Unlike random heteropolymers, proteins fold into unique ordered structures guided by their amino acid sequence. In the folded states proteins are not static but undergo structural changes in response to change in the pH, ligand binding, etc. that governs their function. Understanding the detailed mechanisms underlying these processes is essential to complete knowledge of protein structure and function. To address these questions, we use molecular simulation, statistical mechanics, molecular modeling and massive computational resources.

pH Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway
Deconstructing Activation Events in Rhodopsin
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly.
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling.
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection
Functionally Important Conformations of the Met20 Loop in Dihydrofolate Reductase are Populated by Rapid Thermal Fluctuations