Published in Chem Phys Lipids on January 30, 2013
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure (2015) 1.08
Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature (2015) 1.08
Membrane driven spatial organization of GPCRs. Sci Rep (2013) 1.03
A structural model of the active ribosome-bound membrane protein insertase YidC. Elife (2014) 0.93
Structural evidence for functional lipid interactions in the betaine transporter BetP. EMBO J (2013) 0.92
NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol (2014) 0.91
Computational characterization of structural dynamics underlying function in active membrane transporters. Curr Opin Struct Biol (2015) 0.87
Properties of an inward-facing state of LeuT: conformational stability and substrate release. Biophys J (2015) 0.83
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes. Proteins (2015) 0.83
Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations. Structure (2015) 0.82
Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins. Biophys J (2014) 0.82
Protein and lipid interactions driving molecular mechanisms of in meso crystallization. J Am Chem Soc (2014) 0.81
Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290. J Biol Chem (2016) 0.80
Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models. Biochim Biophys Acta (2016) 0.78
Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles. Biochemistry (2016) 0.77
Functional mechanisms of neurotransmitter transporters regulated by lipid-protein interactions of their terminal loops. Biochim Biophys Acta (2015) 0.77
The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput Biol (2016) 0.76
Grafting Charged Species to Membrane-Embedded Scaffolds Dramatically Increases the Rate of Bilayer Flipping. ACS Cent Sci (2017) 0.75
New Continuum Approaches for Determining Protein-Induced Membrane Deformations. Biophys J (2017) 0.75
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters. Nature (2005) 12.56
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys J (2000) 8.35
Simple allosteric model for membrane pumps. Nature (1966) 7.78
OPM: orientations of proteins in membranes database. Bioinformatics (2006) 5.87
A competitive inhibitor traps LeuT in an open-to-out conformation. Science (2008) 4.86
Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating. Nat Struct Biol (2002) 4.53
Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature (2007) 4.29
The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell (2008) 4.29
Emerging roles for lipids in shaping membrane-protein function. Nature (2009) 4.14
Molecular basis for membrane phospholipid diversity: why are there so many lipids? Annu Rev Biochem (1997) 3.80
Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime. Biophys J (1986) 3.75
Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. J Membr Biol (2006) 3.67
Bilayer thickness and membrane protein function: an energetic perspective. Annu Rev Biophys Biomol Struct (2007) 3.52
Structure and mechanism of a Na+-independent amino acid transporter. Science (2009) 3.30
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
Enzymology, genetics, and regulation of membrane phospholipid synthesis in Escherichia coli. Microbiol Rev (1978) 3.26
X-ray structures of LeuT in substrate-free outward-open and apo inward-open states. Nature (2012) 3.24
A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol (2006) 3.23
Energetics of inclusion-induced bilayer deformations. Biophys J (1998) 3.19
Modulation of rhodopsin function by properties of the membrane bilayer. Chem Phys Lipids (1994) 2.77
The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci (2008) 2.72
On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proc Natl Acad Sci U S A (2007) 2.70
Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature (2010) 2.41
Neurotransmitter transporters as molecular targets for addictive drugs. Drug Alcohol Depend (1998) 2.28
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A (2009) 2.25
Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys J (1999) 2.23
Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes. Biophys J (2006) 2.23
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters. Nat Struct Mol Biol (2010) 2.20
Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue. Nature (2011) 2.18
Antidepressant specificity of serotonin transporter suggested by three LeuT-SSRI structures. Nat Struct Mol Biol (2009) 2.12
Spring constants for channel-induced lipid bilayer deformations. Estimates using gramicidin channels. Biophys J (1999) 2.01
Lateral pressure profile, spontaneous curvature frustration, and the incorporation and conformation of proteins in membranes. Biophys J (2007) 1.90
G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J Am Chem Soc (2007) 1.90
Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys J (1996) 1.89
Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site. Nature (2010) 1.85
A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. Proc Natl Acad Sci U S A (2006) 1.84
Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci U S A (2011) 1.77
Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys J (1999) 1.77
Conformational energetics of rhodopsin modulated by nonlamellar-forming lipids. Biochemistry (2002) 1.71
Capsaicin regulates voltage-dependent sodium channels by altering lipid bilayer elasticity. Mol Pharmacol (2005) 1.70
Snorkeling of lysine side chains in transmembrane helices: how easy can it get? FEBS Lett (2003) 1.57
The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter. PLoS One (2011) 1.48
A functional-phylogenetic system for the classification of transport proteins. J Cell Biochem (1999) 1.45
Cholesterol-induced protein sorting: an analysis of energetic feasibility. Biophys J (2003) 1.45
Experimental conditions can obscure the second high-affinity site in LeuT. Nat Struct Mol Biol (2012) 1.37
Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context. Nat Struct Mol Biol (2012) 1.37
Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophys J (2004) 1.30
Energetics of hydrophobic matching in lipid-protein interactions. Biophys J (2008) 1.30
Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms. Biophys J (2010) 1.27
A continuum method for determining membrane protein insertion energies and the problem of charged residues. J Gen Physiol (2008) 1.27
Contribution of membrane elastic energy to rhodopsin function. Biophys J (2010) 1.21
Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue. PLoS Comput Biol (2010) 1.20
Hydrophobic coupling of lipid bilayer energetics to channel function. J Gen Physiol (2003) 1.20
How did the neurotransmitter cross the bilayer? A closer view. Curr Opin Neurobiol (2005) 1.20
Modeling membrane deformations and lipid demixing upon protein-membrane interaction: the BAR dimer adsorption. Biophys J (2009) 1.17
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins (2009) 1.16
Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors. Biophys J (2011) 1.15
Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. J Chem Inf Model (2011) 1.14
Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment. J Am Chem Soc (2005) 1.14
Lipid-rhodopsin hydrophobic mismatch alters rhodopsin helical content. J Am Chem Soc (2008) 1.10
Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties. PLoS Comput Biol (2012) 1.10
Substrate specificity and ion coupling in the Na+/betaine symporter BetP. EMBO J (2011) 1.07
Substrate and drug binding sites in LeuT. Curr Opin Struct Biol (2010) 1.01
Insights into transport mechanism from LeuT engineered to transport tryptophan. EMBO J (2011) 1.00
Elastic deformation of membrane bilayers probed by deuterium NMR relaxation. J Am Chem Soc (2002) 0.97
Membrane bending is critical for the stability of voltage sensor segments in the membrane. J Gen Physiol (2012) 0.97
Thiazolidinedione insulin sensitizers alter lipid bilayer properties and voltage-dependent sodium channel function: implications for drug discovery. J Gen Physiol (2011) 0.96
Lipid shape is a key factor for membrane interactions of amphipathic helical peptides. Biochim Biophys Acta (2012) 0.94
X-ray diffraction measurement of the monolayer spontaneous curvature of dioleoylphosphatidylglycerol. Chem Phys Lipids (2008) 0.94
Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J Phys Chem B (2010) 0.90
Characterization of membrane-protein interactions for the leucine transporter from Aquifex aeolicus by molecular dynamics calculations. J Phys Chem B (2009) 0.84
Functional selectivity and classical concepts of quantitative pharmacology. J Pharmacol Exp Ther (2006) 7.03
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science (2010) 5.86
The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell (2008) 4.29
Mutations in SLC20A2 link familial idiopathic basal ganglia calcification with phosphate homeostasis. Nat Genet (2012) 3.34
LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell (2009) 3.34
A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol (2006) 3.23
The molecular mechanism governing the oncogenic potential of SOX2 in breast cancer. J Biol Chem (2008) 3.01
Dopamine D2 receptors form higher order oligomers at physiological expression levels. EMBO J (2008) 2.99
Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation. Nat Chem Biol (2009) 2.98
SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc Natl Acad Sci U S A (2006) 2.89
The fourth transmembrane segment forms the interface of the dopamine D2 receptor homodimer. J Biol Chem (2002) 2.75
The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci (2008) 2.72
A-803467, a potent and selective Nav1.8 sodium channel blocker, attenuates neuropathic and inflammatory pain in the rat. Proc Natl Acad Sci U S A (2007) 2.60
PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics (2004) 2.55
A novel regulator of macrophage activation: miR-223 in obesity-associated adipose tissue inflammation. Circulation (2012) 2.55
Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature (2010) 2.41
Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. Proc Natl Acad Sci U S A (2005) 2.33
Quantitative information management for the biochemical computation of cellular networks. Sci STKE (2004) 2.32
Cdk5 regulates EphA4-mediated dendritic spine retraction through an ephexin1-dependent mechanism. Nat Neurosci (2006) 2.30
Twin-spot MARCM to reveal the developmental origin and identity of neurons. Nat Neurosci (2009) 2.26
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A (2009) 2.25
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters. Nat Struct Mol Biol (2010) 2.20
Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue. Nature (2011) 2.18
Local resistance switching at grain and grain boundary surfaces of polycrystalline tungsten oxide films. Nanotechnology (2011) 2.09
An intracellular interaction network regulates conformational transitions in the dopamine transporter. J Biol Chem (2008) 2.07
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. Cancer Prev Res (Phila) (2008) 2.04
State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum. J Biol Chem (2006) 2.01
Additional support for a revised Gibbs analysis. Langmuir (2010) 1.94
cAMP-dependent protein kinase A selects the excited state of the membrane substrate phospholamban. J Mol Biol (2011) 1.90
Mannose-binding lectin is a regulator of inflammation that accompanies myocardial ischemia and reperfusion injury. J Immunol (2005) 1.89
Molecular determinants of selectivity and efficacy at the dopamine D3 receptor. J Med Chem (2012) 1.87
Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach. Proc Natl Acad Sci U S A (2009) 1.79
Mannose-binding lectin-deficient mice display defective apoptotic cell clearance but no autoimmune phenotype. J Immunol (2005) 1.69
Stress erythropoiesis: new signals and new stress progenitor cells. Curr Opin Hematol (2011) 1.68
NEK2 induces drug resistance mainly through activation of efflux drug pumps and is associated with poor prognosis in myeloma and other cancers. Cancer Cell (2013) 1.67
Structural and dynamic basis of phospholamban and sarcolipin inhibition of Ca(2+)-ATPase. Biochemistry (2007) 1.66
Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy. Proc Natl Acad Sci U S A (2011) 1.65
NMR structure of the cathelicidin-derived human antimicrobial peptide LL-37 in dodecylphosphocholine micelles. Biochemistry (2008) 1.65
Synthesis, antiproliferative activity, and structure-activity relationships of 3-aryl-1H-quinolin-4-ones. ChemMedChem (2008) 1.64
SABIO-RK--database for biochemical reaction kinetics. Nucleic Acids Res (2011) 1.63
Metronidazole-flavonoid derivatives as anti-Helicobacter pylori agents with potent inhibitory activity against HPE-induced interleukin-8 production by AGS cells. ChemMedChem (2007) 1.62
An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell (2012) 1.61
HAT4, a Golgi apparatus-anchored B-type histone acetyltransferase, acetylates free histone H4 and facilitates chromatin assembly. Mol Cell (2011) 1.59
microRNA-141 is involved in a nasopharyngeal carcinoma-related genes network. Carcinogenesis (2010) 1.59
Lethal infection of K18-hACE2 mice infected with severe acute respiratory syndrome coronavirus. J Virol (2006) 1.59
A severe acute respiratory syndrome-associated coronavirus-specific protein enhances virulence of an attenuated murine coronavirus. J Virol (2005) 1.59
Rapid learning in cortical coding of visual scenes. Nat Neurosci (2007) 1.58
Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method. Proc Natl Acad Sci U S A (2011) 1.57
Synthesis, crystal structure and antimicrobial activity of deoxybenzoin derivatives from genistein. Eur J Med Chem (2007) 1.57
Respiratory syncytial virus nonstructural protein 2 specifically inhibits type I interferon signal transduction. Virology (2005) 1.54
Specific inhibition of type I interferon signal transduction by respiratory syncytial virus. Am J Respir Cell Mol Biol (2004) 1.49
Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infect Immun (2005) 1.48
The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter. PLoS One (2011) 1.48
Retracted Downregulation of ADAM10 expression inhibits metastasis and invasiveness of human hepatocellular carcinoma HepG2 cells. Biomed Res Int (2013) 1.44
A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol (2008) 1.41
Mechanism of intrauterine infection of hepatitis B virus. World J Gastroenterol (2004) 1.41
Mutations in PRRT2 result in paroxysmal dyskinesias with marked variability in clinical expression. J Med Genet (2011) 1.38
Three-dimensional representations of G protein-coupled receptor structures and mechanisms. Methods Enzymol (2002) 1.38
Experimental conditions can obscure the second high-affinity site in LeuT. Nat Struct Mol Biol (2012) 1.37
Haemophilus influenzae from patients with chronic obstructive pulmonary disease exacerbation induce more inflammation than colonizers. Am J Respir Crit Care Med (2005) 1.34
Re-evaluating the Gibbs analysis of surface tension at the air/water interface. J Am Chem Soc (2009) 1.34
WASH inhibits autophagy through suppression of Beclin 1 ubiquitination. EMBO J (2013) 1.32
Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT. Biophys J (2012) 1.30
Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. J Biol Chem (2005) 1.28
Caloric restriction and age affect synaptic proteins in hippocampal CA3 and spatial learning ability. Exp Neurol (2008) 1.27
Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms. Biophys J (2010) 1.27
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc (2006) 1.27
Membrane localization is critical for activation of the PICK1 BAR domain. Traffic (2008) 1.25
Targeting aberrant glutathione metabolism to eradicate human acute myelogenous leukemia cells. J Biol Chem (2013) 1.25
A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding. Neuropharmacology (2005) 1.24
Electrostatic binding among equilibrating 2-D and 3-D self-assemblies. J Am Chem Soc (2009) 1.24
Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials. Proteins (2003) 1.24
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proc Natl Acad Sci U S A (2009) 1.23
TheV-Go insulin delivery device used in clinical practice: patient perception and retrospective analysis of glycemic control. Endocr Pract (2012) 1.23
Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6. Proc Natl Acad Sci U S A (2005) 1.23
Use of the substituted cysteine accessibility method to study the structure and function of G protein-coupled receptors. Methods Enzymol (2002) 1.21
The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics. FEBS J (2005) 1.20
Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects. J Chem Phys (2007) 1.20
Quantitative trait loci for root morphology in response to low phosphorus stress in Brassica napus. Theor Appl Genet (2010) 1.19
Reduction of miR-21 induces glioma cell apoptosis via activating caspase 9 and 3. Oncol Rep (2010) 1.19
Transgenic rhesus monkeys produced by gene transfer into early-cleavage-stage embryos using a simian immunodeficiency virus-based vector. Proc Natl Acad Sci U S A (2010) 1.18
Hepatocellular carcinoma-associated mesenchymal stem cells promote hepatocarcinoma progression: role of the S100A4-miR155-SOCS1-MMP9 axis. Hepatology (2013) 1.18
Gene silencing of serine proteases affects melanization of Sephadex beads in Anopheles gambiae. Insect Biochem Mol Biol (2006) 1.17
Probing conformational changes in neurotransmitter transporters: a structural context. Eur J Pharmacol (2003) 1.17
Modeling membrane deformations and lipid demixing upon protein-membrane interaction: the BAR dimer adsorption. Biophys J (2009) 1.17
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins (2009) 1.16