A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition

The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state

(2017) Sebastian Stolzenberg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Membrane cholesterol access into a G-protein-coupled receptor

(2017) Ramon Guixà-González et al.   Nature Communications

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

(2017) Asghar M. Razavi et al.   Scientific Reports

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

(2016) Xavier Periole   CHEMICAL REVIEWS

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

X-ray structures and mechanism of the human serotonin transporter

(2016) Jonathan A. Coleman et al.   NATURE

Mapping Cholesterol Interaction Sites on Serotonin Transporter through Coarse-Grained Molecular Dynamics

(2016) Mariarosaria Ferraro et al.   PLoS One

Control of serotonin transporter phosphorylation by conformational state

(2016) Yuan-Wei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

(2016) Moutusi Manna et al.   eLife

Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus

(2015) George Khelashvili et al.   ACS Chemical Neuroscience

The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations

(2015) Julie Grouleff et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

A Dualistic Conformational Response to Substrate Binding in the Human Serotonin Transporter Reveals a High Affinity State for Serotonin

(2015) Henriette Bjerregaard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Neurotransmitter and psychostimulant recognition by the dopamine transporter

(2015) Kevin H. Wang et al.   NATURE

X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine

(2015) Aravind Penmatsa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2-containing membranes

(2015) George Khelashvili et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter

(2015) Mary Hongying Cheng et al.   STRUCTURE

X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine

(2015) Aravind Penmatsa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Monoamine transporters: insights from molecular dynamics simulations

(2015) Julie Grouleff et al.   Frontiers in Pharmacology

Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites

(2014) Xavier Prasanna et al.   BIOPHYSICAL JOURNAL

Conformational dynamics of ligand-dependent alternating access in LeuT

(2014) Kelli Kazmier et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters

(2014) Lina Malinauskaite et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

AlignMe—a membrane protein sequence alignment web server

(2014) Marcus Stamm et al.   NUCLEIC ACIDS RESEARCH

Common Folds and Transport Mechanisms of Secondary Active Transporters

(2013) Yigong Shi   Annual Review of Biophysics

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Dopamine Transporter Endocytic Trafficking in Striatal Dopaminergic Neurons: Differential Dependence on Dynamin and the Actin Cytoskeleton

(2013) L. R. Gabriel et al.   JOURNAL OF NEUROSCIENCE

X-ray structure of dopamine transporter elucidates antidepressant mechanism

(2013) Aravind Penmatsa et al.   NATURE

Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

(2013) Heidi Koldsø et al.   PLoS One

How cholesterol interacts with membrane proteins: an exploration of cholesterol-binding sites including CRAC, CARC, and tilted domains

(2013) Jacques Fantini et al.   Frontiers in Physiology

Visualization of Lipid Raft Membrane Compartmentalization in Living RN46A Neuronal Cells Using Single Quantum Dot Tracking

(2012) Jerry C. Chang et al.   ACS Chemical Neuroscience

Comparative Modeling of the Human Monoamine Transporters: Similarities in Substrate Binding

(2012) Heidi Koldsø et al.   ACS Chemical Neuroscience

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Importance of cholesterol in dopamine transporter function

(2012) Kymry T. Jones et al.   JOURNAL OF NEUROCHEMISTRY

X-ray structures of LeuT in substrate-free outward-open and apo inward-open states

(2012) Harini Krishnamurthy et al.   NATURE

Uncovering the intimate relationship between lipids, cholesterol and GPCR activation

(2011) Joanne Oates et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Flotillin-1 is essential for PKC-triggered endocytosis and membrane microdomain localization of DAT

(2011) M Laura Cremona et al.   NATURE NEUROSCIENCE

SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation

(2011) A. S. Kristensen et al.   PHARMACOLOGICAL REVIEWS

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

(2011) Heidi Koldsø et al.   PLoS Computational Biology

Membrane Cholesterol Modulates the Outward Facing Conformation of the Dopamine Transporter and Alters Cocaine Binding

(2010) Weimin C. Hong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Modeling and Dynamics of the Inward-Facing State of a Na+/Cl− Dependent Neurotransmitter Transporter Homologue

(2010) Saher Afshan Shaikh et al.   PLoS Computational Biology

Recent advances in the understanding of the interaction of antidepressant drugs with serotonin and norepinephrine transporters

(2009) Jacob Andersen et al.   CHEMICAL COMMUNICATIONS

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Genetics of attention-deficit hyperactivity disorder (ADHD)

(2009) Sally I. Sharp et al.   NEUROPHARMACOLOGY

The Rocking Bundle: A Mechanism for Ion-Coupled Solute Flux by Symmetrical Transporters

(2009) Lucy R. Forrest et al.   PHYSIOLOGY

Are specific nonannular cholesterol binding sites present in G-protein coupled receptors?

(2008) Yamuna Devi Paila et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

An Intracellular Interaction Network Regulates Conformational Transitions in the Dopamine Transporter

(2008) Julie Kniazeff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Phorbol ester induced trafficking-independent regulation and enhanced phosphorylation of the dopamine transporter associated with membrane rafts and cholesterol

(2008) James D. Foster et al.   JOURNAL OF NEUROCHEMISTRY

Binding of Serotonin to the Human Serotonin Transporter. Molecular Modeling and Experimental Validation

(2008) Leyla Celik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Mechanism of a Neurotransmitter:Sodium Symporter—Inward Release of Na+ and Substrate Is Triggered by Substrate in a Second Binding Site

(2008) Lei Shi et al.   MOLECULAR CELL

Mechanism for alternating access in neurotransmitter transporters

(2008) L. R. Forrest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate Binding and Formation of an Occluded State in the Leucine Transporter

(2007) Leyla Celik et al.   BIOPHYSICAL JOURNAL

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation