(Q37008252)

17 August 2017

Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations (English)

1 reference

17 August 2017

David N Beratan

3

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author name string

Parag Mukhopadhyay

series ordinal

1

1 reference

PMCID

2599840

17 August 2017

Gérard Zuber

series ordinal

2

1 reference

PMCID

2599840

17 August 2017

language of work or name

English

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publication date

19 September 2008

1 reference

17 August 2017

13

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inferred from page(s)

published in

Biophysical Journal

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17 August 2017

95

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17 August 2017

12

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17 August 2017

5574-5586

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Are current molecular dynamics force fields too helical?

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Conformations of alanine-based peptides in water probed by FTIR, Raman, vibrational circular dichroism, electronic circular dichroism, and NMR spectroscopy.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Further evidence for the absence of polyproline II stretch in the XAO peptide.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Proline zwitterion dynamics in solution, glass, and crystalline state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Conformation of the backbone in unfolded proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Metadynamics as a tool for exploring free energy landscapes of chemical reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Raman optical activity: a tool for protein structure analysis.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Unfolded proteins studied by Raman optical activity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Escaping free-energy minima

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

The lubricant of life: a proposal that solvent water promotes extremely fast conformational fluctuations in mobile heteropolypeptide structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Infrared and Raman vibrational optical activity: theoretical and experimental aspects

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Relevance of the electric-dipole--electric-quadrupole contribution to Raman optical activity spectra

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Spin relaxation enhancement confirms dominance of extended conformations in short alanine peptides

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Can Raman optical activity separate axial from local chirality? A theoretical study of helical deca-alanine.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Solvent effects on Raman optical activity spectra calculated using the polarizable continuum model

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Demonstration of the ring conformation in polyproline by the Raman optical activity.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Towards Raman optical activity calculations of large molecules

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Vibrational Raman optical activity characterization of poly(l-proline) II helix in alanine oligopeptides.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Basis Set and Density Functional Dependence of Vibrational Raman Optical Activity Calculations

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599840

Contribution of a Solute's Chiral Solvent Imprint to Optical Rotation

4 December 2018

1 reference

12 December 2020

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

1 reference

12 December 2020

Class IV charge models: A new semiempirical approach in quantum chemistry

1 reference

12 December 2020

Conformational flexibility of L-alanine zwitterion determines shapes of Raman and Raman optical activity spectral bands

1 reference

12 December 2020

Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution

1 reference

12 December 2020

Effects of H2O and D2O on polyproline II helical structure

1 reference

12 December 2020

Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics

1 reference

12 December 2020

Vibrational raman optical activity as a mean for revealing the helicity of oligosilanes: a quantum chemical investigation

1 reference

12 December 2020

Solvent Effect on Optical Rotation: A Case Study of Methyloxirane in Water

1 reference

12 December 2020

Absolute configuration of chirally deuterated neopentane

1 reference

12 December 2020

10.1529/BIOPHYSJ.108.137596

Identifiers

DOI

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

PMCID

2599840