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Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88

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Abstract

Elucidating the relationship between sequence and conformation is essential for the understanding of functions of proteins. While sharing 88 % sequence identity and differing by only seven residues, GA88 and GB88 have completely different structures and serve as ideal systems for investigating the relationship between sequence and function. Benefiting from the continuous advancement of the computational ability of modern computers, molecular dynamics (MD) simulation is now playing an increasingly important role in the study of proteins. However, the reliability of MD simulations is limited by the accuracy of the force fields and solvent model approximations. In this work, several AMBER force fields (AMBER03, AMBER99SB, AMBER12SB, AMBER14SB, AMBER96) and solvent models (TIP3P, IGB5, IGB7, IGB8) have been employed in the simulations of GA88 and GB88. The statistical results from 19 simulations show that GA88 and GB88 both adopt more compact structures than the native structures. GB88 is more stable than GA88 regardless of the force fields and solvent models utilized. Most of the simulations overestimated the salt bridge interaction. The combination of AMBER14SB force field and IGB8 solvent model shows the best overall performance in the simulations of both GA88 and GB88. AMBER03 and AMBER12SB also yield reasonable results but only in the TIP3P explicit solvent model.

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Acknowledgments

The authors thank the Supercomputer Center of East China Normal University for the support of CPU time.

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Authors and Affiliations

  1. Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China

    Juan Zeng

  2. Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, Hubei Province, South-Central University for Nationalities, Wuhan, 430074, China

    Yongxiu Li

  3. Department of Physics, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China

    John Z.H. Zhang

  4. NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China

    John Z.H. Zhang & Ye Mei

  5. State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China

    Ye Mei

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Correspondence to Juan Zeng.

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Zeng, J., Li, Y., Zhang, J.Z. et al. Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. J Mol Model 22, 177 (2016). https://doi.org/10.1007/s00894-016-3027-8

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