Arginine-phosphate salt bridges in protein-DNA complexes: a Car-Parrinello study
Arginine-phosphate salt bridges in protein-DNA complexes: a Car-Parrinello study
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DOI：
10.1016/s0166-1280(01)00368-2
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发表时间：
2001-11-16
影响因子：
--
通讯作者：
Carloni, P
中科院分区：
文献类型：
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作者：
Frigyes, D;Alber, F;Carloni, P
我们提出了一个梯度校正的密度泛函（DFT）为基础的分子动力学（MD）研究的水化和蛋白质中的磷酸盐加合物的动力学。使用交换相关函数的BLYP配方进行计算。我们专注于两个代表性的H-键模式中发现的蛋白质-DNA复合物中存在和不存在水分子。我们的结构模型包括甲基胍（代表精氨酸侧链），二甲基磷酸盐（代表DNA中的磷酸部分）和水分子H-键合的复合物。我们的DFT-MD模拟，在室温下进行，指出水合作用作为一个可能的关键因素的双齿复合物的分子识别。此外，他们认为，水化伴随着显着的极化效应。(C)2001 Elsevier Science B. V.保留所有权利。
We present a gradient-corrected density functional (DFT)-based molecular dynamics (MD) study on hydration and dynamics of arginine-phosphate adducts in proteins. Calculations are carried out using the BLYP recipe for the exchange-correlation functional. We focus on two representative H-bond patterns found in protein-DNA complexes in the presence and in the absence of water molecules. Our structural models include methylguanidinium (representing die arginine side chain), dimethyl-phosphate (representing the phosphate moiety in DNA) and water molecules H-bonding the complex. Our DFT-MD simulations, carried out at room temperature, point to hydration as a possible key factor for molecular recognition of the bidentate complex. Furthermore they suggest that hydration is accompanied by significant polarization effects. (C) 2001 Elsevier Science B.V. All rights reserved.