This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.This is a renewal of our proposal on employing state-of-the-art molecular simulations to study the catalytic mechanism of enzymes, properties of biomolecular machines and biomaterials. Specifically, the projects include hybrid QM/MM studies of chemical mechanisms in metalloproteins (cytochrome c oxidase) and the ribosome, molecular dynamics simulations of enzyme dynamics (RNase A), signaling protein (CheY), molecular motor (myosin) and DNA binding proteins (IHF), as well as non-natural peptides and peptide transport through membrane. The computations will be mainly carried out using our own developmental version of CHARMM, which is well tuned to take advantage of the parallel architecture at NCSA. The power of the NCSA machines is crucial to the productive simulation of these large and challenging systems.
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