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Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study

机译：Sir2同源活性位点内分子间相互作用的物理性质：分子动力学和从头算研究

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摘要

In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein–ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein–ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component.

机译：在本研究中，我们分析了NAD +依赖性脱乙酰基酶（Sir2同源酵母Hst2）与氨基甲酸酯-烟酰胺-腺嘌呤-二核苷酸（ADP-HPD）的相互作用。对于Sir2同源物，应用酵母Hst2对接程序。在对接过程中获得的蛋白质-ADP-HPD复合物的结构被用作分子动力学模拟的起点。通过分子动力学模拟对蛋白质-ADP-HPD复合物进行了分子间相互作用能分配。对形成脱乙酰酶结合袋的ADP-HPD和15个氨基酸进行了分析。尽管结果表明一阶静电相互作用能很大，但研究的配合物中多个氢键的存在可导致诱导成分的显着价值。

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期刊名称 Springer Open Choice
作者
Przemysław Czeleń; Żaneta Czyżnikowska;
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作者单位

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年(卷),期 -1(22),-1
年度 -1
页码 120
总页数 7
原文格式 PDF
正文语种
中图分类外科学;
关键词
Docking procedure Molecular dynamic simulations Intermolecular interaction energy partitioning;

机译：对接程序;分子动力学模拟;分子间相互作用能分配;

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专利

1. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study [J] . Czelen Przemyslaw, Czyznikowska Zaneta Journal of molecular modeling . 2016,第6期

机译：Sir2同源活性位点内分子间相互作用的物理性质：分子动力学和从头算研究
2. Physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: Differential transition state stabilization in phosphoryl transfer reaction [J] . Szarek P, Dyguda-Kazimierowicz E, Tachibana A, The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical . 2008,第37期

机译：cAMP依赖性蛋白激酶活性位点内分子间相互作用的物理性质：磷酸转移反应中的差异过渡态稳定。
3. Ab initio study of the physical nature of interactions between enzyme active site fragments in vacuo [J] . Sokalski WA., Grembecka J., Kedzierski P. Physical chemistry chemical physics: PCCP . 2001,第5期

机译：从头开始研究真空中酶活性位点片段之间相互作用的物理性质
4. Intermolecular interactions in molecular crystals studied by ab initio methods: From isolated interactions to patterns and crystals [C] . J.J.Novoa, NATO NATO advanced study institute on implications of molecular and materials structure for new technologies . 1999

机译：AB Initio方法研究的分子晶体中的分子间相互作用：从分离的相互作用与图案和晶体
5. Ab initio molecular dynamics of hydrogen-bonded systems: I. Influence of water on atmospheric reaction intermediate stability: Case study of hydroxy isoprene radical, II. Time-translation projection operators for computing temporal signatures in vibrational dynamics: Case study of the zundel cation. [D] . Dietrick, Scott M. 2011

机译：氢键体系的从头算分子动力学：I.水对大气反应中间稳定性的影响：羟基异戊二烯自由基的案例研究，II。时间平移投影算子用于计算振动动力学中的时间签名：zundel阳离子的案例研究。
6. Active Site Cysteine Is Protonated in the PAD4 Michaelis Complex: Evidence from Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations [O] . Zhihong Ke, Yanzi Zhou, Po Hu, -1

机译：活性位点半胱氨酸在PAD4 Michaelis复合体中质子化：来自出生 - oppenheimer AB ININIO QM / MM分子动力学模拟的证据
7. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study [O] . 2016

机译：Sir2同源活性位点内分子间相互作用的物理性质：分子动力学和从头算研究

Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study

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