Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder PredictionReportar como inadecuado




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1

Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

2

Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA

3

Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA

4

Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia





*

Author to whom correspondence should be addressed.



Abstract Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features MoRFs. A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level. View Full-Text

Keywords: reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS





Autor: Bin Xue 1,2,3, A. Keith Dunker 1,2 and Vladimir N. Uversky 1,2,3,4,*

Fuente: http://mdpi.com/



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