Sampling alternative conformational states of transporters and receptors with AlphaFold2

Structures of the glucocorticoid-bound adhesion receptor GPR97–Go complex

(2021) Yu-Qi Ping et al.   NATURE

Structure and dynamics of the CGRP receptor in apo and peptide-bound forms

(2021) Tracy M. Josephs et al.   SCIENCE

Principles of Alternating Access in Multidrug and Toxin Extrusion (MATE) Transporters

(2021) Derek P. Claxton et al.   JOURNAL OF MOLECULAR BIOLOGY

AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP

(2021) Diego del Alamo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mechanism of substrate transport and inhibition of the human LAT1-4F2hc amino acid transporter

(2021) Renhong Yan et al.   Cell Discovery

Cryo-EM structure of constitutively active human Frizzled 7 in complex with heterotrimeric Gs

(2021) Lu Xu et al.   CELL RESEARCH

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

(2021) Rachel-Ann A. Garibsingh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High‐accuracy protein structure prediction in CASP14

(2021) Joana Pereira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5

(2021) Hui Zhang et al.   Nature Communications

Applying and improving AlphaFold at CASP14

(2021) John Jumper et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Beyond structure: emerging approaches to study GPCR dynamics

(2020) Anastasiia Gusach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural features of activated GPCR signaling complexes

(2020) Jingjing Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity

(2020) Vincent Debruycker et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations

(2020) Jing Xue et al.   eLife

Structural basis of human monocarboxylate transporter 1 inhibition by anti-cancer drug candidates

(2020) Nan Wang et al.   CELL

Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter

(2019) Kalyan Immadisetty et al.   ACS Central Science

Structure of the human LAT1–4F2hc heteromeric amino acid transporter complex

(2019) Renhong Yan et al.   NATURE

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

(2019) Melanie P. Muller et al.   CHEMICAL REVIEWS

Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport

(2019) Jonathan A. Coleman et al.   NATURE

Visualizing conformation transitions of the Lipid II flippase MurJ

(2019) Alvin C. Y. Kuk et al.   Nature Communications

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Inward-facing conformation of a multidrug resistance MATE family transporter

(2019) Sandra Zakrzewska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A one-gate elevator mechanism for the human neutral amino acid transporter ASCT2

(2019) Alisa A. Garaeva et al.   Nature Communications

Applications of sequence coevolution in membrane protein biochemistry

(2018) John M. Nicoludis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Crystal structure of the Frizzled 4 receptor in a ligand-free state

(2018) Shifan Yang et al.   NATURE

High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist

(2018) Janosch Ehrenmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct protein-lipid interactions shape the conformational landscape of secondary transporters

(2018) Chloe Martens et al.   Nature Communications

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

(2017) Yi Zheng et al.   IMMUNITY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Shared Molecular Mechanisms of Membrane Transporters

(2016) David Drew et al.   Annual Review of Biochemistry

X-ray structures and mechanism of the human serotonin transporter

(2016) Jonathan A. Coleman et al.   NATURE

The role of protein dynamics in the evolution of new enzyme function

(2016) Eleanor Campbell et al.   Nature Chemical Biology

Crystal structure of the MOP flippase MurJ in an inward-facing conformation

(2016) Alvin C Y Kuk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lipids modulate the conformational dynamics of a secondary multidrug transporter

(2016) Chloé Martens et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structure of the MOP flippase MurJ in an inward-facing conformation

(2016) Alvin C Y Kuk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lipids modulate the conformational dynamics of a secondary multidrug transporter

(2016) Chloé Martens et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

(2015) Zoe Cournia et al.   JOURNAL OF MEMBRANE BIOLOGY

Large-scale determination of previously unsolved protein structures using evolutionary information

(2015) Sergey Ovchinnikov et al.   eLife

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

(2013) Yoshiki Tanaka et al.   NATURE

Protonation drives the conformational switch in the multidrug transporter LmrP

(2013) Matthieu Masureel et al.   Nature Chemical Biology

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Autophosphorylation ActivatesDictyosteliumMyosin II Heavy Chain Kinase A by Providing a Ligand for an Allosteric Binding Site in the α-Kinase Domain

(2010) Scott W. Crawley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology