(Q42871846)

9 November 2017

title

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers (English)

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9 November 2017

1

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9 November 2017

Volodymyr Babin

2

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9 November 2017

Christopher Roland

series ordinal

3

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9 November 2017

Celeste Sagui

series ordinal

4

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9 November 2017

language of work or name

English

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publication date

1 September 2010

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Journal of Chemical Physics

9 November 2017

published in

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9 November 2017

volume

133

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9 November 2017

issue

12

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9 November 2017

page(s)

125104

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Molecular structure of a left-handed double helical DNA fragment at atomic resolution

9 November 2017

cites work

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Preferred proline puckerings in cis and trans peptide groups: implications for collagen stability

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

21 January 2018

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Cis-trans isomerization and puckering of proline residue

21 January 2018

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Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues

21 January 2018

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Hypothesis about the Mechanism of Protein Folding

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Proline cis-trans isomerization and protein folding

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Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP

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Host-guest scale of left-handed polyproline II helix formation.

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Polyproline II helix conformation in a proline-rich environment: a theoretical study

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Host-guest study of left-handed polyproline II helix formation

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Is polyproline II a major backbone conformation in unfolded proteins?

21 January 2018

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

21 January 2018

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

21 January 2018

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Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales

21 January 2018

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

21 January 2018

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Are current molecular dynamics force fields too helical?

21 January 2018

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Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

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Polyproline II structure in a sequence of seven alanine residues.

21 January 2018

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Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study

21 January 2018

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Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy

21 January 2018

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

21 January 2018

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Unusual compactness of a polyproline type II structure

21 January 2018

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

21 January 2018

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Left-handed polyproline II helices commonly occur in globular proteins.

21 January 2018

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Protein modules and signalling networks

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Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building

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Energy transfer: a spectroscopic ruler

21 January 2018

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Distance estimates from paramagnetic enhancements of nuclear relaxation in linear and flexible model peptides

21 January 2018

1 reference

Quantitative single-molecule conformational distributions: a case study with poly-(L-proline).

21 January 2018

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A 10-A spectroscopic ruler applied to short polyprolines

21 January 2018

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Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence.

21 January 2018

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Effect of flexibility and cis residues in single-molecule FRET studies of polyproline

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Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix.

21 January 2018

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Conformations and free energy landscapes of polyproline peptides

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Side-chain effects on peptidyl-prolyl cis/trans isomerisation.

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The X-Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides

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Nmr studies of the molecular conformations in the linear oligopeptides H-(L-Ala)n-L-Pro-OH.

21 January 2018

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Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). II. Molecular Theory in the Absence of Solvent

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Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). III. Molecular Theory in the Presence of Solvent

21 January 2018

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Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay

21 January 2018

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Estimate of the barriers hindering rotation about the C.alpha.-C' bond between the cis' and trans' conformations in an isolated L-proline residue

21 January 2018

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Conformational preferences of proline oligopeptides.

21 January 2018

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Adaptively biased molecular dynamics for free energy calculations

21 January 2018

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The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

21 January 2018

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Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

21 January 2018

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Computation of free energy profiles with parallel adaptive dynamics.

21 January 2018

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Local elevation: a method for improving the searching properties of molecular dynamics simulation.

21 January 2018

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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

21 January 2018

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Escaping free-energy minima

21 January 2018

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Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

21 January 2018

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A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

21 January 2018

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Flexible docking in solution using metadynamics

21 January 2018

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Microscopic Mechanism of Antibiotics Translocation through a Porin

21 January 2018

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Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

21 January 2018

1 reference

Exploring intramolecular reactions in complex systems with metadynamics: the case of the malonate anions

21 January 2018

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Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

21 January 2018

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Hydration structure of Y3+ and La3+ compared: an application of metadynamics.

21 January 2018

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Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.

21 January 2018

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Effect of the disulfide bond on the monomeric structure of human amylin studied by combined Hamiltonian and temperature replica exchange molecular dynamics simulations

21 January 2018

1 reference

Nonequilibrium Equality for Free Energy Differences

21 January 2018

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Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality.

21 January 2018

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A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

21 January 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

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Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics

21 January 2018

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Role of cis-trans isomerism of the peptide bond in protease specificity. Kinetic studies on small proline-containing peptides and on polyproline

21 January 2018

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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

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Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

21 January 2018

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Pairwise solute descreening of solute charges from a dielectric medium

21 January 2018

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Puckering Transition of Proline Residue in Water

21 January 2018

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

21 January 2018

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Equilibrium Free Energies from Nonequilibrium Metadynamics

21 January 2018

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Multidimensional replica-exchange method for free-energy calculations

21 January 2018

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Structure of Poly-L-Proline I

21 January 2018

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Structure of Poly-L-Proline

21 January 2018

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21 January 2018

Identifiers

DOI

10.1063/1.3481087

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9 November 2017

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