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首页> 外文期刊>Journal of Molecular Biology >Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
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Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

机译：利用分子动力学和连续溶剂模型计算HIV蛋白酶二聚体稳定性的自由能

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Dimerization of HIV-I protease (HIV PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disrupting dimerization of the enzyme can inhibit its activity. We have calculated the relative binding free energies between different dimers of the HIV protease using molecular dynamics and a continuum model, which we call MM/PBSA. We examined the dominant negative inhibition of the HIV PR by a mutated form of the protease and found relative dimerization free energies of homo- and hetero-dimerization consistent with experimental data. We also developed a rapid screening method, which was called the virtual mutagenesis method to consider other mutations which might stabilize non-wild-type heterodimers. Using this approach, we considered the mutations near the dimer interface which might cause dominant negative inhibition of the HIV PR. The rapid method we developed can be used in studying any ligand-protein and protein-protein interaction, in order to identify mutations that can enhance the binding affinities of the complex. (C) 2000 Academic Press. [References: 40]
机译：HIV-1蛋白酶（HIV PR）单体的二聚化是病毒蛋白水解活性和随后产生感染性病毒颗粒的必要先决条件。破坏酶的二聚化可以抑制其活性。我们已经使用分子动力学和连续模型（称为MM / PBSA）计算了HIV蛋白酶不同二聚体之间的相对结合自由能。我们检查了蛋白酶的突变形式对HIV PR的显性负抑制作用，发现均二聚和异二聚化的相对二聚自由能与实验数据一致。我们还开发了一种快速筛选方法，称为虚拟诱变方法，以考虑可能稳定非野生型异二聚体的其他突变。使用这种方法，我们考虑了二聚体界面附近的突变，这可能导致对HIV PR的显性负抑制作用。我们开发的快速方法可用于研究任何配体-蛋白质和蛋白质-蛋白质相互作用，以鉴定可增强复合物结合亲和力的突变。 （C）2000学术出版社。 [参考：40]

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