Biochemistry Department

Jefferson Perry


Dr. Jefferson Perry 

Jefferson Perry

Assistant Professor of Biochemistry


Protein Crystallography, Small Angle X-Ray Scattering, Signal Transduction, Genome Stability, Fragment-Based Lead Discovery, Rational-Based Drug Discovery

Perry Research Group
PubMed Citations
Curriculum Vitae


Dr. Jeff Perry obtained his B.Sc. degree in ‘Biochemistry, with a Year in Industry’ from Imperial College of Science, Technology and Medicine, London, U.K, which included a year’s research at Glaxo-Wellcome, U.K. His Ph.D. studies were in Prof. Sir Tom L. Blundell’s laboratory, the former Head of Department, Department of Biochemistry, University of Cambridge, U.K. His doctoral work was sponsored by the BBSRC, U.K. and also Pfizer Central Research, U.K, and focused on structural studies of cell surface glycoproteins. He was a post-doctoral fellow at Lawrence Berkeley National Labs, Berkeley, Ca and at the same time a Visiting Scientist at The Scripps Research Institute, La Jolla, Ca, focusing on defining the structures and molecular mechanisms of proteins involved in DNA repair and genome stability. Dr. Perry was then a Senior Research Fellow and then Staff Scientist at Scripps, studying the SUMOylation and Ubiquitination machinery, in relation to genome stability. Dr. Perry became an International Professor for Amrita University, Kerala, India in 2005, and more recently an adjunct Professor at Francisco de Vitoria, Madrid, Spain in 2015. Dr. Perry joined the UCR Faculty in October 2014, and the focus of his research is on signal transduction pathways control human health and disease. 

Research Interests

Dr. Perry’s research interests are in defining molecular mechanisms of key protein complexes having pathological links to cancer, neurodegenerative disease and/or rapid aging, using macromolecular crystallography, small angle x- ray scattering and biochemistry studies. This research is focused on novel SUMO and ubiquitin pathway proteins, kinases and GTPases, involved in either signal transduction and/or genome stability. The results from the structural-based studies are also being used to identify compounds that can selectively modulate activities of these protein complexes. Such small molecules can be used as tools for more clear definitions of cellular functions, and in certain cases, can potentially open up new research avenues aimed at developing novel therapies.

Awards and Honors
  • 2014 – Present  Arnold O. Beckman Review Panel

  • 2015  UCR Seed Grant

  • 2014  Ad Hoc Review Committee, NIH

  • 2013 – 2014  NIH/NIGMS P50 Collaborative Development Program Award
  • 2011 – 2015  NIH/NIAMS New Investigator R03

  • 1996 – 2000  Pfizer Central Research Ltd, UK, CASE-sponsored Ph.D. studentship

Selected Publications
  • Finley J. Allgaier & J. Jefferson P. Perry. Reactive Oxygen Species in Amyotrophic Lateral Sclerosis.
 Book Chapter. Reactive Oxygen Species in Biology and Human Health. Editor Shamim I. Ahmad. (2016) June 1 CRC Press ISBN 9781498735452. Corresponding author.

  • Andrew Hollands, Ross Corriden, Gabriela Gysler, Samira Dahesh, Joshua Olson, Syed Raza Ali, Maya T. Kunkel, Ann E. Lin, Stefano Forli, Alexandra C. Newton, Geetha B. Kumar, Bipin G. Nair, J. Jefferson P. Perry, and Victor Nizet. Natural product anacardic acid from cashew nut shells stimulates neutrophil extracellular trap production and bactericidal activity J. Biol. Chem (2016) Jul 1;291(27):13964-73.

  • Tsai CL, Williams GJ, Perry JJ, Tainer JA. An AAA+ ATPase Clamshell Targets Transposition. Cell. 2015 Aug 13;162(4):701-3 

  • Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Perry JJ, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. Lanosterol reverses protein aggregation in cataracts. Nature. (2015) 523, 607–611. Epub. Jul 22nd 2015 . Faculty1000prime Recommended
  • Fan H, Hahm J, Diggs S, Perry JJ, Blaha G. Structural and Functional Analysis of BipA, a Regulator of Virulence in enteropathogenic Escherichia coli. J Biol Chem. 2015 Jul 10. [Epub ahead of print].

  • Zhang ZM, Liu S, Lin K, Luo Y, Perry JJP, Wang Y, Song J. Crystal Structure of Human DNA Methyltransferase 1. J Mol Biol. 2015 Jun 10. pii: S0022-2836(15)00341-1. doi: 10.1016/j.jmb.2015.06.001. [Epub ahead of print].
  • Perry JJP, Ballard GD, Albert AE, Dobrolecki LE, Malkas LH, Hoelz DJ. Human C6orf211 encodes Armt1, a protein carboxyl methyltransferase that targets PCNA and is linked to the DNA damage response. Cell Rep. 2015 Mar 3;10(8):1288-96. doi: 10.1016/j.celrep.2015.01.054. Epub 2015 Feb 26.
  • Groocock, LM, Nie M, Prudden J, Moiani D, Wang T, Cheltsov A, Arvai AS, Hitomi C, Tainer JA, Luger K, Perry JJP*, Lazzerini-DenchiE* & Boddy MN*.RNF4Interacts with both SUMO and Nucleosomes to Promote the DNA Damage Response. EMBO Reports (2014) May;15(5):601-8. Epub 2014 Apr 8. *Co-corresponding author.
  • Shibata A, Moiani D, Arvai AS, Perry JJP, Harding SM, Genois MM, Maity R, van Rossum-Fikkert S, Kertokalio A, Romoli F, Ismail A, Ismalaj E, Petricci E, Neale MJ, Bristow RG, Masson JY, Wyman C, Jeggo P & Tainer JA. DNA Double Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities. Mol. Cell (2014) Jan 9;53(1):7-18. Epub 2013 Dec 5. Faculty 1000 – ‘Must read’ Manuscript.
  • Perry JJP & Tainer JA. Developing advanced x-ray scattering methods combined with crystallography and computation. Invited Review. Methods (2013). Mar;59(3):363-71. Epub 2013 Jan 29.
  • Omanakuttan A, Nambiar J, Harris RM, Chinchubose B, Pandurangan N, VargheseRK, Kumar GB, Tainer JA, Banerji A, Perry JJP & Nair BG.Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9. Mol. Pharmacology (2012) Oct;82(4):614-22. Epub June 28th.
  • Pratt A, Getzoff E, Perry JJP*. Amyotrophic lateral sclerosis: Update and New Developments. Review. Degenerative Neurological and Neuromuscular Disease(2012) Feb;2012(2):1-14. *Corresponding author.
  • Groocock L, Prudden J, Perry JJP, Boddy MN. RecQ4 Orthologue Hrq1 is Critical for DNA Interstrand Crosslink Repair and Genome Stability in Fission Yeast. Mol. Cell. Biol. (2012) Jan;32(2):276-87. Epub Nov 7th 2011.
  • Shin DS, Pratt, A, Getzoff ED& Perry JJP*. Amyotrophic Lateral Sclerosis, Advanced Understanding of Neurodegenerative Diseases, Raymond Chuen-Chung Chang (Ed.), (2011) ISBN: 978-953-307-529-7, InTech. http://www.intechopen.com/articles/show/title/amyotrophic-lateral-sclerosis.*Corresponding author.
  • Trego KS, Chernikova SB, Davalos AR, Perry JJP, Finger LD, Ng C, Tsai MS, Yannone SM, Tainer JA, Campisi J, Cooper, PK.The DNA Repair Endonuclease XPG Interacts Directly and Functionally with the WRN Helicase Defective in Werner Syndrome.Cell Cycle (2011). Jun 15;10 (12).
  • Perry JJP &Tainer JA. All Stress Out Without ATM Kinase. Science Signaling (2011) April 5; 4(167):18.
  • Prudden, J* & Perry, JJP*, Minghua Nie, Arvai, A, C. Hitomi, Guenther, G, Tainer J.A, Boddy, M.N. DNA Repair and Global Sumoylation are Regulated by Distinct Ubc9 Non-covalent Complexes. Mol Cell Biol. (2011) Epub March 28th. *Co-first author.
  • Heideker J, Prudden, J, Perry JJP, Tainer JA, Boddy MN. SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability. PLOS genetics (2011). March 3; 7(3): e1001320.
  • Perry JJP, Asiathamby A, Barnebey A, Kiamanesh F, Chen DJ, Han S, Tainer JA & Yannone SM.Identification of a coiled-coil in WRN that facilitates multimerization and promotes exonuclease processivity. Journal of Biological Chemistry (2010) Aug 13: 285 (33):25699-707 Epub June 1st.
  • Perry JJP, Cotner-Gohara, E, Ellenberger T & Tainer, JA. Structural dynamics in DNA damage signaling and repair. Current Opinion in Structural Biology. Invited Review (2010) June 20:1-12. Epub May 1st.
  • Perry JJP, Shin DS, Getzoff ED & Tainer JA. The Structural Biochemistry of the Superoxide Dismutases. Invited Review. Biochemica et Biophysica (2010) Feb; 1804(2):245-262.
  • Perry JJP, Shin DS & Tainer JA. Structural biology of Amyotrophic Lateral Sclerosis, Book Chapter of ‘Molecular mechanisms of DNA repair defects’, Editor Shamim I Ahmad, Landes Biosciences Publication, Adv Exp Med Biol. 2010;685:9-20 (2010). Epub Nov 5 (2009).
  • Perry JJP, Harris R, Moiani, D, Olson A & Tainer JA. MAP kinase p38α C-terminal domain binding pocket characterized by crystallographic and computational Analyses. J. Mol. Biol. (2009) Aug 7; 391 (1): 1-11.
  • Perry JJP*, Hitomi K, Tainer JA. Flexibility Promotes Fidelity. Preview. Structure (2009) May 13;17(5):633-4. *Corresponding author.
  • Prudden J* & Perry JJP*, Arvai A, Tainer JA & Boddy MN. Molecular mimicry of SUMO promotes DNA repair. Nature Struct. & Mol. Biol. (2009) May; 16, 509-516.*Co-first author. Faculty 1000 – 4.8 – ‘Must read’ Manuscript.
  • Perry JJP*, Hearn AS, Cabelli DE, Lepock JR, Tainer JA, Nick HS, Silverman DN*. Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry (2009) April; 48 (15):3417–3424. *Co-corresponding author.
  • Heideker J, Perry JJP & Boddy MN. Genome stability roles for SUMO-targeted ubiquitin ligases. Invited review. DNA repair (2009) Apr 5;8(4):517-24.
  • Mohan SS, Perry JJP, Poulose N, Nair BG, Anilkumar G. Homology modeling of Glut4, an insulin regulated facilitated glucose transporter and docking studies with ATP and its inhibitors. Journal of Biomolecular Structure and Dynamics.(2009) Feb;26(4):455-64.
  • Perbernard S, Perry JJP, Tainer JA, Boddy MN. Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability. Mol Biol Cell. (2008) Oct;19(10):4099-109.
  • Chrencik JE, Brooun A, Zhang H, Irimpam M, Hura GL, Foster SA, Perry JJP, Ramage P, Widmer H, Bokach, Tainer JA, Gisbert Wechbecker, Kuhn P. Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1. J. Mol. Biol. (2008) Jul 25;380(5):828-43.
  • Perry JJP, Tainer JA, Boddy MN, A SIM-ultaneous role for SUMO and Ubiquitin. Invited Review. Trends in Biochemical Science (2008) May;33(5):201-8. Cover Article.
  • Perry JJP* & Tainer JA, Structural biology of Cockayne syndrome, Book Chapter of ‘Molecular mechanisms of Cockayne syndrome’, Editor Shamim I Ahmad, Landes Biosciences Publication, Epub Mar 27 (2008). *Corresponding Author.
  • Prudden J, Pebernard S, Raffa G, Slavin DA, Perry JJP, Tainer JA, McGowan CH, Boddy MN, SUMO-targeted ubiquitin ligases in genome stability. EMBO J. (2007) Sep 19;26(18):4089-101. Faculty 1000 – 6.0 – ‘Must Read’ Manuscript, Nature Reviews Molecular Cell Biology Research Highlight, and Science-STKE Editor’s Choice.
  • Perry JJP, Fan L, Tainer JA. Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair. Neuroscience (2007) Apr 14;145(4):1280-1299.
  • Perry JJP, Yannone SM, Holden LG, Hitomi C, Asaithamby A, Han S, Cooper PK, Chen DJ & Tainer JA.   WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nature Struct. Mol. Biol. (2006) May; 13 (5), p414-422.
  • Ren X, Tu C, Bhatt D, Perry JJP, Tainer JA, Cabelli DE, & Silverman DE. Kinetic and structural characterization of human manganese superoxide dismutase containing 3-fluorotyrosine. Journal of Molecular Structure (2006) 790 (1-3), 168-173, Jun 5.
  • Ayala I, Perry JJP, Szczepanski J, Tainer JA, Vala MT, Nick HS & Silverman DN. Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys. J. (2005) Dec;89(6):4171-9.
  • Greenleaf WB, Perry JJP, Hearn AS, Cabelli DE, Lepock JR, Stroupe ME, Tainer JA, Nick HS & Silverman DN. Role of hydrogen bonding in the active site of human manganese superoxide dismutase. Biochemistry (2004) Jun 8;43(22):7038-7045.
  • Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BV, Soares CM, Steward RE, Williams M, Carrondo MA, Blundell TL, & Mizuguchi K. An iterative structure-assisted approach to sequence alignment and comparative modeling. Proteins: Struct. Funct. Genet. (1999) Suppl. 3(9):55-60.

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