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intrinsically disordered proteins

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By Shelly DeForte A PhD student in molecular medicine.
Ashwini Patil, Kengo Kinoshita, Haruki Nakamura
Hubs are proteins with a large number of interactions in a protein-protein interaction network. They are the principal agents in the interaction network and affect its function and stability. Their specific recognition of many different protein partners is of great interest from the structural viewpoint. Over the last few years, the structural properties of hubs have been extensively studied. We review the currently known features that are particular to hubs, possibly affecting their binding ability. Specifically, we look at the levels of intrinsic disorder, surface charge and domain distribution in hubs, as compared to non-hubs, along with differences in their functional domains...
2010: International Journal of Molecular Sciences
Shunsuke Teraguchi, Ashwini Patil, Daron M Standley
BACKGROUND: In order to characterize mammalian intrinsically disordered domains (IDDs) we examined the patterns in their amino acid abundance as well as overrepresented local sequence motifs. We considered IDDs from mouse proteins associated with innate immune responses as well as a set of generic human genes. These sets were compared with artificially generated random sequences with the same overall amino acid abundance and length distributions. IDDs were then clustered by amino acid abundance, and further analyzed in terms of co-occurrence of clusters with functionally characterized Pfam domains...
2010: BMC Bioinformatics
Alok Sharma, Abdollah Dehzangi, James Lyons, Seiya Imoto, Satoru Miyano, Kenta Nakai, Ashwini Patil
With the exponential increase in the number of sequenced organisms, automated annotation of proteins is becoming increasingly important. Intrinsically disordered regions are known to play a significant role in protein function. Despite their abundance, especially in eukaryotes, they are rarely used to inform function prediction systems. In this study, we extracted seven sequence features in intrinsically disordered regions and developed a scheme to use them to predict Gene Ontology Slim terms associated with proteins...
2014: PloS One
Marco Punta, István Simon, Zsuzsanna Dosztányi
Intrinsically disordered proteins and protein regions (IDPs/IDRs) do not adopt a well-defined folded structure under physiological conditions. Instead, these proteins exist as heterogeneous and dynamical conformational ensembles. IDPs are widespread in eukaryotic proteomes and are involved in fundamental biological processes, mostly related to regulation and signaling. At the same time, disordered regions often pose significant challenges to the structure determination process, which generally requires highly homogeneous proteins samples...
2015: Methods in Molecular Biology
Monika Fuxreiter, Ágnes Tóth-Petróczy, Daniel A Kraut, Andreas Matouschek, Andreas T Matouschek, Roderick Y H Lim, Bin Xue, Lukasz Kurgan, Vladimir N Uversky
No abstract text is available yet for this article.
July 9, 2014: Chemical Reviews
Rita Pancsa, Monika Fuxreiter
Proteins containing intrinsically disordered (ID) regions are widespread in eukaryotic organisms and are mostly utilized in regulatory processes. ID regions can mediate binary interactions of proteins or promote organization of large assemblies. Post-translational modifications of ID regions often serve as decision points in signaling pathways. Why Nature distinguished ID proteins in molecular recognition functions? In a simple view, binding of ID regions is accompanied by a large entropic penalty as compared to folded proteins...
June 2012: IUBMB Life
Monika Fuxreiter
Proteins are dynamic creatures. Intrinsically disordered proteins (IDPs) function as multiplicity of structures and their activities can only be described by stochastic structure-function relationships. In their complex forms, however, IDPs were thought to lose their plasticity and behave similarly to globular proteins. Although various IDPs indeed fold upon binding, this view is not valid in general. IDPs usually interact with their partners via short motifs, which require malleable environments to function...
January 2012: Molecular BioSystems
Priyanka Joshi, Michele Vendruscolo
Although the proteins in all the current major classes considered to be druggable are folded in their native states, intrinsically disordered proteins (IDPs) are becoming attractive candidates for therapeutic intervention by small drug-like molecules. IDPs are challenging targets because they exist as ensembles of structures, thereby making them unsuitable for standard rational drug design approaches, which require the knowledge of the three-dimensional structure of the proteins to be drugged. As we review in this chapter, several different small molecule strategies are currently under investigation to target IDPs, including: (i) to stabilise IDPs in their natively disordered states, (ii) to inhibit interactions with ordered or disordered protein partners, and (iii) to induce allosteric inhibition...
2015: Advances in Experimental Medicine and Biology
Biao Fu, Michele Vendruscolo
Intrinsically disordered proteins (IDPs) are involved in a wide range of essential biological processes, including in particular signalling and regulation. We are only beginning, however, to develop a detailed knowledge of the structure and dynamics of these proteins. It is becoming increasingly clear that, as IDPs populate highly heterogeneous states, they should be described in terms of conformational ensembles rather than as individual structures, as is instead most often the case for the native states of globular proteins...
2015: Advances in Experimental Medicine and Biology
A Keith Dunker, Christopher J Oldfield
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance...
2015: Advances in Experimental Medicine and Biology
Vladimir N Uversky, Christopher J Oldfield
No abstract text is available yet for this article.
September 14, 2015: FEBS Letters
Chad W Lawrence, Sushant Kumar, William G Noid, Scott A Showalter
In this work, we quantitatively investigate the thermodynamic analogy between the folding of monomeric proteins and the interactions of intrinsically disordered proteins (IDPs). Motivated by the hypothesis that similar hydrophobic forces guide both globular protein folding and also IDP interactions, we present a unified experimental and computational investigation of the coupling between the folding and binding of the intrinsically disordered tail of FCP1 when interacting with the cooperatively folding winged-helix domain of Rap74...
March 6, 2014: Journal of Physical Chemistry Letters
Rashmi Sharma, Zsolt Raduly, Marton Miskei, Monika Fuxreiter
Specific molecular recognition is assumed to require a well-defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post-translational modifications or alternative splicing to fine-tune affinity...
September 14, 2015: FEBS Letters
Kaare Teilum, Johan G Olsen, Birthe B Kragelund
In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions...
2015: Frontiers in Molecular Biosciences
Munehito Arai, Kenji Sugase, H Jane Dyson, Peter E Wright
Intrinsically disordered proteins (IDPs) frequently function in protein interaction networks that regulate crucial cellular signaling pathways. Many IDPs undergo transitions from disordered conformational ensembles to folded structures upon binding to their cellular targets. Several possible binding mechanisms for coupled folding and binding have been identified: folding of the IDP after association with the target ("induced fit"), or binding of a prefolded state in the conformational ensemble of the IDP to the target protein ("conformational selection"), or some combination of these two extremes...
August 4, 2015: Proceedings of the National Academy of Sciences of the United States of America
Rebecca B Berlow, H Jane Dyson, Peter E Wright
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size...
September 14, 2015: FEBS Letters
Susan Fishbain, Tomonao Inobe, Eitan Israeli, Sreenivas Chavali, Houqing Yu, Grace Kago, M Madan Babu, Andreas Matouschek
The proteasome controls the concentrations of most proteins in eukaryotic cells. It recognizes its protein substrates through ubiquitin tags and initiates degradation at disordered regions within the substrate. Here we show that the proteasome has pronounced preferences for the amino acid sequence of the regions at which it initiates degradation. Specifically, proteins in which the initiation regions have biased amino acid compositions show longer half-lives in yeast than proteins with unbiased sequences in the regions...
March 2015: Nature Structural & Molecular Biology
Vladimir N Uversky
Proteins are structurally heterogeneous and comprise folded regions with variable conformational stabilities and intrinsically disordered protein regions that do not have well-folded structures. Even small, well-folded single-domain proteins are structurally heterogeneous and contain multiple foldon units with different conformational stability. Although the ability of many intrinsically disordered protein regions to undergo at least partial folding at interaction with specific binding partners is a well-established fact, recent studies have revealed that functions of some ordered proteins rely on the decrease in the amount of their ordered structure and require local or even global functional unfolding...
April 2015: FEBS Journal
Eric B Gibbs, Scott A Showalter
Intrinsically disordered proteins (IDPs) are broadly defined as protein regions that do not cooperatively fold into a spatially or temporally stable structure. Recent research strongly supports the hypothesis that a conserved functional role for structural disorder renders IDPs uniquely capable of functioning in biological processes such as cellular signaling and transcription. Recently, the frequency of application of rigorous mechanistic biochemistry and quantitative biophysics to disordered systems has increased dramatically...
February 17, 2015: Biochemistry
Peter E Wright, H Jane Dyson
Intrinsically disordered proteins (IDPs) are important components of the cellular signalling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signalling. These proteins participate in the assembly of signalling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles...
January 2015: Nature Reviews. Molecular Cell Biology
2015-09-24 23:09:54
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