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Perrin L, Loiseau N, André F, Delaforge M. Metabolism of N-methyl-amide by cytochrome P450s. FEBS J 2011; 278:2167-78. [DOI: 10.1111/j.1742-4658.2011.08133.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res 2007; 6:1899-916. [PMID: 17391015 PMCID: PMC2588346 DOI: 10.1021/pr060393m] [Citation(s) in RCA: 193] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.
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Affiliation(s)
- Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- CORRESPONDING AUTHOR FOOTNOTE: Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
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