Development of modified force field for cation-amino acid interactions:Ab initio-derived empirical correction terms with comments on cation-? interactions
✍ Scribed by Donini, Oreola; Weaver, Donald F.
- Publisher
- John Wiley and Sons
- Year
- 1998
- Tongue
- English
- Weight
- 280 KB
- Volume
- 19
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
The modeling of voltage-gated ion-channel proteins is a continuing challenge for force-field calculations because of the diverse range of interactions involved. In particular, current force fields are not parameterized for either ion᎐amino acid or amino acid᎐electric field interactions. To address the parameterization of ion᎐amino acid interactions, we have tested the use of empirical correction terms, derived from ab initio calculations of single amino Ž .
q acids representing the peptide backbone interacting with K ions. Having demonstrated the utility of such an approach, we then extended the application to the amino acid side chains. The calculation of the interaction of K q with Ž . serine, cysteine, methionine, lysine, arginine, aspartate, histidine uncharged , tyrosine, tryptophan, and phenylalanine, both completes the parameterization of the molecular environments contained in the amino acids, and allows specific comment on these ion᎐functional group interactions. The cation᎐ interactions were of particular interest, given recent proposals in the literature and the fear that force fields would not be able to treat such interactions. We present a Ž w x . comprehensive comparison of the ab initio DFT BLYP , 6-311 G** and force Ž . field CHARMm22.0 assessments of these interactions.