Biomolecular simulation: a computational microscope for molecular biology

RO Dror, RM Dirks, JP Grossman, H Xu… - Annual review of …, 2012 - annualreviews.org
Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

[HTML][HTML] The structural basis of secondary active transport mechanisms

LR Forrest, R Krämer, C Ziegler - Biochimica et Biophysica Acta (BBA) …, 2011 - Elsevier
Secondary active transporters couple the free energy of the electrochemical potential of one
solute to the transmembrane movement of another. As a basic mechanistic explanation for …

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

I Buch, T Giorgino… - Proceedings of the …, 2011 - National Acad Sciences
The understanding of protein–ligand binding is of critical importance for biomedical
research, yet the process itself has been very difficult to study because of its intrinsically …

Molecular simulation approaches to membrane proteins

PJ Stansfeld, MSP Sansom - Structure, 2011 - cell.com
Molecular simulations are an invaluable tool for understanding membrane proteins.
Improvements to both hardware and simulation methods have allowed access to …

Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle

ARJ Murphy, DJ Scanlan, Y Chen, NBP Adams… - Nature …, 2021 - nature.com
The planktonic synthesis of reduced organophosphorus molecules, such as
alkylphosphonates and aminophosphonates, represents one half of a vast global oceanic …

Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate: phosphate antiporter

M Moradi, G Enkavi, E Tajkhorshid - Nature communications, 2015 - nature.com
Membrane transporters actively translocate their substrate by undergoing large-scale
structural transitions between inward-(IF) and outward-facing (OF) states ('alternating …

The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter

J Shan, JA Javitch, L Shi, H Weinstein - PloS one, 2011 - journals.plos.org
Background The dopamine transporter (DAT), a member of the neurotransmitter: Na+
symporter (NSS) family, terminates dopaminergic neurotransmission and is a major …

Transient formation of water-conducting states in membrane transporters

J Li, SA Shaikh, G Enkavi, PC Wen… - Proceedings of the …, 2013 - National Acad Sciences
Membrane transporters rely on highly coordinated structural transitions between major
conformational states for their function, to prevent simultaneous access of the substrate …

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

JC Ruiz, V D'Afonseca, A Silva, A Ali, AC Pinto… - PloS one, 2011 - journals.plos.org
Background Corynebacterium pseudotuberculosi s, a Gram-positive, facultative intracellular
pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL …

Protonation drives the conformational switch in the multidrug transporter LmrP

M Masureel, C Martens, RA Stein, S Mishra… - Nature chemical …, 2014 - nature.com
Multidrug antiporters of the major facilitator superfamily couple proton translocation to the
extrusion of cytotoxic molecules. The conformational changes that underlie the transport …