Theory and simulation of protein dynamics, folding, and function

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We have made significant progress in several areas related to protein dynamics, folding, binding, and function. Structure and dynamics of large multiprotein assemblies. We combined a coarse-grained simulation model and experiments to study the structures and motions of large multiprotein complexes and modular proteins with partially disordered segments. For this we used an ensemble refinement approach that allowed us to combine simulation ensembles and low-resolution x-ray scattering data. In collaboration with the experimental groups of Dr. Hurley and Dr. Eaton (both NIDDK, NIH), we obtained detailed structures of ESCRT-II and of the supercomplex between ESCRT-I and ESCRT-II in solution (1). On the basis of these structures we could propose a detailed model for the function of the ESCRT machinery, which is a major player in membrane protein trafficking and other cellular processes, and is hijacked by viruses, in particular HIV. Dynamic kinase-phosphatase complexes. In collaboration with the groups of Prof. Peti and Prof. Page (Brown University), we used our coarse-grained molecular simulation model to integrate a broad range of experimental data reporting on the structure and dynamics of the complexes formed between MAP kinases and phosphatases. We contributed to the determination of the solution structure of a complete MAPKMAPK-regulatory protein complex, formed between p38alpha and hematopoietic tyrosine phosphatase (HePTP). This structure allowed us to perform a detailed investigation of the molecular basis of specificity and fidelity in MAPK regulation. As part of this collaboration with Profs. Peti and Page, we also determined the structures of MAP kinase ERK2 in complex with HePTP, which is involved in T cell activation in lymphocytes. We found that the resting state of the ERK2:HePTP complex adopts a highly extended, dynamic conformation that becomes compact and ordered in the active state complex. This work demonstrated the significant dynamic structural changes in these complexes, provided the first structural insight into an active state MAPK-phosphatase complex. Computational studies of slow dynamics. We have studied the theoretical foundation and algorithmic realization of string methods to sample slow conformational dynamics (4). We demonstrated that the proper treatment of dynamic effects results in more meaningful transition pathways that capture the reactive flux associated with motion through configuration space. 1. E. Boura, B. Rozycki, H. S. Chung, D. Z. Herrick, B. Canagarajah, D. Cafiso, W. A. Eaton, G. Hummer, J. H. Hurley, Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission, Structure 20, 874-886 (2012). 2. D. M. Francis, B. Rozycki, D. Koveal, G. Hummer, R. Page, W. Peti, Structural basis of p38α regulation and specificity by hematopoietic tyrosine phosphatase, Nature Chem. Biol. 7, 916-924 (2011). 3. D. M. Francis, B. Rozycki, A Tortajada, G. Hummer, W. Peti, R. Page, Resting and Active States of the ERK2:HePTP Complex, J. Am. Chem. Soc. Communication 133, 1713817141 (2011). 4. M. E. Johnson, G. Hummer, Characterization of a dynamic string method for the construction of transition pathways in molecular reactions, J. Phys. Chem. B 116, 8573-8583 (2012).