MOLECULAR SIMULATIONS OF CATALYSIS, MOLECULAR MACHINE FUNCTIONS AND BIOMATERIAL

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 这是我们关于使用最先进的分子模拟来研究酶的催化机理、生物分子机器和生物材料的性质的建议的更新。具体地说，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QM/MM混合研究，酶动力学(RNaseA)、信号蛋白(Chey)、分子马达(Myosin)和DNA结合蛋白(IHF)的分子动力学模拟，以及非天然多肽和多肽通过膜的运输。计算将主要使用我们自己的开发版本CHARMM进行，该版本经过了很好的调整，以利用NCSA的并行架构。NCSA机器的能力对于这些大型和具有挑战性的系统的生产性模拟至关重要。

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.