Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 11, Issue 10, Pages 3725-3747Publisher
MDPI AG
DOI: 10.3390/ijms11103725
Keywords
reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS
Funding
- National Institute of Health [R01 LM007688-01A1, GM071714-01A2]
- Russian Academy of Sciences
- Direct For Biological Sciences
- Emerging Frontiers [0849803] Funding Source: National Science Foundation
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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.
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