MINIMIZATION OF POLYPEPTIDE ENERGY .I. PRELIMINARY STRUCTURES OF BOVINE PANCREATIC RIBONUCLEASE S-PEPTIDE
MINIMIZATION OF POLYPEPTIDE ENERGY .I. PRELIMINARY STRUCTURES OF BOVINE PANCREATIC RIBONUCLEASE S-PEPTIDE
复制标题
DOI：
10.1073/pnas.58.2.420
复制
发表时间：
1967-01-01
影响因子：
11.1
通讯作者：
SCHERAGA, HA
中科院分区：
文献类型：
--
作者：
GIBSON, KD;SCHERAGA, HA
UNB= a b UHf () A (1 r 2 r6 r6 吸引力项的系数 UH 是通过将参与键的一对原子的所有剩余静电和非键能贡献相加计算得出的，并要求当 UNB 为最小值时（f (0) 设置等于 1），氢原子和受体原子之间的距离为 1.85 A。这个过程似乎给出了 UNB 最小值的合理值；然而，它很难与实验结果进行有效的比较，因为后者总是包含许多在 UH 计算中未考虑的原子之间的相互作用。通过函数 f (0) 引入了角度依赖性，其中 0 表示 00< 0< 1350 f (0)=(2) cos4 20 表示 1350< 0< 1800，0 是向量 AH 和 B...H 之间的角度，其中 A 为供体原子，B 为受体原子。对于线性氢键，0=1800。当键为线性时，该函数等于 1.0，并且当键偏离线性时，没有考虑涉及受体原子周围的方向的可能的角度依赖性。在超过几埃的原子间距离处，静电能下降得更慢。原子允许溶剂分子（在本例中为水，介电常数约为 80）
UNB= a b UHf () A (1 r 2 r6 r6 The coefficient UH of the attractive term was calculated by sum-ning all the re-maining electrostatic and nonbonded energy contributions of the pair of atoms in-volved in the bond, and requiring that the distance between the hydrogen atom and the acceptor atom be 1.85 A when UNB is a minimum (with f (0) set equal to 1). This procedure appeared to give reasonable values for UNB at the minimum; however, it is difficult to make a valid comparison with experimental results, since the latter always include many interactions between atoms not taken into account in the calculation of UH. Angular dependence was introduced through the function f (0), where0 for 00< 0< 1350 f (0)=(2) cos4 20for 1350< 0< 1800 and 0 is the angle between the vectors AH and B... H, with A being the donor atom and B the acceptor atom. For a linear hydrogenbond, 0= 1800. This function is equal to 1.0 when the bond is linear and falls off rapidly to zero as the bond departs from linearity. No accountwas taken of possible angulardependence involving the orientation around the acceptor atom. The hydrogen bond and 6-12 potentials become negligible at interatomic distances of more than a few angstroms. The electrostatic energies fall off more slowly with distance; but since a sufficiently large separation of the atoms allows solvent molecules (in this case water, with a dielectric constant of about 80) to