Structural basis for substrate specificity of alphavirus nsP2 proteases.
Structural basis for substrate specificity of alphavirus nsP2 proteases.
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DOI：
10.1016/j.jmgm.2010.04.005
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发表时间：
2010-08-24
影响因子：
2.9
通讯作者：
Watowich, Stanley J.
中科院分区：
文献类型：
--
作者：
Russo, Andrew T.;Malmstrom, Robert D.;White, Mark A.;Watowich, Stanley J.
甲病毒nsP 2蛋白酶对于甲病毒非结构多聚蛋白（nsP 1234）的正确加工和病毒基因组的复制至关重要。我们结合分子动力学模拟与我们的结构研究，揭示了nsP 2蛋白酶催化位点和S1 '-S4亚位点的功能，调节蛋白酶的特异性。nsP 2蛋白酶的催化机制似乎类似于木瓜蛋白酶样半胱氨酸蛋白酶，保守的催化二联体在nsP 2活化状态下形成硫醇盐-咪唑鎓离子对。底物结合可能稳定该离子对。委内瑞拉马脑炎病毒（VEEV）nsP 2蛋白酶与nsP 1234切割位点的双分子复合物的分析确定蛋白酶残基His 510，Ser 511，His 546和Lys 706作为切割位点识别的关键。不同甲病毒及其同源切割位点序列的同源性建模和分子动力学模拟揭示了跨甲病毒株操作的底物识别的一般特征以及结合位点和切割位点残基之间的株特异性协变性。例如，发生在P3和S3亚位点残基的补偿性变化，以保持积极有利的互补结合表面。这些结果有助于解释甲病毒nsP 2蛋白酶如何识别非结构多蛋白内的不同切割位点，并区分密切相关的切割靶点。
The alphavirus nsP2 protease is essential for correct processing of the alphavirus nonstructural polyprotein (nsP1234) and replication of the viral genome. We have combined molecular dynamics simulations with our structural studies to reveal features of the nsP2 protease catalytic site and S1’-S4 subsites that regulate the specificity of the protease. The catalytic mechanism of the nsP2 protease appears similar to the papain-like cysteine proteases, with the conserved catalytic dyad forming a thiolate-imidazolium ion pair in the nsP2-activated state. Substrate binding likely stabilizes this ion pair. Analysis of bimolecular complexes of Venezuelan equine encephalitis virus (VEEV) nsP2 protease with each of the nsP1234 cleavage sites identified protease residues His510, Ser511, His546, and Lys706 as critical for cleavage site recognition. Homology modelling and molecular dynamics simulations of diverse alphaviruses and their cognate cleavage site sequences revealed general features of substrate recognition that operate across alphavirus strains as well as strain specific covariance between binding site and cleavage site residues. For instance, compensatory changes occurred in the P3 and S3 subsite residues to maintain energetically favourable complementary binding surfaces. These results help explain how alphavirus nsP2 proteases recognize different cleavage sites within the non-structural polyprotein and discriminate between closely related cleavage targets.
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DOI：
10.1002/prot.340040208
发表时间：
1988-01-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
BRUNGER, AT;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
16
作者：
Mossessova, E;Lima, CD
通讯作者：
Lima, CD
DOI：
10.1093/protein/8.2.127
发表时间：
1995-02-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
WALLACE, AC;LASKOWSKI, RA;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
5.4
作者：
Aguilar, PV;Paessler, S;Weaver, SC
通讯作者：
Weaver, SC
影响因子：
2.9
作者：
LEWIS, SD;JOHNSON, FA;SHAFER, JA
通讯作者：
SHAFER, JA