(Q36769234)

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Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction

scientific article published on 6 March 2007

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction (English)

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Daniel P Raleigh

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Daniel P Raleigh

4

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author name string

Lauren Wickstrom

1

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Yuan Bi

2

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Viktor Hornak

3

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Europe PubMed Central

PMC publication ID

16 August 2017

Carlos Simmerling

5

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Europe PubMed Central

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16 August 2017

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publication date

6 March 2007

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Europe PubMed Central

PMC publication ID

16 August 2017

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Europe PubMed Central

PMC publication ID

16 August 2017

46

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Europe PubMed Central

PMC publication ID

16 August 2017

12

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

3624-3634

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

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29 September 2017

The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure

1 reference

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29 September 2017

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

1 reference

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29 September 2017

Sub-microsecond protein folding

1 reference

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Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

1 reference

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29 September 2017

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4822197

29 September 2017

The Amber biomolecular simulation programs

1 reference

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29 September 2017

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

1 reference

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29 September 2017

Determination of ultrafast protein folding rates from loop formation dynamics

1 reference

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29 September 2017

Probing site-specific conformational distributions in protein folding with solid-state NMR

1 reference

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29 September 2017

Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements

1 reference

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29 September 2017

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

1 reference

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Measuring the stability of partly folded proteins using TMAO.

1 reference

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Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

1 reference

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29 September 2017

Experimental tests of villin subdomain folding simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4822197

29 September 2017

Large-scale context in protein folding: villin headpiece

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4822197

29 September 2017

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

1 reference

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29 September 2017

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

1 reference

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29 September 2017

Stabilization of alpha-helix structure by polar side-chain interactions: complex salt bridges, cation-pi interactions, and C-H em leader O H-bonds

1 reference

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29 September 2017

The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4822197

29 September 2017

Cation-pi interactions in structural biology

1 reference

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29 September 2017

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

1 reference

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29 September 2017

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

1 reference

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29 September 2017

The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation

1 reference

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29 September 2017

A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation

1 reference

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29 September 2017

NMR structure of the 35-residue villin headpiece subdomain

1 reference

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29 September 2017

How to measure and predict the molar absorption coefficient of a protein

1 reference

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29 September 2017

Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

1 reference

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29 September 2017

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.

1 reference

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Optimized parallel tempering simulations of proteins.

1 reference

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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

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Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe.

1 reference

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5 September 2018

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

1 reference

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5 September 2018

Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: the villin headpiece subdomain

1 reference

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1 reference

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Application of the diffusion-collision model to the folding of three-helix bundle proteins.

1 reference

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5 September 2018

Conformation spaces of proteins

1 reference

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5 September 2018

NMR Characterization of a Peptide Model Provides Evidence for Significant Structure in the Unfolded State of the Villin Headpiece Helical Subdomain†

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dynamic NMR Line-Shape Analysis Demonstrates that the Villin Headpiece Subdomain Folds on the Microsecond Time Scale

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nativelike Structure and Stability in a Truncation Mutant of a Protein Minidomain: The Peripheral Subunit-Binding Domain†

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A thermostable 35-residue subdomain within villin headpiece

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

All-atom fast protein folding simulations: the villin headpiece

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Temperature-dependent Dynamics of the Villin Headpiece Helical Subdomain, An Unusually Small Thermostable Protein

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free-Energy Landscape of the Villin Headpiece in an All-Atom Force Field

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Isotropic periodic sum: a method for the calculation of long-range interactions.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Efficient high level expression of peptides and proteins as fusion proteins with the N-terminal domain of L9: Application to the villin headpiece helical subdomain

1 reference

https://pubmed.ncbi.nlm.nih.gov/17338549

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/BI061785+

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

16 August 2017

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