High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

• Published in: Proteins, structure, function, and bioinformatics Vol. 82; no. 8; pp. 1624 - 1635
• Main Authors: Shirai, Hiroki, Ikeda, Kazuyoshi, Yamashita, Kazuo, Tsuchiya, Yuko, Sarmiento, Jamica, Liang, Shide, Morokata, Tatsuaki, Mizuguchi, Kenji, Higo, Junichi, Standley, Daron M., Nakamura, Haruki
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01.08.2014; Wiley Subscription Services, Inc
• Subjects: Amino Acid Sequence; Animals; Antibodies - chemistry; Complementarity Determining Regions - chemistry; complementary determining region; Computational Biology - methods; Databases, Protein; fragment assembly; H3-rules; homology modeling; Humans; immunoglobulin; Immunoglobulin Variable Region - chemistry; Immunoglobulins - chemistry; Molecular Dynamics Simulation; Molecular Sequence Data; multicanonical molecular dynamics simulation; OSCAR; position specific scoring matrix; Protein Conformation; Spanner; structure prediction; complementary determining region; multicanonical molecular dynamics simulation; homology modeling; structure prediction; immunoglobulin; position specific scoring matrix; H3-rules; fragment assembly; OSCAR; Spanner
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24591

ABSTRACT In the second antibody modeling assessment, we used a semiautomated template‐based structure modeling approach for 11 blinded antibody variable region (Fv) targets. The structural modeling method involved several steps, including template selection for framework and canonical structures of complementary determining regions (CDRs), homology modeling, energy minimization, and expert inspection. The submitted models for Fv modeling in Stage 1 had the lowest average backbone root mean square deviation (RMSD) (1.06 Å). Comparison to crystal structures showed the most accurate Fv models were generated for 4 out of 11 targets. We found that the successful modeling in Stage 1 mainly was due to expert‐guided template selection for CDRs, especially for CDR‐H3, based on our previously proposed empirical method (H3‐rules) and the use of position specific scoring matrix‐based scoring. Loop refinement using fragment assembly and multicanonical molecular dynamics (McMD) was applied to CDR‐H3 loop modeling in Stage 2. Fragment assembly and McMD produced putative structural ensembles with low free energy values that were scored based on the OSCAR all‐atom force field and conformation density in principal component analysis space, respectively, as well as the degree of consensus between the two sampling methods. The quality of 8 out of 10 targets improved as compared with Stage 1. For 4 out of 10 Stage‐2 targets, our method generated top‐scoring models with RMSD values of less than 1 Å. In this article, we discuss the strengths and weaknesses of our approach as well as possible directions for improvement to generate better predictions in the future. Proteins 2014; 82:1624–1635. © 2014 Wiley Periodicals, Inc.