Normal mode analysis of the horseradish peroxidase collective motions: correlation with spectroscopically observed heme distortions.
Normal mode analysis of the horseradish peroxidase collective motions: correlation with spectroscopically observed heme distortions.
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辣根过氧化物酶集体运动的正态模式分析：与光谱观察到的血红素扭曲的相关性。
DOI：
10.1002/bip.20463
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
Fidy,Judit
中科院分区：
文献类型：
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作者：
Laberge,Monique;Kovesi,Istvan;Yonetani,Takashi;Fidy,Judit
辣根过氧化物酶C是一种III类过氧化物酶，其结构通过两个内源性钙原子的存在而稳定。钙去除已被证明降低酶的酶活性，并显着影响血红素的光谱可检测的性能，如铁的自旋状态，血红素正常模式，和平面性的扭曲。在这项工作中，我们报告的正常模式分析（NMA）进行2纳秒的分子动力学模拟模型，以描述钙去除蛋白质集体运动的影响，并调查活性位点（血红素）和蛋白质基质波动之间的相关性。我们表明，在天然过氧化物酶模型中，血红素波动与基质波动相关，而在钙耗尽模型中则不然。© 2006 Wiley Periodicals，Inc. Biopolymers 82：425-429，2006这篇文章最初作为公认的预印本在线发表。“在线发布”日期对应于预印本。您可以通过向Biopolymers编辑部发送电子邮件（biopolymers@wiley.com）索取预印本的副本
Horseradish peroxidase C is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme and significantly affect the spectroscopically detectable properties of the heme, such as the spin state of the iron, heme normal modes, and distortions from planarity. In this work, we report on normal mode analysis (NMA) performed on models subjected to 2 ns of molecular dynamics simulations to describe the effect of calcium removal on protein collective motions and to investigate the correlation between active site (heme) and protein matrix fluctuations. We show that in the native peroxidase model, heme fluctuations are correlated to matrix fluctuations while they are not in the calcium‐depleted model. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 425–429, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com