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首页> 外文期刊>Biochemistry >Experimentally Restrained Molecular Dynamics Simulations for Characterizing the Open States of Cytochrome P450cam
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Experimentally Restrained Molecular Dynamics Simulations for Characterizing the Open States of Cytochrome P450cam

机译：用于表征细胞色素P450cam开放状态的受实验约束的分子动力学模拟

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摘要

Residual dipolar couplings (RDCs) were used as restraints in fully solvated molecular dynamicsnsimulations of reduced substrate- and carbonmonoxy-bound cytochrome P450cam (CYP101A1), a 414-nresidue soluble monomeric heme-containing camphor monooxygenase from the soil bacterium Pseudomonasnputida. Then1nDNH residual dipolar couplings used as restraints were measured in two independent alignmentnmedia. A soft annealing protocol was used to heat the starting structures while incorporating the RDCnrestraints. After production dynamics, structures with the lowest total violation energies for RDC restraintsnwere extracted to identify ensembles of conformers accessible to the enzyme in solution. The simulations resultnin substrate orientations different fromthat seen in crystallographic structures and amore open and accessiblenenzyme active site and largely support previously reported differences between the open and closed states ofnCYP101A1.
机译：残留偶极偶合（RDCs）用作完全还原的底物和碳一单氧结合的细胞色素P450cam（CYP101A1）的完全溶剂化分子动力学的模拟，CYP101A1是一种来自土壤细菌Pseudomonasnputida的414个残基的可溶性单体含血红素的樟脑单加氧酶。然后在两个独立的比对介质中测量了作为约束的1nDNH残留偶极耦合。使用软退火协议来加热起始结构，同时并入RDCn约束。生产动态之后，提取具有RDC约束的最低总违背能量的结构，以鉴定溶液中酶可及的构象体集合。模拟结果导致底物取向不同于晶体结构中所见的取向，并且具有更开放和可访问的酶活性位点，并在很大程度上支持了先前报道的nCYP101A1打开和关闭状态之间的差异。

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    《Biochemistry》 |2011年第10期|p.1664-1671|共8页
  • 作者

    Eliana K. Asciutto Marina Dang Susan Sondej Pochapsky Jeffry D. Madura and Thomas C. Pochapsky;

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    §Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States,) Department of Chemistry, MS 015, Brandeis University, 415 South Street, Waltham, Massachusetts02454-9110,United States, and ^Rosenstiel BasicMedical Sciences Research Institute, BrandeisUniversity,Waltham,Massachusetts02454-9110, United States;

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