprised of two chains of 216 aa, a potential target for anti-infectives and herbicides. The NMR structure of this large dimeric enzyme (47kDa) still remains one of the largest protein structures of its type solved by Nuclear Magnetic Resonancek. These early applications of deuteration in combination with 13C-/15N-labelling, together with efforts from several other labs, have led to the development of a diverse and powerful series of methods able to provide comprehensive descriptions of ligand/partner binding, and monitor changes in structure and dynamics associated with the function of large and complex proteins. The list of studies now includes studies of protein machines such as the proteasome, chaperones, nucleosomes, and nascent protein chains emerging from the ribosome.

    1. Nietlispach D., Clowes R. T., Broadhurst R. W., Ito Y., Keeler J., Kelly M. J. S., Ashurst J., Oschkinat H., Domaille P. J., and E.D Laue (1996). An approach to the structure determination of larger proteins using triple resonance NMR experiments in conjunction with random fractional deuteration. Journal of the American Chemical Society 118:407-415.
    2. Smith B. O., Ito Y., Raine A., Teichmann S., Ben-Tovim L., Nietlispach D., Broadhurst R. W., Terada T., Kelly M. J. S., Oschkinat H., Shibata T., Yokoyama S., and E. D. Laue (1996). An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. Journal of Biomolecular NMR 8:360-368
    3. Kelly M. J. S., Yu Y., Krieger C., Ball L., Schmieder P., Richter G., Bacher A. and H. Oschkinat (1999). Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47kDa homodimer: Potential for NMR structure determination of large proteins. Journal of Biomolecular NMR 14:79-83.
    4. Kelly M. J. S., Ball L. J., Richter G., Fischer M., Krieger C., Yu Y., Bermel W., Schmieder P., Karlsson G., Bacher A. and H. Oschkinat (2001). Structure and Function studies of the 47kDa 3,4-dihydroxy-2-butanone 4-phosphate synthase from Escherichia coli by NMR; an enzyme involved in riboflavin biosynthesis. Proceedings of the National Academy of Sciences of USA, 98:13025-13030. PMCID:

See also

Complete list of published work in MyBibliography