Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Abstract

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure–function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc‐pVxZ//MP2/6‐31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc‐pVQZ//MP2/6‐31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone ϕ, ψ dihedral crossterms or a ϕ, ψ grid‐based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the ϕ, ψ dihedral parameters along with the grid‐based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of ϕ and ψ in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid‐based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1400–1415, 2004