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      Digested disorder : Quarterly intrinsic disorder digest (July–August–September, 2013)

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          Abstract

          The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a new issue of reader’s digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

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          Flexible nets. The roles of intrinsic disorder in protein interaction networks.

          A. Keith Dunker, Marc S. Cortese, Pedro Romero … (2005)
          Proteins participate in complex sets of interactions that represent the mechanistic foundation for much of the physiology and function of the cell. These protein-protein interactions are organized into exquisitely complex networks. The architecture of protein-protein interaction networks was recently proposed to be scale-free, with most of the proteins having only one or two connections but with relatively fewer 'hubs' possessing tens, hundreds or more links. The high level of hub connectivity must somehow be reflected in protein structure. What structural quality of hub proteins enables them to interact with large numbers of diverse targets? One possibility would be to employ binding regions that have the ability to bind multiple, structurally diverse partners. This trait can be imparted by the incorporation of intrinsic disorder in one or both partners. To illustrate the value of such contributions, this review examines the roles of intrinsic disorder in protein network architecture. We show that there are three general ways that intrinsic disorder can contribute: First, intrinsic disorder can serve as the structural basis for hub protein promiscuity; secondly, intrinsically disordered proteins can bind to structured hub proteins; and thirdly, intrinsic disorder can provide flexible linkers between functional domains with the linkers enabling mechanisms that facilitate binding diversity. An important research direction will be to determine what fraction of protein-protein interaction in regulatory networks relies on intrinsic disorder.
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            Understanding protein non-folding.

            Vladimir Uversky, A. Keith Dunker (2010)
            This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of a specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that a unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: how were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? Copyright 2010 Elsevier B.V. All rights reserved.
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              Evidence for a partially folded intermediate in alpha-synuclein fibril formation.

              V N Uversky, J. LI, A. L. Fink (2001)
              Intracellular proteinaceous aggregates (Lewy bodies and Lewy neurites) of alpha-synuclein are hallmarks of neurodegenerative diseases such as Parkinson's disease, dementia with Lewy bodies, and multiple systemic atrophy. However, the molecular mechanisms underlying alpha-synuclein aggregation into such filamentous inclusions remain unknown. An intriguing aspect of this problem is that alpha-synuclein is a natively unfolded protein, with little or no ordered structure under physiological conditions. This raises the question of how an essentially disordered protein is transformed into highly organized fibrils. In the search for an answer to this question, we have investigated the effects of pH and temperature on the structural properties and fibrillation kinetics of human recombinant alpha-synuclein. Either a decrease in pH or an increase in temperature transformed alpha-synuclein into a partially folded conformation. The presence of this intermediate is strongly correlated with the enhanced formation of alpha-synuclein fibrils. We propose a model for the fibrillation of alpha-synuclein in which the first step is the conformational transformation of the natively unfolded protein into the aggregation-competent partially folded intermediate.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Intrinsically Disord Proteins
                Journal ID (iso-abbrev): Intrinsically Disord Proteins
                Journal ID (publisher-id): KIDP
                Journal ID (publisher-id): kidp20
                Title: Intrinsically Disordered Proteins
                Publisher: Taylor & Francis
                ISSN (Print): 2169-0693
                ISSN (Electronic): 2169-0707
                Publication date Collection: 2014
                Publication date (Electronic): 19 May 2014
                Publication date PMC-release: 19 May 2014
                Volume: 2
                Issue: 1
                Electronic Location Identifier: e27833
                Affiliations
                [1 ]Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
                [2 ]USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA
                [3 ]Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia
                [4 ]Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
                Author notes
                [†]

                These authors contributed equally to this work.

                [* ]Correspondence to: Vladimir N Uversky, Email: vuversky@ 123456health.usf.edu
                Article
                Publisher ID: 984013
                DOI: 10.4161/idp.27833
                PMC ID: 5314876
                SO-VID: 1784f10b-e68a-49b2-b24e-927887331fc1
                Copyright © Copyright © 2014 Landes Bioscience
                License:

                This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

                History
                Date received : 13 January 2014
                Date accepted : 13 January 2014
                Page count
                Pages: 10
                Categories
                Subject: Digested Disorder

                Keywords: molecular dynamic simulation,pathogenesis,post-translational modification,protein-protein interaction,viral protein
                Data availability:
                Keywords: molecular dynamic simulation, pathogenesis, post-translational modification, protein-protein interaction, viral protein

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