Literature DB >> 21530234

Constructing ensembles for intrinsically disordered proteins.

Charles K Fisher1, Collin M Stultz.   

Abstract

The relatively flat energy landscapes associated with intrinsically disordered proteins makes modeling these systems especially problematic. A comprehensive model for these proteins requires one to build an ensemble consisting of a finite collection of structures, and their corresponding relative stabilities, which adequately capture the range of accessible states of the protein. In this regard, methods that use computational techniques to interpret experimental data in terms of such ensembles are an essential part of the modeling process. In this review, we critically assess the advantages and limitations of current techniques and discuss new methods for the validation of these ensembles.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21530234      PMCID: PMC3112268          DOI: 10.1016/j.sbi.2011.04.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  58 in total

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Authors:  Yang Shen; Ad Bax
Journal:  J Biomol NMR       Date:  2007-07-04       Impact factor: 2.835

2.  Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings.

Authors:  Gabrielle Nodet; Loïc Salmon; Valéry Ozenne; Sebastian Meier; Malene Ringkjøbing Jensen; Martin Blackledge
Journal:  J Am Chem Soc       Date:  2009-12-16       Impact factor: 15.419

3.  Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations.

Authors:  Nicolas L Fawzi; Aaron H Phillips; Jory Z Ruscio; Michaeleen Doucleff; David E Wemmer; Teresa Head-Gordon
Journal:  J Am Chem Soc       Date:  2008-04-16       Impact factor: 15.419

4.  Domain conformation of tau protein studied by solution small-angle X-ray scattering.

Authors:  Efstratios Mylonas; Antje Hascher; Pau Bernadó; Martin Blackledge; Eckhard Mandelkow; Dmitri I Svergun
Journal:  Biochemistry       Date:  2008-09-05       Impact factor: 3.162

5.  Residual structure within the disordered C-terminal segment of p21(Waf1/Cip1/Sdi1) and its implications for molecular recognition.

Authors:  Mi-Kyung Yoon; Veena Venkatachalam; Austin Huang; Byong-Seok Choi; Collin M Stultz; James J Chou
Journal:  Protein Sci       Date:  2009-02       Impact factor: 6.725

6.  The unfoldomics decade: an update on intrinsically disordered proteins.

Authors:  A Keith Dunker; Christopher J Oldfield; Jingwei Meng; Pedro Romero; Jack Y Yang; Jessica Walton Chen; Vladimir Vacic; Zoran Obradovic; Vladimir N Uversky
Journal:  BMC Genomics       Date:  2008-09-16       Impact factor: 3.969

7.  Structural polymorphism of 441-residue tau at single residue resolution.

Authors:  Marco D Mukrasch; Stefan Bibow; Jegannath Korukottu; Sadasivam Jeganathan; Jacek Biernat; Christian Griesinger; Eckhard Mandelkow; Markus Zweckstetter
Journal:  PLoS Biol       Date:  2009-02-17       Impact factor: 8.029

8.  Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.

Authors:  Aaron T Frank; Andrew C Stelzer; Hashim M Al-Hashimi; Ioan Andricioaei
Journal:  Nucleic Acids Res       Date:  2009-04-15       Impact factor: 16.971

9.  Similarity measures for protein ensembles.

Authors:  Kresten Lindorff-Larsen; Jesper Ferkinghoff-Borg
Journal:  PLoS One       Date:  2009-01-15       Impact factor: 3.240

10.  The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau.

Authors:  Austin Huang; Collin M Stultz
Journal:  PLoS Comput Biol       Date:  2008-08-22       Impact factor: 4.475

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  92 in total

1.  Stochastic simulation of structural properties of natively unfolded and denatured proteins.

Authors:  David Curcó; Catherine Michaux; Guillaume Roussel; Emmanuel Tinti; Eric A Perpète; Carlos Alemán
Journal:  J Mol Model       Date:  2012-05-29       Impact factor: 1.810

2.  On the supertertiary structure of proteins.

Authors:  Peter Tompa
Journal:  Nat Chem Biol       Date:  2012-06-18       Impact factor: 15.040

3.  Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins.

Authors:  Debabani Ganguly; Steve Otieno; Brett Waddell; Luigi Iconaru; Richard W Kriwacki; Jianhan Chen
Journal:  J Mol Biol       Date:  2012-06-19       Impact factor: 5.469

4.  Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings.

Authors:  Vytautas Gapsys; Raghavendran L Narayanan; ShengQi Xiang; Bert L de Groot; Markus Zweckstetter
Journal:  J Biomol NMR       Date:  2015-10-03       Impact factor: 2.835

5.  Mechanism and rate constants of the Cdc42 GTPase binding with intrinsically disordered effectors.

Authors:  Xiaodong Pang; Huan-Xiang Zhou
Journal:  Proteins       Date:  2016-03-09

6.  The role of semidisorder in temperature adaptation of bacterial FlgM proteins.

Authors:  Jihua Wang; Yuedong Yang; Zanxia Cao; Zhixiu Li; Huiying Zhao; Yaoqi Zhou
Journal:  Biophys J       Date:  2013-12-03       Impact factor: 4.033

7.  From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

Authors:  Julie D Forman-Kay; Tanja Mittag
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

8.  HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.

Authors:  Xiaorong Liu; Jianhan Chen
Journal:  Phys Chem Chem Phys       Date:  2017-12-13       Impact factor: 3.676

9.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

10.  Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.

Authors:  Lester Carter; Seung Joong Kim; Dina Schneidman-Duhovny; Jan Stöhr; Guillaume Poncet-Montange; Thomas M Weiss; Hiro Tsuruta; Stanley B Prusiner; Andrej Sali
Journal:  Biophys J       Date:  2015-08-18       Impact factor: 4.033

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