Literature DB >> 17704142

Stretching to understand proteins - a survey of the protein data bank.

Joanna I Sułkowska1, Marek Cieplak.   

Abstract

We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps.

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Year:  2007        PMID： 17704142      PMCID： PMC2134851          DOI： 10.1529/biophysj.107.105973

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


  44 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The packing density in proteins: standard radii and volumes.

Authors:  J Tsai; R Taylor; C Chothia; M Gerstein
Journal:  J Mol Biol       Date:  1999-07-02       Impact factor: 5.469

3.  Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme.

Authors:  G Yang; C Cecconi; W A Baase; I R Vetter; W A Breyer; J A Haack; B W Matthews; F W Dahlquist; C Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

4.  Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.

Authors:  R B Best; B Li; A Steward; V Daggett; J Clarke
Journal:  Biophys J       Date:  2001-10       Impact factor: 4.033

5.  Unfolding pathways of native bacteriorhodopsin depend on temperature.

Authors:  Harald Janovjak; Max Kessler; Dieter Oesterhelt; Hermann Gaub; Daniel J Müller
Journal:  EMBO J       Date:  2003-10-01       Impact factor: 11.598

6.  Reverse engineering of the giant muscle protein titin.

Authors:  Hongbin Li; Wolfgang A Linke; Andres F Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Journal:  Nature       Date:  2002-08-29       Impact factor: 49.962

7.  Pulling geometry defines the mechanical resistance of a beta-sheet protein.

Authors:  David J Brockwell; Emanuele Paci; Rebecca C Zinober; Godfrey S Beddard; Peter D Olmsted; D Alastair Smith; Richard N Perham; Sheena E Radford
Journal:  Nat Struct Biol       Date:  2003-08-17

8.  The folding pathway of a fast-folding immunoglobulin domain revealed by single-molecule mechanical experiments.

Authors:  Ingo Schwaiger; Michael Schleicher; Angelika A Noegel; Matthias Rief
Journal:  EMBO Rep       Date:  2005-01       Impact factor: 8.807

9.  Temperature softening of a protein in single-molecule experiments.

Authors:  Michael Schlierf; Matthias Rief
Journal:  J Mol Biol       Date:  2005-10-10       Impact factor: 5.469

10.  Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape.

Authors:  Michael Schlierf; Matthias Rief
Journal:  Biophys J       Date:  2005-12-16       Impact factor: 4.033
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  10 in total

Review 1.  Pulling single molecules of titin by AFM--recent advances and physiological implications.

Authors:  Wolfgang A Linke; Anika Grützner
Journal:  Pflugers Arch       Date:  2007-12-06       Impact factor: 3.657

Review 2.  Mechanical biochemistry of proteins one molecule at a time.

Authors:  Andres F Oberhauser; Mariano Carrión-Vázquez
Journal:  J Biol Chem       Date:  2008-01-14       Impact factor: 5.157

3.  Stabilizing effect of knots on proteins.

Authors:  Joanna I Sułkowska; Piotr Sulkowski; P Szymczak; Marek Cieplak
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-08       Impact factor: 11.205

4.  Selection of optimal variants of Gō-like models of proteins through studies of stretching.

Authors:  Joanna I Sułkowska; Marek Cieplak
Journal:  Biophys J       Date:  2008-06-20       Impact factor: 4.033

Review 5.  Finding the weakest link: exploring integrin-mediated mechanical molecular pathways.

Authors:  Pere Roca-Cusachs; Thomas Iskratsch; Michael P Sheetz
Journal:  J Cell Sci       Date:  2012-07-13       Impact factor: 5.285

6.  Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations.

Authors:  Gali Arad-Haase; Silvia G Chuartzman; Shlomi Dagan; Reinat Nevo; Maksim Kouza; Binh Khanh Mai; Hung Tien Nguyen; Mai Suan Li; Ziv Reich
Journal:  Biophys J       Date:  2010-07-07       Impact factor: 4.033

7.  In vivo optophysiology reveals that G-protein activation triggers osmotic swelling and increased light scattering of rod photoreceptors.

Authors:  Pengfei Zhang; Robert J Zawadzki; Mayank Goswami; Phuong T Nguyen; Vladimir Yarov-Yarovoy; Marie E Burns; Edward N Pugh
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-20       Impact factor: 11.205

8.  Cooperative dynamics of proteins unraveled by network models.

Authors:  Eran Eyal; Anindita Dutta; Ivet Bahar
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2011-04-11

9.  Analysis of the REJ Module of Polycystin-1 Using Molecular Modeling and Force-Spectroscopy Techniques.

Authors:  Meixiang Xu; Liang Ma; Paul J Bujalowski; Feng Qian; R Bryan Sutton; Andres F Oberhauser
Journal:  J Biophys       Date:  2013-05-26

10.  Mechanical strength of 17,134 model proteins and cysteine slipknots.

Authors:  Mateusz Sikora; Joanna I Sułkowska; Marek Cieplak
Journal:  PLoS Comput Biol       Date:  2009-10-30       Impact factor: 4.475
  10 in total

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