Deciphering the preference and predicting the viability of circular permutations in proteins

• Type of Material: Article
• Authors: Wei-Cheng Lo, National Tsing Hua University; Tian Dai, Emory University; Yen-Yi Liu, National Chiao Tung University; Li-Fen Wang, National Chiao Tung University; Jenn-Kang Hwang, National Chiao Tung University; Ping-Chiang Lyu, National Tsing Hua University
• Language: English
• Date: 2012-02-16
• Publisher: Public Library of Science
• Publication Version: Final Published Version
• Copyright Statement: © 2012 Lo et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1371/journal.pone.0031791
• Title of Journal or Parent Work: PLoS ONE
• ISSN: 1932-6203
• Volume: 7
• Issue: 2
• Start Page: e31791
• End Page: e31791
• Grant/Funding Information: This work was funded by the National Science Council, Taiwan (http://www.nsc.gov.tw) with NSC grant number 99-2745-B-009-001-ASP (Academic Summit Program) to JH; 99-2811-M-007-073 and 99-3112-B-007-003 to PL.; The Ministry of Education, Taiwan (http://english.moe.gov.tw/) also funded this study with the Development Plan for World Class University and Research Centers of Excellence (MOU ATU Plan).
• Keywords: Computer Simulation; Support Vector Machine; Amino Acid Sequence; Models, Molecular; Proteins; Protein Engineering
• Research Categories: Biology, Molecular; Biology, Biostatistics

Abstract

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology.