Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase (Q30477296)

13 October 2017

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase (English)

1 reference

13 October 2017

Nobuyasu Koga

1

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13 October 2017

Shoji Takada

series ordinal

2

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13 October 2017

language of work or name

English

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publication date

27 March 2006

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

13 October 2017

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13 October 2017

103

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13 October 2017

14

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13 October 2017

5367-5372

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Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Rotation of F1-ATPase: how an ATP-driven molecular machine may work

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Exploring the range of protein flexibility, from a structural proteomics perspective

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Mechanically driven ATP synthesis by F1-ATPase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Catalysis and rotation of F1 motor: cleavage of ATP at the catalytic site occurs in 1 ms before 40 degree substep rotation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

The ATP-waiting conformation of rotating F1-ATPase revealed by single-pair fluorescence resonance energy transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Accurate computer-based design of a new backbone conformation in the second turn of protein L

20 June 2018

1 reference

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Structure of bovine mitochondrial F(1)-ATPase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Folding and binding cascades: dynamic landscapes and population shifts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

A simple model for calculating the kinetics of protein folding from three-dimensional structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Energy transduction in the F1 motor of ATP synthase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

F1-ATPase is a highly efficient molecular motor that rotates with discrete 120 degree steps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Folding funnels and frustration in off-lattice minimalist protein landscapes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

The ATP synthase--a splendid molecular machine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Direct observation of the rotation of F1-ATPase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Structural correlations in protein folding funnels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Specific placement of tryptophan in the catalytic sites of Escherichia coli F1-ATPase provides a direct probe of nucleotide binding: maximal ATP hydrolysis occurs with three sites occupied

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Rotation of subunits during catalysis by Escherichia coli F1-ATPase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Theoretical Studies of Protein Folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Hypothesis. The mechanism of ATP synthase. Conformational change by rotation of the beta-subunit

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Spin glasses and the statistical mechanics of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Protein folding funnels: a kinetic approach to the sequence-structure relationship

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459361

Elastic energy storage in beta-sheets with application to F1-ATPase

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

Protein and polymer analyses up tom/z 100 000 by laser ionization time-of-flight mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

The role of the DELSEED motif of the beta subunit in rotation of F1-ATPase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

F1-ATPase changes its conformations upon phosphate release

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

Intersubunit rotation in active F-ATPase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0509642103

A single myosin head moves along an actin filament with regular steps of 5.3 nanometres

21 January 2018

1 reference

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A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16567655

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0509642103

1 reference

13 October 2017

0 references

1 reference

13 October 2017

PubMed publication ID

16567655

1 reference