(Q41115469)

26 September 2017

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics (English)

1 reference

26 September 2017

Zachary T Campbell

1

1 reference

26 September 2017

Thomas O Baldwin

series ordinal

2

1 reference

26 September 2017

Osamu Miyashita

series ordinal

3

1 reference

26 September 2017

language of work or name

English

0 references

publication date

1 December 2010

1 reference

26 September 2017

1 reference

26 September 2017

99

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26 September 2017

12

1 reference

26 September 2017

4012-4019

1 reference

describes a project that uses

26 September 2017

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

cites work

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Recent advances in implicit solvent-based methods for biomolecular simulations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Network analysis of protein dynamics

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Complex network analysis of free-energy landscapes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Comparison of multiple Amber force fields and development of improved protein backbone parameters

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Computational redesign of endonuclease DNA binding and cleavage specificity

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Development and testing of a general amber force field

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Exploring protein native states and large-scale conformational changes with a modified generalized born model

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

ModLoop: automated modeling of loops in protein structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Cytoscape: a software environment for integrated models of biomolecular interaction networks

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Proteolytic inactivation of luciferases from three species of luminous marine bacteria, Beneckea harveyi, Photobacterium fischeri, and Photobacterium phosphoreum: evidence of a conserved structural feature

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Random and site-directed mutagenesis of bacterial luciferase: investigation of the aldehyde binding site

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Covalent structure of subunits of bacterial luciferase: NH2-terminal sequence demonstrates subunit homology

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Proteolytic inactivation of the luciferase from the luminous marine bacterium Beneckea harveyi

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Two lysine residues in the bacterial luciferase mobile loop stabilize reaction intermediates

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Mutationally altered bacterial luciferase. Implications for subunit functions.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Bacterial luciferase. Chemistry of the reactive sulfhydryl

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Nucleotide sequence of the luxA gene of Vibrio harveyi and the complete amino acid sequence of the alpha subunit of bacterial luciferase

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Atomic simulations of protein folding, using the replica exchange algorithm.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Functional roles of conserved residues in the unstructured loop of Vibrio harveyi bacterial luciferase

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Functional implications of the unstructured loop in the (beta/alpha)(8) barrel structure of the bacterial luciferase alpha subunit

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3000479

Tryptophan 250 on the .alpha. Subunit Plays an Important Role in Flavin and Aldehyde Binding to Bacterial Luciferase. Effects of W.fwdarw.Y Mutations on Catalytic Function

4 November 2018

1 reference

12 December 2020

Bacterial luciferase: demonstration of a catalytically competent altered conformational state following a single turnover

1 reference

12 December 2020

Potentials of mean force between ionizable amino acid side chains in water

1 reference

12 December 2020

A sensitive assay for proteolytic enzymes using bacterial luciferase as a substrate

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Relationship between the conserved alpha subunit arginine 107 and effects of phosphate on the activity and stability of Vibrio harveyi luciferase

1 reference

12 December 2020

The effects of phosphate on the structure and stability of the luciferases from Beneckea harveyi, Photobacterium fischeri, and Photobacterium phosphoreum

1 reference

12 December 2020

Stopped-flow kinetic analysis of the bacterial luciferase reaction

1 reference

12 December 2020

10.1016/J.BPJ.2010.11.001

Identifiers

DOI

1 reference

26 September 2017

1 reference

26 September 2017

PubMed publication ID

21156144

1 reference