The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis
The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis
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DOI：
10.1002/jmr.658
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发表时间：
2004-03-01
影响因子：
2.7
通讯作者：
Jelesarov, I
中科院分区：
文献类型：
--
作者：
Gorfe, AA;Caflisch, A;Jelesarov, I
Tn 916整合酶蛋白（INT-DBD）的N-末端结构域负责Tn 916接合转座子转座所需的链切割和连接反应过程中的DNA结合。位点特异性结合是由插入大沟的三链β折叠表面的大量蛋白质-DNA接触促进的。蛋白质经历了一个微妙的构象转变，并在蛋白质-DNA复合物中轻微展开。NMR数据对许多带电残基的构象定义不明确，但突变研究表明，去除极性侧链会降低结合亲和力，而非极性接触具有延展性。根据结合焓和结合热容量的分析，我们认为蛋白质-DNA界面的脱水是不完全的。本研究提出了从分子动力学调查的INT-DBD-DNA复合物的目的是在更详细的了解构象动力学和水合作用的位点特异性结合的作用的结果。比较模拟（共13 ns）的游离蛋白质和结合蛋白质构象（在隔离或DNA结合）揭示了内在的灵活性，在某些部分的分子。与部分展开相关的构象适应似乎是由蛋白质-DNA接触诱导的。蛋白质-DNA氢键网络是高度动态的。模拟识别蛋白质-DNA相互作用，解决不好或仅从NMR系综推测。单个水分子和水分子团动态优化“湿”蛋白质-DNA界面极性相互作用的互补性。模拟结果是有用的，以建立一个定性的实验数据之间的联系，个别残基的贡献，结合亲和力和热力学性质的INT-DBD单独和复杂的DNA。版权所有（C）2004约翰威利父子有限公司。
The N-terminal domain of the Tn916 integrase protein (INT-DBD) is responsible for DNA binding in the process of strand cleavage and joining reactions required for transposition of the Tn916 conjugative transposon. Site-specific association is facilitated by numerous protein-DNA contacts from the face of a three-stranded beta-sheet inserted into the major groove. The protein undergoes a subtle conformational transition and is slightly unfolded in the protein-DNA complex. The conformation of many charged residues is poorly defined by NMR data but mutational studies have indicated that removal of polar side chains decreases binding affinity, while non-polar contacts are malleable. Based on analysis of the binding enthalpy and binding heat capacity, we have reasoned that dehydration of the protein-DNA interface is incomplete. This study presents results from a molecular dynamics investigation of the INT-DBD-DNA complex aimed at a more detailed understanding of the role of conformational dynamics and hydration in site-specific binding. Comparison of simulations (total of 13 ns) of the free protein and of the bound protein conformation (in isolation or DNA-bound) reveals intrinsic flexibility in certain parts of the molecule. Conformational adaptation linked to partial unfolding appears to be induced by protein-DNA contacts. The protein-DNA hydrogen-bonding network is highly dynamic. The simulation identifies protein-DNA interactions that are poorly resolved or only surmised from the NMR ensemble. Single water molecules and water clusters dynamically optimize the complementarity of polar interactions at the 'wet' protein-DNA interface. The simulation results are useful to establish a qualitative link between experimental data on individual residue's contribution to binding affinity and thermodynamic properties of INT-DBD alone and in complex with DNA. Copyright (C) 2004 John Wiley Sons, Ltd.