金黄色葡萄球菌谷氨酰胺依赖性酰胺转移酶（GatCAB）中沿两条分子内隧道的氨转移的计算分析。
Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).
作者信息
Dewage Sajeewa Walimuni, Cisneros G Andrés
机构信息
Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States.
出版信息
J Phys Chem B. 2015 Mar 5;119(9):3669-77. doi: 10.1021/jp5123568. Epub 2015 Feb 20.
Most bacteria and all archaea misacylate the tRNAs corresponding to Asn and Gln with Asp and Glu (Asp-tRNA(Asn) and Glu-tRNA(Gln)).The GatCAB enzyme of most bacteria converts misacylated Glu-tRNA(Gln) to Gln-tRNA(Gln) in order to enable the incorporation of glutamine during protein synthesis. The conversion process involves the intramolecular transfer of ammonia between two spatially separated active sites. This study presents a computational analysis of the two putative intramolecular tunnels that have been suggested to describe the ammonia transfer between the two active sites. Molecular dynamics simulations have been performed for wild-type GatCAB of S. aureus and its mutants: T175(A)V, K88(B)R, E125(B)D, and E125(B)Q. The two tunnels have been analyzed in terms of free energy of ammonia transfer along them. The probability of occurrence of each type of tunnel and the variation of the probability for wild-type GatCAB and its mutants is also discussed.
大多数细菌和所有古细菌会用天冬氨酸（Asp）和谷氨酸（Glu）对与天冬酰胺（Asn）和谷氨酰胺（Gln）相对应的tRNA进行错误酰化（Asp-tRNA(Asn)和Glu-tRNA(Gln)）。大多数细菌的GatCAB酶会将错误酰化的Glu-tRNA(Gln)转化为Gln-tRNA(Gln)，以便在蛋白质合成过程中掺入谷氨酰胺。该转化过程涉及氨在两个空间分离的活性位点之间的分子内转移。本研究对两条推测的分子内隧道进行了计算分析，这两条隧道被认为可描述两个活性位点之间的氨转移。对金黄色葡萄球菌的野生型GatCAB及其突变体：T175(A)V、K88(B)R、E125(B)D和E125(B)Q进行了分子动力学模拟。根据氨沿这两条隧道转移的自由能对它们进行了分析。还讨论了每种类型隧道出现的概率以及野生型GatCAB及其突变体概率的变化。
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