computer modeling in molecular biology.pdf

142 Benoft RouxTable 6-1. Interaction energies for the Gramicidin channel systema.H,O to Na+NMA C=O to Na'HzO to HzONMA C=O to HOHNMA N-H to OHHNMA to NMAModel system Energy in kJ/mol Distance in nmeXPHF/6-31G*CHARMMTIP3PHF/6-31G*CHARMMeXPHF/6-31G*TIP3PHF/6-31G*CHARMM-TIP3PHF/6-31G*CHARMM-TIP3PHF/6-31G*CHARMM100.3100.3114.5160.5158.022.627.427.432.030.026.328.532.434.00.2210.2200.2100.2100.2020.1810,1980.1910.2130.1930.2080.193a The ab inito interaction energies of Na' with water and NMA were calculated using theGaussian 82 [72] and Gaussian 86 [73] programs with the 6-31G* basis sets [74]. To accountfor the overestimated bond polarities the ab initio interactions energies were scaled accordingto Escaled = (Escf - Eb.s.) ,uexp/pscf, where pexp and pScf are the experimental and the computedab initio electric dipole of the molecule in the absence of the ion and Eb,s, is the correctionfor the basis set superposition error. The experimental ion-water affinity is from [66], the experimentalwater-water affinity is from [76], the results on hydrogen bonding systems are takenfrom [67].An ion-induced polarization term was found to be required to obtain the steeperthan-Coulombicdistance dependence of the ion-peptide interaction in the range of0.2 to 0.5 nm. The parameters of the potential function, i. e., the polarizability coefficients,the van der Waals and the core size, were adjusted to reproduce the salientfeatures of the ab initio potential surface accurately; the parameters of the ion-peptideand ion-water energy functions are given in [38], the partial charges and the Lennard-Jonesparameters assigned to the peptide backbone have been taken fromprevious work on the peptide-peptide potential [65, 681. All the interaction energiesinvolving Na', water and NMA are given in Table 6-1. The agreement between theempirical potential energy function and the ab initio results is satisfactory.6.3.1.3 Limitations of the Potential Energy FunctionThe present ion-peptide energy function only represents a first step in obtaining anaccurate potential function. Geometries and interaction energies obtained fromsmall isolated fragments are not always sufficient to construct an appropriate poten-