Literature DB >> 28282172

Distinguishing Signatures of Multipathway Conformational Transitions.

Christopher A Pierse1, Olga K Dudko1.   

Abstract

The folding and binding of biomolecules into functional conformations are thought to be commonly mediated by multiple pathways rather than a unique route. Yet even in experiments where one can "see" individual conformational transitions, their stochastic nature generally precludes one from determining whether the transitions occurred through one or multiple pathways. We establish model-free, observable signatures in the response of macromolecules to force that unambiguously identify multiple pathways-even when the pathways themselves cannot be resolved. The unified analytical description reveals that, through multiple pathways, the response of molecules to external forces can be shaped in diverse ways, resulting in a rich design space for a tailored biological function already at the single-molecule level.

Entities:  

Year:  2017        PMID: 28282172      PMCID: PMC6863504          DOI: 10.1103/PhysRevLett.118.088101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  20 in total

1.  Transition path sampling: throwing ropes over rough mountain passes, in the dark.

Authors:  Peter G Bolhuis; David Chandler; Christoph Dellago; Phillip L Geissler
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  Direct observation of catch bonds involving cell-adhesion molecules.

Authors:  Bryan T Marshall; Mian Long; James W Piper; Tadayuki Yago; Rodger P McEver; Cheng Zhu
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

3.  Single-molecule rupture dynamics on multidimensional landscapes.

Authors:  Yohichi Suzuki; Olga K Dudko
Journal:  Phys Rev Lett       Date:  2010-01-25       Impact factor: 9.161

4.  Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins.

Authors:  Olga K Dudko; Jérôme Mathé; Attila Szabo; Amit Meller; Gerhard Hummer
Journal:  Biophys J       Date:  2007-03-23       Impact factor: 4.033

5.  Theory, analysis, and interpretation of single-molecule force spectroscopy experiments.

Authors:  Olga K Dudko; Gerhard Hummer; Attila Szabo
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-13       Impact factor: 11.205

Review 6.  Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy.

Authors:  Keir C Neuman; Attila Nagy
Journal:  Nat Methods       Date:  2008-06       Impact factor: 28.547

Review 7.  Theory of protein folding: the energy landscape perspective.

Authors:  J N Onuchic; Z Luthey-Schulten; P G Wolynes
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

Review 8.  From Levinthal to pathways to funnels.

Authors:  K A Dill; H S Chan
Journal:  Nat Struct Biol       Date:  1997-01

Review 9.  Single-molecule nanometry for biological physics.

Authors:  Hajin Kim; Taekjip Ha
Journal:  Rep Prog Phys       Date:  2012-12-18

10.  Multiple native states reveal persistent ruggedness of an RNA folding landscape.

Authors:  Sergey V Solomatin; Max Greenfeld; Steven Chu; Daniel Herschlag
Journal:  Nature       Date:  2010-02-04       Impact factor: 49.962

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  13 in total

1.  Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds.

Authors:  Katelyn Dahlke; Jing Zhao; Charles E Sing; Edward J Banigan
Journal:  Biophys J       Date:  2019-08-02       Impact factor: 4.033

2.  Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase.

Authors:  Qing Li; Zackary N Scholl; Piotr E Marszalek
Journal:  Biophys J       Date:  2018-07-03       Impact factor: 4.033

3.  Critical phenomena in the temperature-pressure-crowding phase diagram of a protein.

Authors:  Andrei G Gasic; Mayank M Boob; Maxim B Prigozhin; Dirar Homouz; Anna Jean Wirth; Caleb M Daugherty; Martin Gruebele; Margaret S Cheung
Journal:  Phys Rev X       Date:  2019-11-18       Impact factor: 15.762

4.  On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.

Authors:  Zongan Wang; John M Jumper; Karl F Freed; Tobin R Sosnick
Journal:  Biophys J       Date:  2019-09-17       Impact factor: 4.033

5.  Proteins Breaking Bad: A Free Energy Perspective.

Authors:  Jessica Valle-Orero; Rafael Tapia-Rojo; Edward C Eckels; Jaime Andrés Rivas-Pardo; Ionel Popa; Julio M Fernández
Journal:  J Phys Chem Lett       Date:  2017-07-25       Impact factor: 6.475

6.  Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms.

Authors:  Florian Berger; A J Hudspeth
Journal:  PLoS Comput Biol       Date:  2017-05-26       Impact factor: 4.475

7.  Conformational dynamics of the frameshift stimulatory structure in HIV-1.

Authors:  Dustin B Ritchie; Tonia R Cappellano; Collin Tittle; Negar Rezajooei; Logan Rouleau; William K A Sikkema; Michael T Woodside
Journal:  RNA       Date:  2017-05-18       Impact factor: 4.942

8.  Multiple stochastic pathways in forced peptide-lipid membrane detachment.

Authors:  Milica Utjesanovic; Tina R Matin; Krishna P Sigdel; Gavin M King; Ioan Kosztin
Journal:  Sci Rep       Date:  2019-01-24       Impact factor: 4.379

9.  High force catch bond mechanism of bacterial adhesion in the human gut.

Authors:  Zhaowei Liu; Haipei Liu; Andrés M Vera; Rafael C Bernardi; Philip Tinnefeld; Michael A Nash
Journal:  Nat Commun       Date:  2020-08-28       Impact factor: 14.919

10.  Structural-elastic determination of the force-dependent transition rate of biomolecules.

Authors:  Shiwen Guo; Qingnan Tang; Mingxi Yao; Huijuan You; Shimin Le; Hu Chen; Jie Yan
Journal:  Chem Sci       Date:  2018-05-29       Impact factor: 9.825

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