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Archaic Chaos: Intrinsically Disordered Proteins In Archaea, Bin Xue, Robert W. Williams, Christopher J. Oldfield, A. Keith Dunker, Vladimir N. Uversky
Archaic Chaos: Intrinsically Disordered Proteins In Archaea, Bin Xue, Robert W. Williams, Christopher J. Oldfield, A. Keith Dunker, Vladimir N. Uversky
Molecular Medicine Faculty Publications
Background: Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion …
Retro-Morfs: Identifying Protein Binding Sites By Normal And Reverse Alignment And Intrinsic Disorder Prediction, Bin Xue, A. Keith Dunker, Vladimir N. Uversky
Retro-Morfs: Identifying Protein Binding Sites By Normal And Reverse Alignment And Intrinsic Disorder Prediction, Bin Xue, A. Keith Dunker, Vladimir N. Uversky
Molecular Medicine Faculty Publications
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 …