Simulating Protein Structures, Complexes, And Dynamics

我们改进了人类钙受体的同源模型，并发表了一篇分析环缺失突变的论文。另外两篇论文正在出版中；一篇包括酿酒酵母芳烷基胺N-乙酰转移酶同源模型，另一篇涉及水母晶状体J3-晶体蛋白的建模。另一项研究羧基肽酶E的结构和功能的研究已经提交发表。我们还使用朗之万动力学和简化的非键势模拟了短肽在溶液中的动力学。一份描述这部作品的手稿正在准备中。此外，我们对抗生素与二氢叶酸还原酶结合的研究正在进行中。 我们模拟了底物3，4-二羟基苯乙醇醛及其衍生物在醛糖还原酶活性部位的结合模式(提交发表)。我们还研究了反式-1，2-二氢二酚氧化醛糖还原酶的反应机理。我们利用量子力学和分子力学的结合势，研究了分支酸变位酶(提交申请)和5-羟色胺N-乙酰转移酶(准备稿)的催化机理。

We refined our homology model of the human calcium receptor, and a paper analyzing loop-deletion mutants was published. Two additional papers are in press; one includes a homology model of the Saccharomyces cerevisiae homolog of arylalkylamine N-acetyltransferase, and the other involves modeling of the J3-crystallin of the jellyfish lens. Another study that investigates the structure and function of carboxypeptidase E has been submitted for publication. We have also simulated the dynamics of short peptides in solution using Langevin dynamics and a simplified nonbond potential. A manuscript describing this work is in preparation. Also, our study of antibiotic binding to dihydrofolate reductase is ongoing. We modeled the binding mode of substrate 3,4-dihydroxyphenylglycolaldehyde and its derivatives at the active site of aldose reductase (submitted for publication). We have also studied the oxidation mechansim of aldose reductase with trans-naphthalene-1,2 dihydrodiol (in press). Utilizing combined potentials of quantum mechanics and molecular mechanics, we have investigated the catalytic mechansim of chorismate mutase (submitted for pubilcation) and Serotonin N-acetyltransferase (manuscript in preparation).