(Q34350870)

1 August 2017

Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization (English)

1 reference

1 August 2017

Kurt D Berndt

3

0 references

Lennart Nilsson

object named as

Lennart Nilsson

series ordinal

4

0 references

author name string

Ana Caballero-Herrera

series ordinal

1

1 reference

PubMed ID

15908578

1 August 2017

Kerstin Nordstrand

series ordinal

2

1 reference

PubMed ID

15908578

1 August 2017

language of work or name

English

0 references

publication date

20 May 2005

1 reference

1 August 2017

1 reference

1 August 2017

89

1 reference

1 August 2017

2

1 reference

1 August 2017

842-857

1 reference

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

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Aqueous urea solution destabilizes Abeta(16-22) oligomers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Water and urea interactions with the native and unfolded forms of a beta-barrel protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The present view of the mechanism of protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The molecular basis for the chemical denaturation of proteins by urea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Recent advances in helix-coil theory.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Use of chemical shifts in macromolecular structure determination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Residence times of water molecules in the hydration sites of myoglobin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Helix nucleation kinetics from molecular simulations in explicit solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

On the truncation of long-range electrostatic interactions in DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The alpha-helix folds on the millisecond time scale

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Is protein folding hierarchic? I. Local structure and peptide folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Folding studies on ribonuclease A, a model protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Fast events in protein folding: helix melting and formation in a small peptide.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Solution structure and dynamics of PEC-60, a protein of the Kazal type inhibitor family, determined by nuclear magnetic resonance spectroscopy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Stability of alpha-helices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Helix design, prediction and stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Salt-stabilized globular protein structure in 7 M aqueous urea solution.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Hydrogen bonding in globular proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The interpretation of protein structures: Estimation of static accessibility

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Protein denaturation. C. Theoretical models for the mechanism of denaturation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Effect of side chain-backbone electrostatic interactions on the stability of alpha-helices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Nature of the charged-group effect on the stability of the C-peptide helix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Thermodynamic parameters for the helix-coil thermal transition of ribonuclease-S-peptide and derivatives from 1H-NMR data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Structure of phosphate-free ribonuclease A refined at 1.26 .ANG

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Quantitation of aspartate and glutamate in HPLC analysis of phenylthiocarbamyl amino acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The mechanism of alpha-helix formation by peptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Alpha-helix to random coil transitions: determination of peptide concentration from the CD at the isodichroic point

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Impact of protein denaturants and stabilizers on water structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics study on hydrophobic effects in aqueous urea solutions

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366634

The (i, i + 4) Phe-His interaction studied in an alanine-based alpha-helix

27 October 2018

1 reference

12 December 2020

Low-temperature 1H-NMR evidence of the folding of isolated ribonuclease S-peptide

1 reference

12 December 2020

1H n.m.r. parameters of the N-terminal 19-residue S-peptide of ribonuclease in aqueous solution

1 reference

12 December 2020

1H-n.m.r. study of the folding of ribonuclease 12-(beta-(3-pyridyl)-L-Ala) S-peptide (1-14)

1 reference

12 December 2020

Side-chain interactions in the C-peptide helix: Phe 8 ... His 12+

1 reference

12 December 2020

Conformation-dependent antibacterial activity of the naturally occurring human peptide LL-37

1 reference

12 December 2020

Conformational study of two synthetic peptides with sequence analogies to the N-terminal fragment of RNase A

1 reference

12 December 2020

THE SOLUBILITY OF AMINO ACIDS AND RELATED COMPOUNDS IN AQUEOUS UREA SOLUTIONS

1 reference

12 December 2020

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations

1 reference

12 December 2020

The Glu 2- ... Arg 10+ side-chain interaction in the C-peptide helix of ribonuclease A

1 reference

12 December 2020

Urea effects on protein stability: hydrogen bonding and the hydrophobic effect

1 reference

12 December 2020

Structural details of urea binding to barnase: a molecular dynamics analysis

1 reference

12 December 2020

Structure of ribonuclease A: results of joint neutron and X-ray refinement at 2.0-A resolution

1 reference

12 December 2020

A helix stop signal in the isolated S-peptide of ribonuclease A

1 reference

12 December 2020

NH resonances of Ribonuclease S-peptide in aqueous solution. Low temperature n.m.r. study

1 reference

12 December 2020

Protein stabilization and destabilization by guanidinium salts

1 reference

12 December 2020

On the fundamental role of the Glu 2- ... Arg 10+ salt bridge in the folding of isolated ribonuclease A S-peptide

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.061978

Identifiers

DOI

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

PubMed ID

15908578