Thermally induced protein unfolding probed by isotope-edited IR spectroscopy. (Q36294499)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22853174%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

title

Thermally induced protein unfolding probed by isotope-edited IR spectroscopy (English)

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9 February 2020

1

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9 February 2020

author name string

James L Skinner

series ordinal

2

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9 February 2020

language of work or name

English

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publication date

1 August 2012

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Journal of Physical Chemistry B

9 February 2020

published in

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9 February 2020

volume

116

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9 February 2020

issue

32

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9 February 2020

page(s)

9627-9634

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Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation

9 February 2020

cites work

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Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding

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Identifying residual structure in intrinsically disordered systems: a 2D IR spectroscopic study of the GVGXPGVG peptide

30 September 2017

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Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations

30 September 2017

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Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

30 September 2017

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Spectroscopic studies of protein folding: linear and nonlinear methods

30 September 2017

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Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

30 September 2017

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Vibrational spectroscopy of water at interfaces.

30 September 2017

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Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides

30 September 2017

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2DIR spectroscopy of human amylin fibrils reflects stable β-sheet structure

30 September 2017

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Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

30 September 2017

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Role of water in protein aggregation and amyloid polymorphism

30 September 2017

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Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments

30 September 2017

1 reference

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Development and validation of transferable amide I vibrational frequency maps for peptides.

30 September 2017

1 reference

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Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy

30 September 2017

1 reference

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Challenges in protein folding simulations: Timescale, representation, and analysis

30 September 2017

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Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back

30 September 2017

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Taming the complexity of protein folding

30 September 2017

1 reference

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Stable and metastable states of human amylin in solution.

30 September 2017

1 reference

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Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

30 September 2017

1 reference

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Solution structures of rat amylin peptide: simulation, theory, and experiment

30 September 2017

1 reference

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2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece

30 September 2017

1 reference

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Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis.

30 September 2017

1 reference

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Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges

30 September 2017

1 reference

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Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution

30 September 2017

1 reference

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Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles.

30 September 2017

1 reference

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Tracking fiber formation in human islet amyloid polypeptide with automated 2D-IR spectroscopy

30 September 2017

1 reference

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Coherent two-dimensional optical spectroscopy

30 September 2017

1 reference

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Amide I two-dimensional infrared spectroscopy of proteins

30 September 2017

1 reference

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Two-dimensional spectroscopy at infrared and optical frequencies

30 September 2017

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Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

30 September 2017

1 reference

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Structural disorder of the CD3zeta transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations.

30 September 2017

1 reference

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Isotope-edited IR spectroscopy for the study of membrane proteins

30 September 2017

1 reference

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

30 September 2017

1 reference

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Protein misfolding, functional amyloid, and human disease

30 September 2017

1 reference

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Picosecond dynamics of a membrane protein revealed by 2D IR.

30 September 2017

1 reference

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Simulation protocols for coherent femtosecond vibrational spectra of peptides

30 September 2017

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

GROMACS: fast, flexible, and free

30 September 2017

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

Unfolded proteins and protein folding studied by NMR.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

30 September 2017

1 reference

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Protein folding and misfolding

30 September 2017

1 reference

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Experimental tests of villin subdomain folding simulations

30 September 2017

1 reference

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What vibrations tell us about proteins.

30 September 2017

1 reference

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Native-like mean structure in the unfolded ensemble of small proteins

30 September 2017

1 reference

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Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures

30 September 2017

1 reference

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From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

30 September 2017

1 reference

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Use of a new label, (13)==(18)O, in the determination of a structural model of phospholamban in a lipid bilayer. Spatial restraints resolve the ambiguity arising from interpretations of mutagenesis data.

30 September 2017

1 reference

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Protein misfolding, evolution and disease

30 September 2017

1 reference

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Canonical dynamics: Equilibrium phase-space distributions

30 September 2017

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

30 September 2017

1 reference

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

30 September 2017

1 reference

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Theory of protein folding: the energy landscape perspective

30 September 2017

1 reference

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NMR structure of the 35-residue villin headpiece subdomain

30 September 2017

1 reference

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Exploring the energy landscape in proteins

30 September 2017

1 reference

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Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment

30 September 2017

1 reference

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30 September 2017

How does a protein fold?

1 reference

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Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins

30 September 2017

1 reference

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Dominant forces in protein folding

30 September 2017

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Does Fourier-transform infrared spectroscopy provide useful information on protein structures?

30 September 2017

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The Two Dimensional Vibrational Echo of a Nitrile Probe of the Villin HP35 Protein.

30 September 2017

1 reference

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Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

30 September 2017

1 reference

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Comparative study of electrostatic models for the amide-I and -II modes: linear and two-dimensional infrared spectra

29 June 2018

1 reference

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Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein

29 June 2018

1 reference

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Mutation of Charged Residues to Neutral Ones Accelerates Urea Denaturation of HP-35

29 June 2018

1 reference

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Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations.

22 September 2018

1 reference

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Analysis of core packing in a cooperatively folded miniature protein: the ultrafast folding villin headpiece helical subdomain

22 September 2018

1 reference

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Gating mechanism of the influenza A M2 channel revealed by 1D and 2D IR spectroscopies.

22 September 2018

1 reference

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Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent

22 September 2018

1 reference

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Direct and high resolution characterization of cytochrome c equilibrium folding

22 September 2018

1 reference

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Electrostatic DFT map for the complete vibrational amide band of NMA.

22 September 2018

1 reference

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Optimized parallel tempering simulations of proteins.

22 September 2018

1 reference

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Multistate folding of the villin headpiece domain

22 September 2018

1 reference

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Optimal allocation of replicas in parallel tempering simulations.

22 September 2018

1 reference

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Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches

22 September 2018

1 reference

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

22 September 2018

1 reference

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

22 September 2018

1 reference

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Parallel tempering simulations of HP-36.

22 September 2018

1 reference

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Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

Site-specific examination of secondary structure and orientation determination in membrane proteins: the peptidic (13)C=(18)O group as a novel infrared probe

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463243

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

5 December 2018

1 reference

12 December 2020

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

1 reference

12 December 2020

Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy

1 reference

12 December 2020

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

1 reference

12 December 2020

Interpretation of the water surface vibrational sum-frequency spectrum

1 reference

12 December 2020

Residue Specific Resolution of Protein Folding Dynamics Using Isotope-Edited Infrared Temperature Jump Spectroscopy†

1 reference

12 December 2020

Resolution-enhanced Fourier transform infrared spectroscopy of enzymes

1 reference

12 December 2020

IR and Raman spectra of liquid water: theory and interpretation

1 reference

12 December 2020

Two-dimensional infrared spectra of the 13C=18O isotopomers of alanine residues in an alpha-helix

1 reference

12 December 2020

Rational Design, Structural and Thermodynamic Characterization of a Hyperstable Variant of the Villin Headpiece Helical Subdomain†

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Elucidation of residue-level structure and dynamics of polypeptides via isotope-edited infrared spectroscopy

1 reference

12 December 2020

Surface of liquid water: three-body interactions and vibrational sum-frequency spectroscopy

1 reference

12 December 2020

Infrared study of the effect of hydration on the amide I band and aggregation properties of helical peptides

1 reference

12 December 2020

Vibrational sum-frequency spectroscopy of the liquid/vapor interface for dilute HOD in D(2)O

1 reference

12 December 2020

Dynamical effects in line shapes for coupled chromophores: time-averaging approximation

1 reference

12 December 2020

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

1 reference

12 December 2020

2D IR line shapes probe ovispirin peptide conformation and depth in lipid bilayers

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP304613B

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22853174%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22853174%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

22853174

1 reference