A METHOD FOR DETERMINING THE POSITIONS OF POLAR HYDROGENS ADDED TO A PROTEIN-STRUCTURE THAT MAXIMIZES PROTEIN HYDROGEN-BONDING
A METHOD FOR DETERMINING THE POSITIONS OF POLAR HYDROGENS ADDED TO A PROTEIN-STRUCTURE THAT MAXIMIZES PROTEIN HYDROGEN-BONDING
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DOI：
10.1002/prot.340120305
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发表时间：
1992-03-01
期刊：
影响因子：
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通讯作者：
ORNSTEIN, RL
中科院分区：
文献类型：
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作者：
BASS, MB;HOPKINS, DF;ORNSTEIN, RL
描述了一种用于蛋白质结构中极性氢的最佳位置的自动化方法。该方法处理赖氨酸、丝氨酸、苏氨酸和酪氨酸的极性侧链氢和蛋白质的氨基末端。该程序名为NETWORK，将蛋白质的潜在氢键对分成相互作用的供体和受体组。对每个局部基团进行搜索，以找到形成最多氢键的排列。如果两种或更多种排列具有相同数目的氢键，则选择具有最短氢键组的排列。组氨酰侧链的极性氢被特别处理，并且允许该残基的电离状态改变，如果这种改变导致局部基团的额外氢键。该程序将接受蛋白质数据库以及生物系统格式的坐标文件。输入和输出例程可以很容易地修改，以接受其他坐标文件格式。从这种方法的预测相比，已知的氢位置牛胰腺胰蛋白酶抑制剂，胰岛素，RNase-A，胰蛋白酶的中子衍射结构已被确定。该程序的有用性进一步证明了酶细胞色素P-450 CAM与不使用网络的分子动力学模拟的比较。
An automated method for the optimal placement of polar hydrogens in a protein structure is described. This method treats the polar, side chain hydrogens of lysine, serine, threonine, and tyrosine and the amino terminus of a protein. The program, called NETWORK, divides the potential hydrogen-bonding pairs of a protein into groups of interacting donors and acceptors. A search is conducted on each of the local groups to find an arrangement which forms the most hydrogen bonds. If two or more arrangements have the same number of hydrogen bonds, the arrangement with the shortest set of hydrogen bonds is selected. The polar hydrogens of the histidyl side chain are specifically treated, and the ionization state of this residue is allowed to change, if this change results in additional hydrogen bonds for the local group. The program will accept Protein Data Bank as well as Biosym-format coordinate files. Input and output routines can be easily modified to accept other coordinate file formats. The predictions from this method are compared to known hydrogen positions for bovine pancreatic trypsin inhibitor, insulin, RNase-A, and trypsin for which the neutron diffraction structures have been determined. The usefulness of this program is further demonstrated by a comparison of molecular dynamics simulations for the enzyme cytochrome P-450cam with and without using NETWORK.