Literature DB >> 21156127

How sequence determines elasticity of disordered proteins.

Shanmei Cheng1, Murat Cetinkaya, Frauke Gräter.   

Abstract

How nature tunes sequences of disordered protein to yield the desired coiling properties is not yet well understood. To shed light on the relationship between protein sequence and elasticity, we here investigate four different natural disordered proteins with elastomeric function, namely: FG repeats in the nucleoporins; resilin in the wing tendon of dragonfly; PPAK in the muscle protein titin; and spider silk. We obtain force-extension curves for these proteins from extensive explicit solvent molecular dynamics simulations, which we compare to purely entropic coiling by modeling the four proteins as entropic chains. Although proline and glycine content are in general indicators for the entropic elasticity as expected, divergence from simple additivity is observed. Namely, coiling propensities correlate with polyproline II content more strongly than with proline content, and given a preponderance of glycines for sufficient backbone flexibility, nonlocal interactions such as electrostatic forces can result in strongly enhanced coiling, which results for the case of resilin in a distinct hump in the force-extension curve. Our results, which are directly testable by force spectroscopy experiments, shed light on how evolution has designed unfolded elastomeric proteins for different functions.
Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 21156127      PMCID: PMC3000487          DOI: 10.1016/j.bpj.2010.10.011

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  33 in total

1.  Multiple conformations of PEVK proteins detected by single-molecule techniques.

Authors:  H Li; A F Oberhauser; S D Redick; M Carrion-Vazquez; H P Erickson; J M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-28       Impact factor: 11.205

2.  Segmented nanofibers of spider dragline silk: atomic force microscopy and single-molecule force spectroscopy.

Authors:  E Oroudjev; J Soares; S Arcdiacono; J B Thompson; S A Fossey; H G Hansma
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-16       Impact factor: 11.205

3.  Polyproline II helical structure in protein unfolded states: lysine peptides revisited.

Authors:  Adam L Rucker; Trevor P Creamer
Journal:  Protein Sci       Date:  2002-04       Impact factor: 6.725

4.  Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field.

Authors:  Justin L MacCallum; D Peter Tieleman
Journal:  J Comput Chem       Date:  2003-11-30       Impact factor: 3.376

5.  A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors:  Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

6.  Dissecting entropic coiling and poor solvent effects in protein collapse.

Authors:  Frauke Gräter; Pascal Heider; Ronen Zangi; B J Berne
Journal:  J Am Chem Soc       Date:  2008-08-12       Impact factor: 15.419

7.  Entropic elasticity of lambda-phage DNA.

Authors:  C Bustamante; J F Marko; E D Siggia; S Smith
Journal:  Science       Date:  1994-09-09       Impact factor: 47.728

8.  Tentative identification of a resilin gene in Drosophila melanogaster.

Authors:  D H Ardell; S O Andersen
Journal:  Insect Biochem Mol Biol       Date:  2001-09       Impact factor: 4.714

Review 9.  Polyproline II structure in proteins: identification by chiroptical spectroscopies, stability, and functions.

Authors:  Brigida Bochicchio; Antonio Mario Tamburro
Journal:  Chirality       Date:  2002-11       Impact factor: 2.437

Review 10.  The mechanical design of spider silks: from fibroin sequence to mechanical function.

Authors:  J M Gosline; P A Guerette; C S Ortlepp; K N Savage
Journal:  J Exp Biol       Date:  1999-12       Impact factor: 3.312

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  23 in total

1.  Elasticity, structure, and relaxation of extended proteins under force.

Authors:  Guillaume Stirnemann; David Giganti; Julio M Fernandez; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-13       Impact factor: 11.205

2.  KAP-1 promotes resection of broken DNA ends not protected by γ-H2AX and 53BP1 in G₁-phase lymphocytes.

Authors:  Anthony T Tubbs; Yair Dorsett; Elizabeth Chan; Beth Helmink; Baeck-Seung Lee; Putzer Hung; Rosmy George; Andrea L Bredemeyer; Anuradha Mittal; Rohit V Pappu; Dipanjan Chowdhury; Nima Mosammaparast; Michael S Krangel; Barry P Sleckman
Journal:  Mol Cell Biol       Date:  2014-05-19       Impact factor: 4.272

3.  Can Dissipative Properties of Single Molecules Be Extracted from a Force Spectroscopy Experiment?

Authors:  Fabrizio Benedetti; Yulia Gazizova; Andrzej J Kulik; Piotr E Marszalek; Dmitry V Klinov; Giovanni Dietler; Sergey K Sekatskii
Journal:  Biophys J       Date:  2016-09-20       Impact factor: 4.033

4.  Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153.

Authors:  Sigrid Milles; Edward A Lemke
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

5.  The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization.

Authors:  Elizabeth S Freeman Rosenzweig; Bin Xu; Luis Kuhn Cuellar; Antonio Martinez-Sanchez; Miroslava Schaffer; Mike Strauss; Heather N Cartwright; Pierre Ronceray; Jürgen M Plitzko; Friedrich Förster; Ned S Wingreen; Benjamin D Engel; Luke C M Mackinder; Martin C Jonikas
Journal:  Cell       Date:  2017-09-21       Impact factor: 41.582

6.  Phase Separation of Toxic Dipeptide Repeat Proteins Related to C9orf72 ALS/FTD.

Authors:  Hamidreza Jafarinia; Erik van der Giessen; Patrick R Onck
Journal:  Biophys J       Date:  2020-07-16       Impact factor: 4.033

Review 7.  Titin-based tension in the cardiac sarcomere: molecular origin and physiological adaptations.

Authors:  Brian R Anderson; Henk L Granzier
Journal:  Prog Biophys Mol Biol       Date:  2012-08-11       Impact factor: 3.667

8.  The giant keyhole limpet radular teeth: A naturally-grown harvest machine.

Authors:  Tina Ukmar-Godec; Gregor Kapun; Paul Zaslansky; Damien Faivre
Journal:  J Struct Biol       Date:  2015-10-03       Impact factor: 2.867

Review 9.  Hepatitis C Virus Structure: Defined by What It Is Not.

Authors:  Altaira D Dearborn; Joseph Marcotrigiano
Journal:  Cold Spring Harb Perspect Med       Date:  2020-01-02       Impact factor: 6.915

10.  GFP's mechanical intermediate states.

Authors:  John Saeger; Vesa P Hytönen; Enrico Klotzsch; Viola Vogel
Journal:  PLoS One       Date:  2012-10-31       Impact factor: 3.240

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