Curcó David, Rodríguez-Ropero Francisco, Alemán Carlos
Departament d'Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, E-08028, Barcelona, Spain.
J Comput Aided Mol Des. 2006 Jan;20(1):13-25. doi: 10.1007/s10822-005-9032-0. Epub 2006 Apr 19.
Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.
利用量子力学计算得出了用于逆反向修饰肽分子力学研究的扭转和静电参数。将所得参数与常规肽计算得到的参数进行了比较。通过去除与所研究扭转之外的相互作用变化相关的能量贡献，对跨越相应二面角获得的旋转轮廓进行了校正。为此，将轮廓各点的扭转能量估计为相应的量子力学能量减去所跨越二面角变化在键长、键角和其他二面角中引起的扰动所产生的键合和非键合能量贡献。这些能量使用力场表达式进行计算。将校正后的轮廓拟合为三项傅里叶展开式以推导扭转参数。逆反向修饰残基的原子电荷源自严格计算的量子力学静电势。此外，还检验了基于几何相关电荷和固定电荷的静电模型的可靠性。
