4.6 Article

Topological analyses of the L-lysine exporter LysO reveal a critical role for a conserved pair of intramembrane solvent-exposed acidic residues

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Integrative Structural Biology in the Era of Accurate Structure Prediction

Gal Masrati et al.

Summary: The accurate modeling methods of protein structures, especially with the breakthrough advance by AlphaFold2, can be combined with experimental techniques to enhance integrative structural biology. This will lead to better and quicker investigation of structure-function relationships.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Dissection of Protonation Sites for Antibacterial Recognition and Transport in QacA, a Multi-Drug Efflux Transporter

Puja Majumder et al.

JOURNAL OF MOLECULAR BIOLOGY (2019)

Review Biochemical Research Methods

Coupling efficiency of secondary active transporters

Ryan K. Henderson et al.

CURRENT OPINION IN BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection

Erik J. Hasenoehrl et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Topology of membrane proteins - predictions, limitations and variations

Konstantinos D. Tsirigos et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

Review Biochemistry & Molecular Biology

Shared Molecular Mechanisms of Membrane Transporters

David Drew et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 85 (2016)

Article Multidisciplinary Sciences

Structural basis for amino acid export by DMT superfamily transporter YddG

Hirotoshi Tsuchiya et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

Konstantinos D. Tsirigos et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

CCTOP: a Consensus Constrained TOPology prediction web server

Laszlo Dobson et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

JPred4: a protein secondary structure prediction server

Alexey Drozdetskiy et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

Dissection of Mechanistic Principles of a Secondary Multidrug Efflux Protein

Nir Fluman et al.

MOLECULAR CELL (2012)

Article Microbiology

Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli

Carmelita N. Marbaniang et al.

JOURNAL OF BACTERIOLOGY (2011)

Article Biochemical Research Methods

Jalview Version 2-a multiple sequence alignment editor and analysis workbench

Andrew M. Waterhouse et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Transmembrane protein topology prediction using support vector machines

Timothy Nugent et al.

BMC BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Transport mechanism of a bacterial homologue of glutamate transporters

Nicolas Reyes et al.

NATURE (2009)

Article Multidisciplinary Sciences

Prediction of membrane-protein topology from first principles

Andreas Bernsel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation

Jin Hwan Park et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Biochemistry & Molecular Biology

Membrane protein structure: Prediction versus reality

Arne Elofsson et al.

ANNUAL REVIEW OF BIOCHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

Tomoya Baba et al.

MOLECULAR SYSTEMS BIOLOGY (2006)

Article Microbiology

Characterization of methionine export in Corynebacterium glutamicum

C Trötschel et al.

JOURNAL OF BACTERIOLOGY (2005)

Review Biochemistry & Molecular Biology

Properties of integral membrane protein structures: Derivation of an implicit membrane potential

MB Ulmschneider et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Experimentally based topology models for E-coli inner membrane proteins

M Rapp et al.

PROTEIN SCIENCE (2004)

Article Multidisciplinary Sciences

Structure of a glutamate transporter homologue from Pyrococcus horikoshii

D Yernool et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

A combined transmembrane topology and signal peptide prediction method

L Käll et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Multidisciplinary Sciences

Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code

BC Jester et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Multidisciplinary Sciences

Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis

D Drew et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Review Biotechnology & Applied Microbiology

Bacterial amino acid transport proteins: occurrence, functions, and significance for biotechnological applications

A Burkovski et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2002)

Article Biochemical Research Methods

The HMMTOP transmembrane topology prediction server

GE Tusnády et al.

BIOINFORMATICS (2001)

Article Biochemistry & Molecular Biology

Amino acid distributions in integral membrane protein structures

MB Ulmschneider et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2001)

Article Biochemistry & Molecular Biology

Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes

A Krogh et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Multidisciplinary Sciences

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

KA Datsenko et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)