SIMULATING PROTEIN STRUCTURES, COMPLEXES, AND DYNAMICS

我们对HIV-1包膜糖蛋白gp120的V3环进行了结构计算。使用了来自液态和固态核磁共振数据的实验约束，并使用CHARMM程序评估了不同的模拟退火方案。一篇论文已经发表，另一篇手稿即将提交出版。我们总结了我们的研究，通过突变实验和分子模拟来确定底物结合部位。研究结果发表了。我们继续在CHARMM程序中开发蒙特卡罗模拟技术，包括对主链和侧链二面体构象的偏向搜索。这些方法通过使用溶剂化自由能的广义Born处理的α螺旋的初步折叠模拟来测试。根据肺炎链球菌二氢叶酸还原酶(DHFR)的晶体结构，建立了DHFR的同源模型。对抗生素甲氧苄啶结合的同源模型进行了蒙特卡罗模拟。研究了Ile 100突变为亮氨酸或蛋氨酸的结构效应。模拟表明，突变Ile100Leu导致主链松弛，打破残基100与甲氧嘧啶之间的氢键，从而对甲氧普林产生抗药性。根据大肠杆菌亮氨酸/异亮氨酸/缬氨酸周质结合蛋白的晶体结构，我们建立了人钙受体胞外区(Hcar ECD)的同源模型。实验数据和模型用于推测Hcar ECD的二聚体界面。已经发表了一篇论文。-分子建模、结构-功能关系、计算机模拟

We performed structure calculations for the V3 loop of the HIV-1 envelope glycoprotein gp120. Experimental restraints derived from liquid- and solid-state NMR data were used, and different simulated annealing protocols were evaluated using the CHARMM program. One paper has been published and another manuscript will soon be submitted for publication. We concluded our study of peptide binding to cyclin- dependent kinase 5. Mutagenesis experiments and molecular modeling were used to identify the substrate binding site. The results were published. We continued to develop Monte Carlo simulation techniques in the CHARMM program, incorporating biased searching of main-chain and side-chain dihedral conformations. The methods were tested with preliminary folding simulations of an alpha helix using a Generalized Born treatment of the solvation free energy. We made a homology model of dihydrofolate reductase (DHFR) from Streptococcus pneumonia from the crystal structure of DHFR from E. coli. Monte Carlo simulations were performed on the homology model with the antibiotic trimethoprim bound. The structural effects of mutating Ile 100 to Leu or Met were investigated. Simulations suggested that the mutation Ile100Leu results in main-chain relaxation that breaks a hydrogen bond between residue 100 and trimethoprim and thus confers resistance to trimethoprim. A manuscript is in preparation.We made a homology model of the extracellular domain of the human calcium receptor (hCaR ECD) based on the crystal structure of E. coli leucine/isoleucine/valine periplasmic binding protein. Experimental data and the model were used to infer the putative dimer interface of hCaR ECD. A paper has been published. - molecular modeling, structure-function relationship, computer simulation