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Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant

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Abstract

The replica-exchange Monte Carlo method based on the single amino acid potential (SAAP) force field, i.e., REMC/SAAP3D, was recently developed by our group for the molecular simulation of short peptides. In this study, the method has been improved by applying a distance-dependent dielectric (DDD) constant and extended to the peptides containing d-amino acid (AA) residues. For chignolin (10 AAs), a sigmoidal DDD model reasonably allocated the native-like β-hairpin structure with all-atom root mean square deviation (RMSD) = 2.0 Å as a global energy minimum. The optimal DDD condition was subsequently applied for Trp-cage (20 AAs) and its G10q mutant. The native-like α-rich folded structures with main-chain RMSD = 3.7 and 3.8 Å were obtained as global energy minima for Trp-cage and G10q, respectively. The results suggested that the REMC/SAAP3D method with the sigmoidal DDD model is useful for structural prediction for the short peptides comprised of up to 20 AAs. In addition, the relative contributions of SAAP to the total energy (%SAAP) were evaluated by energetic component analysis. The ratios of %SAAP were about 40 and 20% for chignolin and Trp-cage (or G10q), respectively. It was proposed that SAAP is more important for the secondary structure formation than for the assembly to a higher-order folded structure, in which the attractive van der Waals interaction may play a more important role.

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Data Availability

Supplementary data are available from the journal web page.

Code Availability

The program code of REMC/SAAP3D is available from the corresponding author at a request.

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Funding

This work was supported by Grant-in-Aid for Scientific Research on Innovative Areas (No. 2120005) from the Ministry of Education, Culture, Sports, Science and Technology, Japan (MI).

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  1. Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa, 259-1292, Japan

    Michio Iwaoka, Koji Yoshida & Taku Shimosato

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  1. Michio Iwaoka
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  2. Koji Yoshida
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  3. Taku Shimosato
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Contributions

MI organized the SAAP project and prepared the manuscript. KY modified the source code and carried out simulations and data analysis. TS managed the SAAP force field parameters, including those for D-amino acids.

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Correspondence to Michio Iwaoka.

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This paper is dedicated to late Dr. Harold A. Scheraga.

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Iwaoka, M., Yoshida, K. & Shimosato, T. Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant. Protein J 39, 402–410 (2020). https://doi.org/10.1007/s10930-020-09936-7

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