(Q30155447)

16 October 2017

A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding (English)

1 reference

16 October 2017

0 references

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3

1 reference

16 October 2017

Daniel Hsieh

1

1 reference

PMCID

3323780

16 October 2017

Alexander Davis

series ordinal

2

1 reference

16 October 2017

23 November 2011

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16 October 2017

1 reference

16 October 2017

21

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16 October 2017

1

1 reference

16 October 2017

50-62

1 reference

Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Strategies and perspectives in ion-channel engineering.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Engineering of the E. coli outer membrane protein FhuA to overcome the hydrophobic mismatch in thick polymeric membranes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Association of neighboring β-strands of outer membrane protein A in lipid bilayers revealed by site-directed fluorescence quenching

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Redesign of a plugged beta-barrel membrane protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Membrane protein folding makes the transition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

The transition state for folding of an outer membrane protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

A continuum method for determining membrane protein insertion energies and the problem of charged residues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Outer membrane protein G: Engineering a quiet pore for biosensing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Highly active and selective endopeptidases with programmed substrate specificities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

The role of a hydrogen bonding network in the transmembrane beta-barrel OMPLA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Positioning of proteins in membranes: a computational approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Energetics of outer membrane phospholipase A (OMPLA) dimerization.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Recognition of transmembrane helices by the endoplasmic reticulum translocon.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Asymmetric amino acid compositions of transmembrane beta-strands

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Omp85, an evolutionarily conserved bacterial protein involved in outer-membrane-protein assembly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Molecular basis of bacterial outer membrane permeability revisited

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Secondary and tertiary structure formation of the beta-barrel membrane protein OmpA is synchronized and depends on membrane thickness

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Folding free energy function selects native-like protein sequences in the core but not on the surface

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Structure and assembly of beta-barrel membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

How proteins adapt to a membrane-water interface

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

EMBOSS: the European Molecular Biology Open Software Suite

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Structural evidence for dimerization-regulated activation of an integral membrane phospholipase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Membrane assembly of the Escherichia coli outer membrane protein OmpA: exploring sequence constraints on transmembrane beta-strands

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Architecture of beta-barrel membrane proteins: analysis of trimeric porins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Oligomeric states and siderophore binding of the ligand-gated FhuA protein that forms channels across Escherichia coli outer membranes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Folding of a bacterial outer membrane protein during passage through the periplasm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Folding intermediates of a beta-barrel membrane protein. Kinetic evidence for a multi-step membrane insertion mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Experimentally determined hydrophobicity scale for proteins at membrane interfaces

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Folding and membrane insertion of the trimeric beta-barrel protein OmpF.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Structural basis of amino acid alpha helix propensity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Reduced representation model of protein structure prediction: statistical potential and genetic algorithms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

A thermodynamic scale for the beta-sheet forming tendencies of the amino acids.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Protein structure. Born to be beta

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

The hydrophobic moment detects periodicity in protein hydrophobicity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Purification and characterization of eight class 5 outer membrane protein variants from a clone of Neisseria meningitidis serogroup A.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Refolding and oriented insertion of a membrane protein into a lipid bilayer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Reconstitution in planar lipid bilayers of a voltage-dependent anion-selective channel obtained from paramecium mitochondria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3323780

Characterization of the translocon of the outer envelope of chloroplasts

3 June 2018

1 reference

Biogenesis of the gram-negative bacterial outer membrane.

21 January 2018

1 reference

Molecular basis of bacterial outer membrane permeability

21 January 2018

1 reference

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.

21 January 2018

1 reference

Snorkeling preferences foster an amino acid composition bias in transmembrane helices.

21 January 2018

1 reference

Effective energy function for proteins in lipid membranes

21 January 2018

1 reference

Computational design of peptides that target transmembrane helices.

21 January 2018

1 reference

Proline substitutions are not easily accommodated in a membrane protein

21 January 2018

1 reference

Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms.

21 January 2018

1 reference

21 January 2018

1 reference

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

21 January 2018

1 reference

Measurement of the β-sheet-forming propensities of amino acids

21 January 2018

1 reference

The assembly pathway of outer membrane protein PhoE of Escherichia coli

21 January 2018

1 reference

12 December 2020

Reconstitution of Channel Proteins in (Polymerized) ABA Triblock Copolymer Membranes This work was supported by the Swiss National Science Foundation. We thank Dr. T. Hirt and Dr. J. Leukel for the synthesis of the triblock copolymer, Dr. P. Van Gel

1 reference

12 December 2020

Interhelical hydrogen bonding drives strong interactions in membrane proteins

1 reference

12 December 2020

Energy transduction between membranes. TonB, a cytoplasmic membrane protein, can be chemically cross-linked in vivo to the outer membrane receptor FepA

1 reference

12 December 2020

Membrane protein folding and oligomerization: the two-stage model

1 reference

12 December 2020

Aromatic rescue of glycine in beta sheets

1 reference

12 December 2020

Asparagine-mediated self-association of a model transmembrane helix

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.758

1 reference

16 October 2017

1 reference

16 October 2017

1 reference

PMCID

3323780