Atomic-level description of ubiquitin folding (Q36762717)

16 August 2017

Atomic-level description of ubiquitin folding (English)

1 reference

16 August 2017

Kresten Lindorff-Larsen

object named as

Kresten Lindorff-Larsen

series ordinal

2

0 references

author name string

Stefano Piana

series ordinal

1

1 reference

16 August 2017

David E Shaw

series ordinal

3

1 reference

16 August 2017

language of work or name

English

0 references

publication date

15 March 2013

1 reference

Proceedings of the National Academy of Sciences of the United States of America

16 August 2017

1 reference

16 August 2017

110

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16 August 2017

15

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16 August 2017

5915-5920

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

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Single-molecule fluorescence experiments determine protein folding transition path times

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

How fast-folding proteins fold

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Behind the folding funnel diagram

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Malleability of folding intermediates in the homeodomain superfamily

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Water's role in the force-induced unfolding of ubiquitin.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Computational design and experimental testing of the fastest-folding β-sheet protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Atomic-level characterization of the structural dynamics of 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=3625349

Protein vivisection reveals elusive intermediates in folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Kinetic barriers and the role of topology in protein and RNA folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared 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=3625349

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

An experimental survey of the transition between two-state and downhill protein folding scenarios

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Protein folding and unfolding studied at atomic resolution by fast two-dimensional 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=3625349

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Sub-microsecond protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Reaction coordinates and rates from transition paths

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

The N-terminal to C-terminal motif in protein folding and function

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Protein folding and the organization of the protein topology universe.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Differences in the folding transition state of ubiquitin indicated by phi and psi analyses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

The folding pathway of ubiquitin from all-atom molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Folding lambda-repressor at its speed limit

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

The protein folding 'speed limit'.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Fast and faster: a designed variant of the B-domain of protein A folds in 3 microsec

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Discerning the structure and energy of multiple transition states in protein folding using psi-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=3625349

Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Is there a unifying mechanism for protein folding?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Absolute comparison of simulated and experimental protein-folding dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Designing a 20-residue protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Computer-based redesign of a protein folding pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Three key residues form a critical contact network in a protein folding transition 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=3625349

Protein folding intermediates and pathways studied by hydrogen exchange

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Contact order, transition state placement and the refolding rates of single domain 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=3625349

Backbone dynamics and structural characterization of the partially folded A state of ubiquitin by 1H, 13C, and 15N nuclear magnetic resonance 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=3625349

Thermodynamics of ubiquitin unfolding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Navigating the folding routes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60% methanol and in water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Structure of ubiquitin refined at 1.8 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Early hydrogen-bonding events in the folding reaction of ubiquitin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Molecular conservation of 74 amino acid sequence of ubiquitin between cattle and man

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Resolution of the ATP-dependent proteolytic system from reticulocytes: a component that interacts with ATP

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

How robust are protein folding simulations with respect to force field parameterization?

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Kinetics of unfolding and folding from amide hydrogen exchange in native ubiquitin

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Characterization of the heat-stable polypeptide of the ATP-dependent proteolytic system from reticulocytes.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Markov models of molecular kinetics: generation and validation

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Reducing lambda repressor to the core

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Determination of the transition state ensemble for the folding of ubiquitin from a combination of Phi and Psi analyses.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Transition state contact orders correlate with protein folding rates.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Ubiquitin folds through a highly polarized transition state.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction coordinates by changing the pulling geometry.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

From transition paths to transition states and rate coefficients.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Toward minimalist models of larger proteins: a ubiquitin-like protein

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625349

Reversible multiple time scale molecular dynamics

5 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1218321110

Direct Observation of Dipolar Couplings and Hydrogen Bonds across a β-Hairpin in 8 M Urea

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1218321110

Multiple folding mechanisms of protein ubiquitin

21 January 2018

1 reference

12 December 2020

Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: an investigation by steered molecular dynamics simulation

1 reference

12 December 2020

Rapid Cooperative Two-state Folding of a Miniature α–β Protein and Design of a Thermostable Variant

1 reference

12 December 2020

Thermal versus mechanical unfolding of ubiquitin

1 reference

12 December 2020

Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability

1 reference

12 December 2020

Temperature- and pressure-induced unfolding and refolding of ubiquitin: a static and kinetic Fourier transform infrared spectroscopy study

1 reference

12 December 2020

Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis

1 reference

12 December 2020

Structure of very early protein folding intermediates: new insights through a variant of hydrogen exchange labelling

1 reference

12 December 2020

Immunochemical analysis of the turnover of ubiquitin-protein conjugates in intact cells. Relationship to the breakdown of abnormal proteins

1 reference

12 December 2020

Distinguishing between two-state and three-state models for ubiquitin folding

1 reference

12 December 2020

A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip

1 reference

12 December 2020

Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues

1 reference

12 December 2020

Nanosecond folding dynamics of a three-stranded beta-sheet

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1218321110

1 reference

release_aii3ko4gpvb7vp7sxj4r43qdxi

16 August 2017

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1 reference

Fatcat

https://api.fatcat.wiki/v0/release/aii3ko4gpvb7vp7sxj4r43qdxi

24 November 2022

mapped directly with Wikidata item

1 reference

16 August 2017

1 reference