(Q55560897)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

title

Atomistic picture of conformational exchange in a T4 lysozyme cavity mutant: an experiment-guided molecular dynamics study (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

4

Lewis E. Kay

1 reference

15 July 2018

Pramodh Vallurupalli

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

Nilmadhab Chakrabarti

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

Régis Pomès

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

Lewis E Kay

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

publication date

7 January 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

page(s)

3602-3613

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

EMMA: A Software Package for Markov Model Building and Analysis.

12 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Kinetic characterization of the critical step in HIV-1 protease maturation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

How should we think about the ribosome?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Structure of an intermediate state in protein folding and aggregation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Single-molecule fluorescence experiments determine protein folding transition path times

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

How fast-folding proteins fold

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Transient Hoogsteen base pairs in canonical duplex DNA.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Lessons from the lysozyme of phage T4

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

The role of dynamic conformational ensembles in biomolecular recognition

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Transition networks for modeling the kinetics of conformational change in macromolecules

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Measurement of bond vector orientations in invisible excited states of proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Mechanism of coupled folding and binding of an intrinsically disordered protein

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Direct observation of base-pair stepping by RNA polymerase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

GROMACS: fast, flexible, and free

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Molecular dynamics and protein function

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

UCSF Chimera--a visualization system for exploratory research and analysis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Protein folding and misfolding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Absolute comparison of simulated and experimental protein-folding dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Escaping free-energy minima

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

VMD: visual molecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Analysis of the effectiveness of proline substitutions and glycine replacements in increasing the stability of phage T4 lysozyme

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Dynamics of folded proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Temperature dependent molecular motion of a tyrosine residue of ferrocytochromeC

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI)

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Ion permeation in K⁺ channels occurs by direct Coulomb knock-on.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Perspective: Markov models for long-timescale biomolecular dynamics

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

All-atom empirical potential for molecular modeling and dynamics studies of proteins

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Markov state models of biomolecular conformational dynamics

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Single-molecule fluorescence probes dynamics of barrier crossing

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Recovery from slow inactivation in K+ channels is controlled by water molecules

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Allosteric inhibition through suppression of transient conformational states

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

A transient and low-populated protein-folding intermediate at atomic resolution

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Large conformational changes in proteins: signaling and other functions

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Hidden alternative structures of proline isomerase essential for catalysis

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

CPMG relaxation dispersion NMR experiments measuring glycine 1H alpha and 13C alpha chemical shifts in the 'invisible' excited states of proteins

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Expanding the realm of ultrafast protein folding: gpW, a midsize natural single-domain with alpha+beta topology that folds downhill.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Characterization of chemical exchange using residual dipolar coupling

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Reverse translocation of tRNA in the ribosome.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

The dynamic energy landscape of dihydrofolate reductase catalysis

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

From transition paths to transition states and rate coefficients.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

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

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Im7 folding mechanism: misfolding on a path to the native state

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Slow dynamics in folded and unfolded states of an SH3 domain

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Studying excited states of proteins by NMR spectroscopy.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

The Energy Landscapes and Motions of Proteins

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3-->Pro

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Fluorotyrosine M13 coat protein: fluorine-19 nuclear magnetic resonance study of the motional properties of an integral membrane protein in phospholipid vesicles

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6008728

Dynamics of ligand binding to myoglobin

12 August 2018

1 reference

12 December 2020

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

1 reference

12 December 2020

Access of ligands to cavities within the core of a protein is rapid

1 reference

12 December 2020

A TROSY CPMG sequence for characterizing chemical exchange in large proteins

1 reference

12 December 2020

Intrawell relaxation of overdamped Brownian particles

1 reference

12 December 2020

Folding at the speed limit

1 reference

12 December 2020

Probing Chemical Shifts of Invisible States of Proteins with Relaxation Dispersion NMR Spectroscopy: How Well Can We Do?

1 reference

12 December 2020

Probing structure in invisible protein states with anisotropic NMR chemical shifts

1 reference

12 December 2020

Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states

1 reference

12 December 2020

Increasing the exchange time-scale that can be probed by CPMG relaxation dispersion NMR

1 reference

12 December 2020

Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories

1 reference

12 December 2020

Identifiers

DOI

10.1039/C5SC03886C

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30008994%20AND%20SRC:MED&resulttype=core&format=json

12 April 2020

1 reference