Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

• Published in: Journal of computational chemistry Vol. 29; no. 12; pp. 1930 - 1944
• Main Authors: Katagiri, Daisuke, Fuji, Hideyoshi, Neya, Saburo, Hoshino, Tyuji
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.09.2008; Wiley Subscription Services, Inc
• Subjects: Analytical chemistry; Computational Biology; Computer Simulation; force field; Models, Molecular; Molecular biology; molecular dynamics; Molecular structure; prediction of protein structure; Protein Conformation; Protein Structure, Secondary; Proteins; Proteins - chemistry; Quantum Theory; Simulation; Water - chemistry; water phase
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.20963

Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between α-helix and β-sheet structures was significantly improved by the modification of charge parameters.