Mutations as trapdoors to two competing native conformations of the Rop-dimer (Q36140604)

12 August 2017

Mutations as trapdoors to two competing native conformations of the Rop-dimer (English)

1 reference

12 August 2017

4

José N Onuchic

1 reference

12 August 2017

Alexander Schug

1

1 reference

12 August 2017

Paul C Whitford

series ordinal

2

1 reference

12 August 2017

Yaakov Levy

series ordinal

3

1 reference

12 August 2017

language of work or name

English

0 references

publication date

29 October 2007

1 reference

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

12 August 2017

1 reference

12 August 2017

104

1 reference

12 August 2017

45

1 reference

12 August 2017

17674-17679

1 reference

Conformational transitions of adenylate kinase: switching by cracking

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Dynamics of allosteric transitions in GroEL.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Molecular dynamics: survey of methods for simulating the activity of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Comparative modeling for protein structure prediction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Scalable molecular dynamics with NAMD

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Determination of barrier heights and prefactors from protein folding rate data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Probing the instabilities in the dynamics of helical fragments from mouse PrPC.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

The effects of nonnative interactions on protein folding rates: theory and simulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

The protein folding 'speed limit'.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Theory of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

A cell-based screen for function of the four-helix bundle protein Rop: a new tool for combinatorial experiments in biophysics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Protein topology determines binding mechanism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Force fields for protein simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Automated analysis of interatomic contacts in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

The Alacoil: a very tight, antiparallel coiled-coil of helices

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Funnels, pathways, and the energy landscape of protein folding: a synthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Bent helix formation between RNA hairpins with complementary loops

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Control of ColE1 DNA replication: the rop gene product negatively affects transcription from the replication primer promoter

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Structure of the ColE1 rop protein at 1.7 A resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

The structure of ColE1 rop in solution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

The Energy Landscapes and Motions of Proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Atomic-level description of amyloid beta-dimer formation

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Complete change of the protein folding transition state upon circular permutation.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Mapping the cytochrome C folding landscape

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Protein folding funnels: the nature of the transition state ensemble

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2077020

Control of cole 1 plasmid replication: Enhancement of binding of RNA I to the primer transcript by the rom protein

5 December 2018

1 reference

12 December 2020

Reproducible Protein Folding with the Stochastic Tunneling Method

1 reference

12 December 2020

Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude

1 reference

12 December 2020

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

1 reference

12 December 2020

Low barrier kinetics: dependence on observables and free energy surface

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0706077104

1 reference

release_n74mcb46onb77kbqtwtbhmruuy

12 August 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/n74mcb46onb77kbqtwtbhmruuy

24 November 2022

mapped directly with Wikidata item

1 reference

12 August 2017

PubMed publication ID

17968016

1 reference