ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations

Structural basis for the binding of DNP and purine nucleotides onto UCP1

(2023) Yunlu Kang et al.   NATURE

Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling

(2023) Antoine Gagelin et al.   Nature Communications

Structural basis of purine nucleotide inhibition of human uncoupling protein 1

(2023) Scott A. Jones et al.   Science Advances

PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations

(2022) Wanling Song et al.   Journal of Chemical Theory and Computation

Mitochondrial uncouplers induce proton leak by activating AAC and UCP1

(2022) Ambre M. Bertholet et al.   NATURE

Scalable Constant pH Molecular Dynamics in GROMACS

(2022) Noora Aho et al.   Journal of Chemical Theory and Computation

Brown adipose tissue is associated with cardiometabolic health

(2021) Tobias Becher et al.   NATURE MEDICINE

ANT1 Activation and Inhibition Patterns Support the Fatty Acid Cycling Mechanism for Proton Transport

(2021) Jürgen Kreiter et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT

(2021) Yu Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anti-obesity drug discovery: advances and challenges

(2021) Timo D. Müller et al.   NATURE REVIEWS DRUG DISCOVERY

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial uncoupler BAM15 reverses diet-induced obesity and insulin resistance in mice

(2020) Stephanie J. Alexopoulos et al.   Nature Communications

Identification of New Potent Human Uncoupling Protein 1 (UCP1) Agonists Using Virtual Screening and In Vitro Approaches

(2019) Hong‐Yuan Lu et al.   Molecular Informatics

H+ transport is an integral function of the mitochondrial ADP/ATP carrier

(2019) Ambre M. Bertholet et al.   NATURE

Antidiabetic and cardiovascular beneficial effects of a liver-localized mitochondrial uncoupler

(2019) Naohide Kanemoto et al.   Nature Communications

A single K+-binding site in the crystal structure of the gastric proton pump

(2019) Kenta Yamamoto et al.   eLife

K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase

(2018) Vikas Dubey et al.   Scientific Reports

Reactive molecular dynamics: From small molecules to proteins

(2018) Markus Meuwly   Wiley Interdisciplinary Reviews-Computational Molecular Science

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

(2017) Brian K. Radak et al.   Journal of Chemical Theory and Computation

Specific Interaction of the Human Mitochondrial Uncoupling Protein 1 with Free Long-Chain Fatty Acid

(2017) Linlin Zhao et al.   STRUCTURE

The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion

(2016) Huan Rui et al.   eLife

Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin

(2015) Yang Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Expression, Folding, and Proton Transport Activity of Human Uncoupling Protein-1 (UCP1) in Lipid Membranes

(2013) Tuan Hoang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2

(2013) Manuela Zoonens et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Lipids of mitochondria

(2013) Susanne E. Horvath et al.   PROGRESS IN LIPID RESEARCH

Mechanism of Fatty-Acid-Dependent UCP1 Uncoupling in Brown Fat Mitochondria

(2012) Andriy Fedorenko et al.   CELL

The mitochondrial transporter family SLC25: Identification, properties and physiopathology

(2012) Ferdinando Palmieri   MOLECULAR ASPECTS OF MEDICINE

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

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching

(2011) Marcelo J. Berardi et al.   NATURE

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess 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

Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein

(2008) Yuki Takayama et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding of ADP in the Mitochondrial ADP/ATP Carrier Is Driven by an Electrostatic Funnel

(2008) François Dehez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Electrostatic funneling of substrate in mitochondrial inner membrane carriers

(2008) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA