Kang Young Kee, Scheraga Harold A
Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea.
J Phys Chem B. 2008 May 1;112(17):5470-8. doi: 10.1021/jp711484f. Epub 2008 Apr 10.
An efficient method is presented to calculate atomic charges of peptides and proteins derived from Mulliken electronic populations for terminally blocked amino acids (Ac-X-NHMe, X = any neutral or charged residue) calculated at the B3LYP/6-31G(d,p)//HF/6-31G(d,p) level of theory. This electronic population-derived atomic charges (EPAC) method is based on the geometry-dependent atomic charge (GDAC) method proposed by Cho et al. (J. Phys. Chem. B 2001, 105, 3624), in which atomic charges are calculated by using the partial equalization of atomic electronegativities with electronegativity parameters and damping factors given by interatomic distances between covalently bonded atoms in a molecule. The overall mean absolute difference (mad) and root-mean-square deviation (rmsd) between dipole moments micro(EPAC) and micro(B3LYP), obtained from EPAC charges and from B3LYP/6-31G(d,p) level calculations, respectively, for Ac-X-NHMe are estimated to be 0.38 and 0.59 D, respectively, for 26 representative conformations in the training set, and 0.54 and 0.79 D, respectively, for 172 representative conformations not used for parametrization. For Ac-(Ala)(n)-NHMe (n = 2-6), the EPAC method reasonably predicts the increase of the dipole moment with increase of the chain length, although the deviations from the micro(B3LYP) values are somewhat larger. For Ac-Ala-NHMe and Ac-(Ala)(3)-NHMe, the EPAC charge for a specific type of atom does not depend on its position in the sequence or on the length of the sequence. In addition, charge neutrality holds for any Ala residue of these two peptides. Thus, these results suggest that the EPAC charges derived from B3LYP/6-31G(d,p) Mulliken populations can be used reliably for conformational analysis of peptides and proteins.
本文提出了一种有效的方法，用于计算在B3LYP/6 - 31G(d,p)//HF/6 - 31G(d,p)理论水平下计算得到的末端封闭氨基酸（Ac - X - NHMe，X = 任何中性或带电荷残基）的肽和蛋白质的Mulliken电子布居衍生的原子电荷。这种基于电子布居的原子电荷（EPAC）方法是基于Cho等人提出的几何相关原子电荷（GDAC）方法（《物理化学杂志B》2001年，105卷，3624页），其中原子电荷是通过使用原子电负性的部分均衡来计算的，电负性参数和阻尼因子由分子中共价键合原子之间的原子间距离给出。对于Ac - X - NHMe，分别从EPAC电荷和B3LYP/6 - 31G(d,p)水平计算得到的偶极矩μ(EPAC)和μ(B3LYP)之间的总体平均绝对差（mad）和均方根偏差（rmsd），对于训练集中的26个代表性构象，估计分别为0.38 D和0.59 D，对于未用于参数化的172个代表性构象，分别为0.54 D和0.79 D。对于Ac - (Ala)n - NHMe（n = 2 - 6），尽管与μ(B3LYP)值的偏差稍大，但EPAC方法合理地预测了偶极矩随链长增加而增加。对于Ac - Ala - NHMe和Ac - (Ala)3 - NHMe，特定类型原子的EPAC电荷不取决于其在序列中的位置或序列长度。此外，这两种肽的任何Ala残基都保持电荷中性。因此，这些结果表明，从B3LYP/6 - 31G(d,p) Mulliken布居衍生的EPAC电荷可可靠地用于肽和蛋白质的构象分析。
