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Computational Prediction of Association Free Energies for the C3d-CR2 Complex and Comparison to Experimental Data Alexander S. Cheung 292:1725-1728. 8. Guthridge, JM, Rakstang, JK, Young, KA, Hinshelwood, J, Aslam, M, Robertson, A, Gipson, MG, Sarrias, MR, Moore, WT, Meagher, M, Karp, D, Lambris, JD, Perkins, SJ, & Holers, VM (2001) Structural studies in solution of the recombinant N-terminal pair of short consensus/complement repeat domains of complement receptor type 2 (CR2/CD21) and interactions with its ligand C3dg, Biochemistry 40:5931-5941. 9. Clemenza, L, & Isenman, DE (2000) Structureguided identification of C3d residues essential for its binding to complement receptor 2 (CD21), Journal of Immunology 165:3839-3848. 10. Nagar, B, Jones, RG, Diefenbach, RJ, Isenman, DE, & Rini, JM (1998) X-ray crystal structure of C3d: A C3 fragment and ligand for complement receptor 2, Science 280:1277-1281. 11. Mallik, B, Zhang, L, Koide, S, & Morikis, D (2008) pH dependence of stability of the 10th human fibronectin type III domain: a computational study, Biotechnology Progress 24:48-55. 12. Morikis, D, Elcock, AH, Jennings, PA, & McCammon, JA (2001) Native state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations, Protein Science 10:2363-2378. 13. Morikis, D, Elcock, AH, Jennings, PA, & McCammon, JA (2001) Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations, Protein Science 10:2379-2392. 14. Zhang, L, & Morikis, D (2006) Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics, Biophysical Journal 90:3106-3119. 15. Wu, J & Morikis, D (2006) Molecular thermodynamics for charged biomacromolecules, Fluid Phase Equlibria 241:317-333. 16. Berman, HM, Westbrook, J, Feng, Z, Gilliland, G, Bhat, TN, Weissig, H, Shindyalov, IN, & Bourne, PE (2000) The Protein Data Bank, Nucleic Acids Research 28:235-242. 17. Guex, N, Peitsch, MC (1997) Swiss-model and the Swiss-Pdb-Viewer: an environment for comparative protein modeling, Electrophoresis 18:2714-2723. 18. Vriend, G (1990) WHAT IF: A molecular modeling and drug design program, Journal of Molecular Graphics 8:52-56. 19. Yang, J (2007) Implementation of a high throughput computational protocol for calculation and clustering of electrostatic potentials of protein families, M.S. Thesis, University of California, Riverside. 20. Dolinsky, TJ, Nielsen, JE, McCammon, JA, & Baker, NA (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmaann electrostatics calculations, Nucleic Acids Research 32:W665-W667 21. Sitkoff, D, Sharp, KA, & Honig, B (1994) Calculation of alkane to water solvation free energies using continuum solvent models, Journal of Physical Chemistry 98:1978–1988. 22. Baker, NA, Sept, D, Joseph, S, Holst, MJ, & McCammon, JA (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences (USA) 98:10037-10041. 23. Humphrey, W, Dalke, A, & Schulten, K (1996) VMD - Visual Molecular Dynamics Journal of Molecular Graphics 14:33-38. 22 UCR Un d e r g r a d u a t e Re s e a r c h Jo u r n a l
Phosphorylation of Crk Adaptor Protein by Cdc42-Activated Pak2 and Identification of Phosphorylation Sites Jisun Lee 1 , Jin-Hun Jung 2 , Jolinda A. Traugh 2 1 Department of Biology, 2 Department of Biochemistry University of California, Riverside ABSTRACT The p21-activated protein kinase Pak2 is activated in response to a variety of stresses. Pak2 is activated by binding of Cdc42(GTP) followed by autophosphorylation or by caspase3 cleavage. Pak2 modifies various targeted substrates. In this study Crk, an adaptor protein, was phosphorylated by Pak2 using (γ- 32 P)ATP. Phosphorylation of Crk was analyzed by SDS-polyacrylamide gel electrophoresis and phosphorimaging. Results from scintillation counting showed 0.6 mol/mol of 32P incorporated into Crk. Phosphoaminoacid analysis showed that Crk was phosphorylated on serine, not threonine. To identify the sites of phosphorylation, phosphorylated Crk was digested by the proteases Glu-C or trypsin and subjected to two-dimensional phosphopeptide mapping. The maps yielded two phosphopeptides, which suggested two phosphopeptides contained the same phosphorylation site or two distinctive phosphorylation sites on Crk. Potential phosphorylation sites in two sequences of Crk are located near the SH2 and SH3 domains. Faculty Mentors Jolinda Traugh Department of Biochemistry Jisun Lee worked as a dishwasher in my laboratory for several years, and also prepared electrophoresis buffer and solutions for staining and destaining proteins. She became interested in our research on the protein kinase Pak2, and received a campus Nova Award last summer to enable her to work in the laboratory full time. She has mastered a number of techniques to analyze phosphorylated proteins and identify the sites phosphorylated by Pak2. Jisun is a delight to work with. Her interest and motivation in writing this paper attests to her rapid growth and outstanding potential as a scientist. A U T H O R Jisun Lee Biology JinSun Lee is a fourth year student majoring in Biology. Her research interest involves the study of phosphorylation of proteins such as Crk, and she is currently working on the identification of phosphorylation sites of Crk. She hopes that research in this field may contribute to study of progression of tumor cells and its therapeutic solution in the future. Jisun would like to thank her family and two faculty mentors for their support and generous advice throughout her academic years. She plans to continue her studies in graduate school and work for the public interest in the future. Jin-Hun Jung Department of Biochemistry We have been studying a protein kinase, Pak2, which is activated under a variety of stress conditions, such as DNAdamaging and hyperosmolarity. Jisun Lee has been working on phosphorylation of a proto-oncoprotein Crk by Pak2. She has made a significant contribution to identification of the site of phosphorylation on Crk, which can lead us to study afunctional relationship of the two proteins in cells. She has successfully developed the research skills and related knowledge on her project. It has been a great pleasure to work with her. UCR Un d e r g r a d u a t e Re s e a r c h Jo u r n a l 23
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