Published in Structure on July 01, 2007
Crystal structure of a eukaryotic phosphate transporter. Nature (2013) 1.60
Molecular dynamics simulations of membrane channels and transporters. Curr Opin Struct Biol (2009) 1.58
Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. Proc Natl Acad Sci U S A (2013) 1.45
Transport and signaling via the amino acid binding site of the yeast Gap1 amino acid transceptor. Nat Chem Biol (2008) 1.16
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol (2010) 1.11
Site-directed alkylation studies with LacY provide evidence for the alternating access model of transport. Biochemistry (2011) 0.98
Protonation drives the conformational switch in the multidrug transporter LmrP. Nat Chem Biol (2013) 0.97
Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol (2014) 0.92
Gating at both ends and breathing in the middle: conformational dynamics of TolC. Biophys J (2008) 0.91
Proton-coupled dynamics in lactose permease. Structure (2012) 0.89
An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency. Structure (2012) 0.89
Molecular dynamics simulation studies of GLUT4: substrate-free and substrate-induced dynamics and ATP-mediated glucose transport inhibition. PLoS One (2010) 0.87
Simulations of substrate transport in the multidrug transporter EmrD. Proteins (2012) 0.83
Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation. J Comput Theor Nanosci (2010) 0.79
Relating protein conformational changes to packing efficiency and disorder. Protein Sci (2009) 0.78
Modulation of the conformational state of the SV2A protein by an allosteric mechanism as evidenced by ligand binding assays. Br J Pharmacol (2013) 0.77
Mechanism of Substrate Translocation in an Alternating Access Transporter. Cell (2017) 0.77
Evidence for the transport of maltose by the sucrose permease, CscB, of Escherichia coli. J Membr Biol (2009) 0.76
Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol:fumarate reductase. Biophys J (2012) 0.75
Emulating proton-induced conformational changes in the vesicular monoamine transporter VMAT2 by mutagenesis. Proc Natl Acad Sci U S A (2016) 0.75
Proline-induced distortions of transmembrane helices. J Mol Biol (2002) 2.76
Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1. Science (2010) 2.52
Liquid-vapor oscillations of water in hydrophobic nanopores. Proc Natl Acad Sci U S A (2003) 2.48
Acquisition of siderophores in gram-negative bacteria. Nat Rev Mol Cell Biol (2003) 2.24
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores. Phys Biol (2004) 2.13
Insertion and assembly of membrane proteins via simulation. J Am Chem Soc (2006) 2.12
Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J (2010) 2.05
H bonding at the helix-bundle crossing controls gating in Kir potassium channels. Neuron (2007) 2.02
Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure (2008) 1.98
Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J Struct Biol (2006) 1.91
Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol (2008) 1.86
Setting up and optimization of membrane protein simulations. Eur Biophys J (2002) 1.79
Functional analysis of a structural model of the ATP-binding site of the KATP channel Kir6.2 subunit. EMBO J (2005) 1.79
Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins (2005) 1.74
A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Phys Biol (2006) 1.70
3-D structural and functional characterization of the purified KATP channel complex Kir6.2-SUR1. EMBO J (2005) 1.66
Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc Natl Acad Sci U S A (2007) 1.59
The pore structure and gating mechanism of K2P channels. EMBO J (2011) 1.56
Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states. Proc Natl Acad Sci U S A (2013) 1.54
Molecular simulation approaches to membrane proteins. Structure (2011) 1.52
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry (2008) 1.51
Outer membrane protein G: Engineering a quiet pore for biosensing. Proc Natl Acad Sci U S A (2008) 1.48
Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer. J Mol Biol (2003) 1.47
How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure (2007) 1.46
Not ions alone: barriers to ion permeation in nanopores and channels. J Am Chem Soc (2004) 1.46
The structural basis of ZMPSTE24-dependent laminopathies. Science (2013) 1.43
K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study. Biophys J (2002) 1.42
Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis. EMBO J (2007) 1.41
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations. J Am Chem Soc (2010) 1.41
PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations. Biochemistry (2009) 1.40
Structural and functional analysis of the putative pH sensor in the Kir1.1 (ROMK) potassium channel. EMBO Rep (2006) 1.39
Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Comput Biol (2011) 1.37
Transmembrane helix prediction: a comparative evaluation and analysis. Protein Eng Des Sel (2005) 1.33
A gating mutation at the internal mouth of the Kir6.2 pore is associated with DEND syndrome. EMBO Rep (2005) 1.32
Viral ion channels: structure and function. Biochim Biophys Acta (2002) 1.31
Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins (2004) 1.31
OmpA: a pore or not a pore? Simulation and modeling studies. Biophys J (2002) 1.28
Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues. J Gen Physiol (2008) 1.28
Analysis and evaluation of channel models: simulations of alamethicin. Biophys J (2002) 1.25
The selectivity of K+ ion channels: testing the hypotheses. Biophys J (2008) 1.24
Structure of the TatC core of the twin-arginine protein transport system. Nature (2012) 1.23
Identification of residues contributing to the ATP binding site of Kir6.2. EMBO J (2003) 1.22
Multiscale methods for macromolecular simulations. Curr Opin Struct Biol (2008) 1.19
Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization. Biochemistry (2008) 1.18
Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA. Biophys J (2003) 1.18
Anionic phospholipid interactions with the potassium channel KcsA: simulation studies. Biophys J (2005) 1.18
Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol (2012) 1.18
Reduced lateral mobility of lipids and proteins in crowded membranes. PLoS Comput Biol (2013) 1.17
Ion channel gating: insights via molecular simulations. FEBS Lett (2003) 1.17
Filter flexibility in a mammalian K channel: models and simulations of Kir6.2 mutants. Biophys J (2003) 1.17
Control of pH and PIP2 gating in heteromeric Kir4.1/Kir5.1 channels by H-Bonding at the helix-bundle crossing. Channels (Austin) (2007) 1.17
Open-state models of a potassium channel. Biophys J (2002) 1.17
A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophys J (2007) 1.15
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study. Structure (2010) 1.14
Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies. Biopolymers (2002) 1.13
Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component. J Biol Chem (2006) 1.12
Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics (2012) 1.12
Lipid-protein interactions of integral membrane proteins: a comparative simulation study. Biophys J (2004) 1.12
Increased ATPase activity produced by mutations at arginine-1380 in nucleotide-binding domain 2 of ABCC8 causes neonatal diabetes. Proc Natl Acad Sci U S A (2007) 1.11
Insight into the mechanism of inactivation and pH sensitivity in potassium channels from molecular dynamics simulations. Biochemistry (2008) 1.10
OmpA: gating and dynamics via molecular dynamics simulations. Biochim Biophys Acta (2007) 1.09
Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states. Biophys J (2003) 1.09
Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor. J Biol Chem (2006) 1.09
The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating. Biophys J (2005) 1.07
The simulation approach to bacterial outer membrane proteins. Mol Membr Biol (2004) 1.07
Potassium channel regulation. EMBO Rep (2003) 1.07
Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class. Biophys J (2011) 1.06
Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1. Biophys J (2004) 1.06
Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2. Biophys J (2002) 1.05
Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain. Structure (2011) 1.05
Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer. Biochemistry (2006) 1.04
Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components. Biochemistry (2007) 1.04
A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore. J Biol Chem (2011) 1.04
Lipidbook: a public repository for force-field parameters used in membrane simulations. J Membr Biol (2010) 1.04
MD simulations of spontaneous membrane protein/detergent micelle formation. J Am Chem Soc (2004) 1.04
Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys J (2008) 1.03
Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. Acc Chem Res (2010) 1.03
Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett (2003) 1.02
Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol (2011) 1.02
Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces. Biophys J (2012) 1.02
Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions. Biophys J (2005) 1.01
Structural model for the protein-translocating element of the twin-arginine transport system. Proc Natl Acad Sci U S A (2013) 1.01
Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment. J Phys Chem B (2005) 1.01
Lipid/protein interactions and the membrane/water interfacial region. J Am Chem Soc (2003) 1.01
Multiscale simulations suggest a mechanism for integrin inside-out activation. Proc Natl Acad Sci U S A (2011) 1.00
Focus on Kir6.2: a key component of the ATP-sensitive potassium channel. J Mol Cell Cardiol (2005) 1.00
Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis. Mol Membr Biol (2006) 1.00
Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins. Structure (2013) 1.00
Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA. Biophys J (2006) 1.00
OmpT: molecular dynamics simulations of an outer membrane enzyme. Biophys J (2004) 0.99
Side pockets provide the basis for a new mechanism of Kv channel-specific inhibition. Nat Chem Biol (2013) 0.99
Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations. Biochemistry (2005) 0.99
Comparative molecular dynamics--similar folds and similar motions? Proteins (2005) 0.98
Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating. Biophys J (2005) 0.98
Novel alpha7-like nicotinic acetylcholine receptor subunits in the nematode Caenorhabditis elegans. Protein Sci (2002) 0.98
Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1. Eur Biophys J (2004) 0.98
The pore of voltage-gated potassium ion channels is strained when closed. Nat Commun (2013) 0.97
Insights into how nucleotide-binding domains power ABC transport. Structure (2009) 0.97
Modeling, docking, and simulation of the major facilitator superfamily. Biophys J (2006) 0.97
Asymmetric switching in a homodimeric ABC transporter: a simulation study. PLoS Comput Biol (2010) 0.97