Simulation of Protein Dynamics, Folding, and Function

Diabetes, Digestive, Kidney Diseases

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Abstract

We have made significant progress in three major areas related to protein dynamics, folding, and function. (1) Nucleic acid translocation across membranes. Using extensive molecular dynamics simulations, we were able to study the translocation of RNA across membrane pores of ~1.5 nm diameter in full atomic detail (Yeh and Hummer, Proc. Natl. Acad. Sci. USA, 2004; Yeh and Hummer, Biophys. J., 2004). We found that conformational dynamics and hydrophobic attachment to the pore wells determined the translocation kinetics. A kinetic model based on the simulations could explain a series of recent experimental measurements. (2) Functional protein dynamics. Using molecular dynamics simulations, we succeeded in performing the first atomically detailed comparison of functional protein dynamics from theory and picosecond time-resolved X-ray crystallography experiments (Hummer, Schotte, and Anfinrud, Proc. Natl. Acad. Sci. USA, 2004, in press). The successful comparison of theory and experiment establishes the state of current simulations. Moreover, the single-molecule information provided by the simulation led to new insights into the role of protein motions in their function. (3) Accelerated molecular dynamics. We made significant progress in the development of new approaches to overcome the time-scale limitation in molecular simulation through path-sampling approaches (Hummer, J. Chem. Phys., 2004) and coarse-graining (Kevrekidis, Gear, and Hummer, AIChE J, 2004). (4) Single-molecule biophysics. We successfully applied our theory for extracting equilibrium thermodynamics information from non-equilibrium single-molecule pulling experiments to the unfolding of RNA (Hummer and Szabo, Acc. Chem. Res., submitted 2004).