LIFE SCIENCES

Most biological functions are mediated by conformational changes and specific association of protein molecules. Atomistic simulations are ideal to study the molecular details of such systems. However, often the associated timescales are beyond the maximum simulation times that can be reached even on supercomputers. In this project, researchers developed and tested advanced sampling simulations to accelerate protein domain motions and association of partner molecules. These techniques allow to study domain motions and association of protein molecules on currently accessible time scales. They were successfully applied to study the Hsp90 chaperone protein and to several protein-protein and protein-peptide systems of biological importance.

Heat shock protein 90 (Hsp90) is a molecular chaperone essential for the folding and stabilization of a wide variety of client proteins in eukaryotes. Many of these processes are associated with cancer and other diseases, making Hsp90 an attractive drug target. Hsp90 is a highly flexible protein that can adopt a wide range of distinct conformational states, which in turn are tightly coupled to the enzyme’s ATPase activity. In this project, atomistic molecular dynamics simulations, free energy calculations, and hybrid quantum mechanics/classical mechanics simulations were performed on both monomeric and full-length dimeric Hsp90 models to probe how long-range effects in the global Hsp90 structure regulate ATP-binding and hydrolysis.

Complex I is the largest and most intricate respiratory enzyme, which couples the free energy released from quinone reduction to transfer protons across a biological membrane. Recent X-ray structures of bacterial and eukaryotic complex I have advanced our understanding of the enzyme’s function, but the mechanism of its long-range energy conversion remains unsolved. Here, we use atomistic molecular dynamics simulations and free energy calculations to study how the protonation state, hydration dynamics, and conformational dynamics of complex I regulate its proton pumping activity. Our simulations mimic transient states in the enzyme’s pumping cycle to draw a molecular picture of the protonation signals along the membrane domain of complex I.