(Q28477196)

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Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories

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Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories (English)

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author name string

Violeta Beleva Guthrie

1

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Jennifer Allen

2

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Manel Camps

3

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Rachel Karchin

4

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language of work or name

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publication date

September 2011

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PLOS Computational Biology

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7

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9

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e1002184

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copyright license

Creative Commons Attribution 4.0 International

22 September 2011

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April 2022 Public Data File from Crossref

copyright status

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describes a project that uses

object named as

CytoScape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Three decades of beta-lactamase inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Updated functional classification of beta-lactamases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

In the light of directed evolution: pathways of adaptive protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Genetic and Structural Characterization of an L201P Global Suppressor Substitution in TEM-1 β-Lactamase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Increased folding stability of TEM-1 beta-lactamase by in vitro selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

PAML 4: phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Tools for integrated sequence-structure analysis with UCSF Chimera

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

RAISE: a simple and novel method of generating random insertion and deletion mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Predicting the emergence of antibiotic resistance by directed evolution and structural analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

PAML: a program package for phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

Rapid evolution of a protein in vitro by DNA shuffling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

19 March 2017

SIFT: Predicting amino acid changes that affect protein function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

7 April 2017

Darwinian evolution can follow only very few mutational paths to fitter proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

7 April 2017

Prediction of deleterious human alleles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

7 April 2017

An evolutionary trace method defines binding surfaces common to protein families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

7 April 2017

Initial mutations direct alternative pathways of protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Mutational effects and the evolution of new protein functions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Natural evolution of TEM-1 β-lactamase: experimental reconstruction and clinical relevance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Structural and functional roles of coevolved sites in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

The changing epidemiology of resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Protein dynamism and evolvability.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Potential role of phenotypic mutations in the evolution of protein expression and stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Ohno's model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Intense neutral drifts yield robust and evolvable consensus proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Mutational events in cefotaximase extended-spectrum beta-lactamases of the CTX-M-1 cluster involved in ceftazidime resistance.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Analysis of the residue-residue coevolution network and the functionally important residues in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Evolution of extended-spectrum beta-lactamases by mutation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Protein engineers turned evolutionists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Genetic constraints on protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

RNA mutagenesis yields highly diverse mRNA libraries for in vitro protein evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Unexpected enzyme TEM-126: role of mutation Asp179Glu

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

One-step random mutagenesis by error-prone rolling circle amplification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Biochemical characterization of laboratory mutants of extended-spectrum beta-lactamase TEM-60.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Experimental Prediction of the Natural Evolution of Antibiotic Resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Predicting evolution by in vitro evolution requires determining evolutionary pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Mutant TEM beta-lactamase producing resistance to ceftazidime, ampicillins, and beta-lactamase inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Why are proteins so robust to site mutations?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Selection of naturally occurring extended-spectrum TEM beta-lactamase variants by fluctuating beta-lactam pressure.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Inhibitor-resistant TEM beta-lactamases: phenotypic, genetic and biochemical characteristics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Selection and characterization of beta-lactam-beta-lactamase inactivator-resistant mutants following PCR mutagenesis of the TEM-1 beta-lactamase gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

A237T as a modulating mutation in naturally occurring extended-spectrum TEM-type beta-lactamases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Clinical inhibitor-resistant mutants of the beta-lactamase TEM-1 at amino-acid position 69. Kinetic analysis and molecular modelling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Catalytic properties of class A beta-lactamases: efficiency and diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

A novel extended-spectrum TEM-type beta-lactamase (TEM-52) associated with decreased susceptibility to moxalactam in Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

A natural polymorphism in beta-lactamase is a global suppressor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

An additional ionic bond suggested by molecular modelling of TEM-2 might induce a slight discrepancy between catalytic properties of TEM-1 and TEM-2 beta-lactamases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Extended-spectrum and inhibitor-resistant TEM-type beta-lactamases: mutations, specificity, and three-dimensional structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Single amino acid replacements at positions altered in naturally occurring extended-spectrum TEM beta-lactamases.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Beta-lactamases and bacterial resistance to antibiotics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Site-directed mutagenesis at the active site of Escherichia coli TEM-1 beta-lactamase. Suicide inhibitor-resistant mutants reveal the role of arginine 244 and methionine 69 in catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

29 September 2017

Mutagenesis and functional selection protocols for directed evolution of proteins in E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

2 June 2018

Rapid in vivo evolution of a beta-lactamase using phagemids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

2 June 2018

Stability of TEM beta-lactamase mutants hydrolyzing third generation cephalosporins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

2 June 2018

A standard numbering scheme for the class A beta-lactamases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

2 June 2018

Substitution of lysine at position 104 or 240 of TEM-1pTZ18R beta-lactamase enhances the effect of serine-164 substitution on hydrolysis or affinity for cephalosporins and the monobactam aztreonam.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

2 June 2018

Experimental evolution of gene duplicates in a bacterial plasmid model

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Finding local community structure in networks.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Effects on substrate profile by mutational substitutions at positions 164 and 179 of the class A TEM(pUC19) beta-lactamase from Escherichia coli.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Statistical mechanics of complex networks

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

A novel extended-spectrum TEM-type beta-lactamase, TEM-138, from Salmonella enterica serovar Infantis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Structural determinants of allosteric ligand activation in RXR heterodimers.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif A functions in base selection.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

TEM beta-lactamase mutants hydrolysing third-generation cephalosporins. A kinetic and molecular modelling analysis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Detrimental effect of the combination of R164S with G238S in TEM-1 beta-lactamase on the extended-spectrum activity conferred by each single mutation.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Structure of the wild-type TEM-1 beta-lactamase at 1.55 A and the mutant enzyme Ser70Ala at 2.1 A suggest the mode of noncovalent catalysis for the mutant enzyme

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002184

21 January 2018

Site-directed mutagenesis using the megaprimer method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

27 November 2018

Improving a circularly permuted TEM-1 beta-lactamase by directed evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

27 November 2018

The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3178621

27 November 2018

The asparagine to aspartic acid substitution at position 276 of TEM-35 and TEM-36 is involved in the beta-lactamase resistance to clavulanic acid

1 reference

https://pubmed.ncbi.nlm.nih.gov/21966264

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolution of extended-spectrum beta-lactamases in a MutS-deficient Pseudomonas aeruginosa hypermutator

1 reference

https://pubmed.ncbi.nlm.nih.gov/21966264

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of residue 238 of TEM-1 beta-lactamase in the hydrolysis of extended-spectrum antibiotics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21966264

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PCBI.1002184

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

DBLP publication ID

journals/ploscb/GuthrieACK11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

0 references

PubMed publication ID

0 references

ResearchGate publication ID

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