Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1. (Q34497324)

2 August 2017

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1. (English)

1 reference

2 August 2017

0 references

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Olivier Tenaillon

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

author name string

Matteo Figliuzzi

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Hervé Jacquier

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Alexander Schug

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

language of work or name

1 reference

6 October 2015

1 reference

Molecular Biology and Evolution

2 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

volume

33

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

page(s)

268-280

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

Dissecting enzyme function with microfluidic-based deep mutational scanning

4 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

How structural and physicochemical determinants shape sequence constraints in a functional enzyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Sequence co-evolution gives 3D contacts and structures of protein complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Empirical fitness landscapes and the predictability of evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Inferring fitness landscapes by regression produces biased estimates of epistasis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

A comprehensive, high-resolution map of a gene's fitness landscape

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Mutational effects on stability are largely conserved during protein evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Pfam: the protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Maximum allowed solvent accessibilites of residues in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

The network of stabilizing contacts in proteins studied by coevolutionary data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Capturing the mutational landscape of the beta-lactamase TEM-1.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Evolutionary biochemistry: revealing the historical and physical causes of protein properties.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Emerging methods in protein co-evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Analyses of the effects of all ubiquitin point mutants on yeast growth rate

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Protein structure prediction from sequence variation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

The spatial architecture of protein function and adaptation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Genomics-aided structure prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Three-dimensional structures of membrane proteins from genomic sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Amino acid coevolution induces an evolutionary Stokes shift.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Predicting the functional impact of protein mutations: application to cancer genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Diminishing returns epistasis among beneficial mutations decelerates adaptation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

A biophysical protein folding model accounts for most mutational fitness effects in viruses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Uncovering the roles of rare variants in common disease through whole-genome sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

A method and server for predicting damaging missense mutations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

High-resolution protein complexes from integrating genomic information with molecular simulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Protein sectors: evolutionary units of three-dimensional structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

The role of a second-shell residue in modifying substrate and inhibitor interactions in the SHV beta-lactamase: a study of ambler position Asn276.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Identification of direct residue contacts in protein-protein interaction by message passing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

SPROUTS: a database for the evaluation of protein stability upon point mutation.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Empirical fitness landscapes reveal accessible evolutionary paths

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Predicting the effects of amino acid substitutions on protein function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Thermodynamic prediction of protein neutrality

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

SIFT: Predicting amino acid changes that affect protein function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

What is antibiotic resistance and how can we measure it?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Reduced surface: an efficient way to compute molecular surfaces

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Towards a general theory of adaptive walks on rugged landscapes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

A standard numbering scheme for the class A beta-lactamases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4693977

Large pseudocounts and L2-norm penalties are necessary for the mean-field inference of Ising and Potts models.

7 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV211

Epistasis as the primary factor in molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV211

Predicting functionally important residues from sequence conservation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV211

Prediction of protein stability changes for single-site mutations using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV211

Negative epistasis between beneficial mutations in an evolving bacterial population

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV211

Reproducible Protein Folding with the Stochastic Tunneling Method

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26446903

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Basin hopping simulations for all-atom protein folding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26446903

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural determinants of protein evolution are context-sensitive at the residue level

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26446903

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSV211

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

1 reference

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26446903%20AND%20SRC:MED&resulttype=core&format=json