(Q31133660)

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A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).

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scholarly article

1 reference

Europe PubMed Central

17 October 2017

A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). (English)

1 reference

Europe PubMed Central

17 October 2017

1 reference

based on heuristic

inferred from title

5

object named as

George D Rose

1 reference

Europe PubMed Central

17 October 2017

Patrick J. Fleming

1

object named as

Patrick J Fleming

1 reference

Europe PubMed Central

17 October 2017

Nicholas C Fitzkee

2

object named as

Nicholas C Fitzkee

1 reference

Europe PubMed Central

17 October 2017

Rajgopal Srinivasan

4

object named as

Rajgopal Srinivasan

1 reference

Europe PubMed Central

17 October 2017

author name string

Mihaly Mezei

3

1 reference

Europe PubMed Central

17 October 2017

publication date

2 December 2004

1 reference

Europe PubMed Central

17 October 2017

Protein Science

1 reference

Europe PubMed Central

17 October 2017

14

1 reference

Europe PubMed Central

17 October 2017

1

1 reference

Europe PubMed Central

17 October 2017

111-118

1 reference

Europe PubMed Central

17 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

H-bonding in protein hydration revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Unfolded state of polyalanine is a segmented polyproline II helix.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Ab initio protein folding using LINUS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Hydration dynamics near a model protein surface.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Configurational temperature density of states simulations of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Stereochemistry of polypeptide chain configurations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

PISCES: a protein sequence culling server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

A simple model for polyproline II structure in unfolded states of alanine-based peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Evaluation of a fast implicit solvent model for molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Rotamer strain energy in protein helices - quantification of a major force opposing protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

The penultimate rotamer library

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

A physical basis for protein secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Interaction between water and polar groups of the helix backbone: an important determinant of helix propensities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Prediction of binding energetics from structure using empirical parameterization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Free energy of burying hydrophobic residues in the interface between protein subunits.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Solvation: how to obtain microscopic energies from partitioning and solvation experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

The interpretation of protein structures: Estimation of static accessibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Turns in peptides and proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Calculation of the free energy of association for protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

21 June 2018

Short sequences of non-proline residues can adopt the polyproline II helical conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Role of solvent in determining conformational preferences of alanine dipeptide in water.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Structural energetics of peptide recognition: Angiotensin II/antibody binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

LINUS: a hierarchic procedure to predict the fold of a protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2253334

25 November 2018

The sensitivity of conformational free energies of the alanine dipeptide to atomic site charges

1 reference

https://pubmed.ncbi.nlm.nih.gov/15576559

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamic mechanism and consequences of the polyproline II (PII) structural bias in the denatured states of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/15576559

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/15576559

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1110/PS.041047005

1 reference

Europe PubMed Central

17 October 2017

1 reference

Europe PubMed Central

17 October 2017

1 reference

Europe PubMed Central

17 October 2017

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