MOLECULAR SIMULATIONS OF CATALYSIS, MOLECULAR MACHINE FUNCTIONS AND BIOMATERIAL

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 这是对我们提出的采用最先进的分子模拟来研究酶的催化机制、生物分子机器和生物材料的性质的更新。具体而言，这些项目包括金属蛋白（细胞色素c氧化酶）和核糖体化学机制的混合QM/MM研究，酶动力学（RNase A），信号蛋白（CheY），分子马达（肌球蛋白）和DNA结合蛋白（IHF）的分子动力学模拟，以及非天然肽和肽通过膜的转运。计算将主要使用我们自己的CHARMM开发版本进行，该版本经过很好的调整，可以利用NCSA的并行架构。NCSA机器的强大功能对于这些大型且具有挑战性的系统的高效仿真至关重要。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for 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.