New force replica exchange method and protein folding pathways probed by force-clamp technique. (Q51894579)

17 April 2018

title

New force replica exchange method and protein folding pathways probed by force-clamp technique. (English)

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2

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author name string

Maksim Kouza

series ordinal

1

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Mai Suan Li

series ordinal

3

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language of work or name

English

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publication date

1 January 2008

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Journal of Chemical Physics

published in

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volume

128

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issue

4

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page(s)

045103

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Recognition of the polyubiquitin proteolytic signal

cites work

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A ubiquitin ligase complex assembles linear polyubiquitin chains

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Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair

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Cell cycle-regulated modification of the ribosome by a variant multiubiquitin chain

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Ubiquitin lys63 is involved in ubiquitination of a yeast plasma membrane protein

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Ubiquitin folds through a highly polarized transition state.

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Characterizing the protein folding transition state using psi analysis

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Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.

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Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.

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Molecular dynamics simulations of hydrophobic collapse of ubiquitin

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Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin

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The mechanical stability of ubiquitin is linkage dependent

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The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques

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Mechanical resistance of proteins explained using simple molecular models

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Dissecting the mechanical unfolding of ubiquitin

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Force-clamp spectroscopy monitors the folding trajectory of a single protein

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Replica-exchange molecular dynamics method for protein folding

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Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange molecular dynamics simulations.

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Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

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Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions

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Intrinsic rates and activation free energies from single-molecule pulling experiments.

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Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices

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Folding of the protein domain hbSBD

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Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation

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Effect of finite size on cooperativity and rates of protein folding.

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Time-resolved backbone desolvation and mutational hot spots in folding proteins.

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Models for the Specific Adhesion of Cells to Cells

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Kinetics from nonequilibrium single-molecule pulling experiments

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Beyond the conventional description of dynamic force spectroscopy of adhesion bonds

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Reversible mechanical unfolding of single ubiquitin molecules

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Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction coordinates by changing the pulling geometry

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Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

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Folding and stability of a tryptophan-containing mutant of ubiquitin

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Secondary structure, mechanical stability, and location of transition state of proteins

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Contact order, transition state placement and the refolding rates of single domain proteins.

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Internal protein dynamics shifts the distance to the mechanical transition state.

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Dynamic strength of molecular adhesion bonds

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A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

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Conformation-dependent environments in folding proteins

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Comment on "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein"

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Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

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Protein folding in a force clamp

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Protein-folding dynamics

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Identifiers

DOI

10.1063/1.2822272

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17 April 2018