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Nucleic Acids Res. 2006 Apr 26;34(7):2117-27. doi: 10.1093/nar/gkl182. Print 2006.
2
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A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.钙调蛋白结构中钙离子去除效应的分子动力学研究
Biophys J. 2006 Jun 1;90(11):3842-50. doi: 10.1529/biophysj.105.077792. Epub 2006 Mar 13.
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Reducing CDK4/6-p16(INK4a) interface. Computational alanine scanning of a peptide bound to CDK6 protein.减少细胞周期蛋白依赖性激酶4/6-p16（INK4a）相互作用界面。与细胞周期蛋白依赖性激酶6蛋白结合的肽段的计算丙氨酸扫描。
Proteins. 2006 Jun 1;63(4):797-810. doi: 10.1002/prot.20943.
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Insights into voltage-gated calcium channel regulation from the structure of the CaV1.2 IQ domain-Ca2+/calmodulin complex.从CaV1.2 IQ结构域 - Ca2+/钙调蛋白复合物结构洞察电压门控钙通道调节机制
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Mlc1p蛋白与两种IQ模体肽复合物的分子动力学研究及自由能分析。

A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.

作者信息

Ganoth Assaf, Friedman Ran, Nachliel Esther, Gutman Menachem

机构信息

Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

出版信息

Biophys J. 2006 Oct 1;91(7):2436-50. doi: 10.1529/biophysj.106.085399. Epub 2006 Jul 14.

DOI:10.1529/biophysj.106.085399
PMID:16844751
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1562369/
Abstract

The Mlc1p protein from the budding yeast Saccharomyces cerevisiae is a Calmodulin-like protein, which interacts with IQ-motif peptides located at the yeast's myosin neck. In this study, we report a molecular dynamics study of the Mlc1p-IQ2 protein-peptide complex, starting with its crystal structure, and investigate its dynamics in an aqueous solution. The results are compared with those obtained by a previous study, where we followed the solution structure of the Mlc1p-IQ4 protein-peptide complex by molecular dynamics simulations. After the simulations, we performed an interaction free-energy analysis using the molecular mechanics Poisson-Boltzmann surface area approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the light-chain-binding domain of myosin V from the yeast S. cerevisiae is discussed.

摘要

来自芽殖酵母酿酒酵母的Mlc1p蛋白是一种类钙调蛋白，它与位于酵母肌球蛋白颈部的IQ基序肽相互作用。在本研究中，我们报告了从Mlc1p-IQ2蛋白-肽复合物的晶体结构开始的分子动力学研究，并研究了其在水溶液中的动力学。将结果与之前的一项研究进行了比较，在之前的研究中，我们通过分子动力学模拟追踪了Mlc1p-IQ4蛋白-肽复合物的溶液结构。模拟之后，我们使用分子力学泊松-玻尔兹曼表面积方法进行了相互作用自由能分析。基于Mlc1p-IQ蛋白-肽复合物的动力学，讨论了来自酿酒酵母的肌球蛋白V轻链结合结构域的结构。