(Q41039362)

25 September 2017

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes (English)

1 reference

25 September 2017

3

Pemra Doruker

1 reference

25 September 2017

2

Turkan Haliloglu

1 reference

25 September 2017

Nigar Kantarci-Carsibasi

series ordinal

1

1 reference

PMCID

2599820

25 September 2017

language of work or name

English

0 references

publication date

1 August 2008

1 reference

25 September 2017

1 reference

25 September 2017

95

1 reference

25 September 2017

5862-5873

1 reference

25 September 2017

12

1 reference

Intrinsic motions along an enzymatic reaction trajectory

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

HingeProt: automated prediction of hinges in protein structures

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Conformational transitions of adenylate kinase: switching by cracking

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Can conformational change be described by only a few normal modes?

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Coarse-grained normal mode analysis in structural biology

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Normal-modes-based prediction of protein conformational changes guided by distance constraints

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Molecular dynamics simulations of peptides and proteins with amplified collective motions

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Efficient generation of feasible pathways for protein conformational transitions

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Anisotropy of fluctuation dynamics of proteins with an elastic network model

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The T-to-R transformation in hemoglobin: a reevaluation

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Structure of human oxyhaemoglobin at 2.1 A resolution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

A third quaternary structure of human hemoglobin A at 1.7-A resolution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

How well can we understand large-scale protein motions using normal modes of elastic network models?

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Molecular dynamics of apo-adenylate kinase: a principal component analysis

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Rigid-cluster models of conformational transitions in macromolecular machines and assemblies

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Conformational change of proteins arising from normal mode calculations

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

The allosteric mechanism of yeast chorismate mutase: a dynamic analysis

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Sampling protein conformations and pathways

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599820

Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18676657

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18676657

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18676657

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1529/BIOPHYSJ.107.128447

1 reference

25 September 2017

1 reference

25 September 2017

1 reference

PMCID

2599820