Department of Biochemistry,
Center for Biophysics and Quantitative Biology,
Beckman Institute for Advanced Science and Technology
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Control of the selectivity of the aquaporin water channel family by global orientational tuning.
Science (New York, N.Y.) Apr, 2002 | Pubmed ID: 11964478
Energetics of glycerol conduction through aquaglyceroporin GlpF.
Proceedings of the National Academy of Sciences of the United States of America May, 2002 | Pubmed ID: 11997475
Pressure-induced water transport in membrane channels studied by molecular dynamics.
Biophysical journal Jul, 2002 | Pubmed ID: 12080108
Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle.
Biophysical journal Sep, 2002 | Pubmed ID: 12202355
Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin.
Biophysical journal Dec, 2002 | Pubmed ID: 12496081
Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2003 | Pubmed ID: 12799468
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics.
Biophysical journal Jul, 2003 | Pubmed ID: 12829462
Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore.
Biophysical journal Sep, 2003 | Pubmed ID: 12944261
Electrostatic tuning of permeation and selectivity in aquaporin water channels.
Biophysical journal Nov, 2003 | Pubmed ID: 14581193
Theory and simulation of water permeation in aquaporin-1.
Biophysical journal Jan, 2004 | Pubmed ID: 14695248
Classical force field parameters for the heme prosthetic group of cytochrome c.
Journal of computational chemistry Oct, 2004 | Pubmed ID: 15264255
Collective diffusion model for water permeation through microscopic channels.
Physical review letters Nov, 2004 | Pubmed ID: 15601094
Molecular dynamics simulations of proteins in lipid bilayers.
Current opinion in structural biology Aug, 2005 | Pubmed ID: 16043343
What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF.
Structure (London, England : 1993) Aug, 2005 | Pubmed ID: 16084383
Scalable molecular dynamics with NAMD.
Journal of computational chemistry Dec, 2005 | Pubmed ID: 16222654
Dynamics of K+ ion conduction through Kv1.2.
Biophysical journal Sep, 2006 | Pubmed ID: 16844753
Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1.
Structure (London, England : 1993) Sep, 2006 | Pubmed ID: 16962972
Sugar binding and protein conformational changes in lactose permease.
Biophysical journal Dec, 2006 | Pubmed ID: 16963502
Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics.
Journal of structural biology Mar, 2007 | Pubmed ID: 17306562
Sugar transport across lactose permease probed by steered molecular dynamics.
Biophysical journal Jul, 2007 | Pubmed ID: 17434947
Mechanics of force propagation in TonB-dependent outer membrane transport.
Biophysical journal Jul, 2007 | Pubmed ID: 17449669
Molecular mechanisms of conduction and selectivity in aquaporin water channels.
The Journal of nutrition 06, 2007 | Pubmed ID: 17513417
Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.
Biophysical journal Feb, 2008 | Pubmed ID: 17921212
Substrate binding and formation of an occluded state in the leucine transporter.
Biophysical journal Mar, 2008 | Pubmed ID: 18024499
Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors.
Structure (London, England : 1993) Jan, 2008 | Pubmed ID: 18184585
Resolution enhancement in solid-state NMR of oriented membrane proteins by anisotropic differential linebroadening.
Journal of the American Chemical Society Apr, 2008 | Pubmed ID: 18341279
Indirect role of Ca2+ in the assembly of extracellular matrix proteins.
Biophysical journal Jul, 2008 | Pubmed ID: 18359797
Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.
Biophysical journal Jul, 2008 | Pubmed ID: 18390613
Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter.
Biophysical journal Sep, 2008 | Pubmed ID: 18515371
Electrostatic funneling of substrate in mitochondrial inner membrane carriers.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2008 | Pubmed ID: 18621725
Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study.
Biophysical journal Nov, 2008 | Pubmed ID: 18676652
Blood clotting reactions on nanoscale phospholipid bilayers.
Thrombosis research , 2008 | Pubmed ID: 18691494
Potential cation and H+ binding sites in acid sensing ion channel-1.
Biophysical journal Dec, 2008 | Pubmed ID: 18790845
Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.
Biophysical journal Dec, 2008 | Pubmed ID: 18790847
Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation.
Biophysical journal Jan, 2009 | Pubmed ID: 19167292
Molecular dynamics simulations of membrane channels and transporters.
Current opinion in structural biology Apr, 2009 | Pubmed ID: 19345092
Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT.
Biophysical journal Sep, 2009 | Pubmed ID: 19720022
Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.
Journal of molecular biology Nov, 2009 | Pubmed ID: 19747487
Nitric oxide conduction by the brain aquaporin AQP4.
Proteins Feb, 2010 | Pubmed ID: 19842162
Ion-releasing state of a secondary membrane transporter.
Biophysical journal Dec, 2009 | Pubmed ID: 19948113
Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT.
Biochemistry Feb, 2010 | Pubmed ID: 20058936
Protein-phospholipid interactions in blood clotting.
Thrombosis research Apr, 2010 | Pubmed ID: 20129649
Functional interplay between acetylation and methylation of the RelA subunit of NF-kappaB.
Molecular and cellular biology May, 2010 | Pubmed ID: 20160011
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor.
Journal of thrombosis and haemostasis : JTH May, 2010 | Pubmed ID: 20180816
Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel.
Biophysical journal May, 2010 | Pubmed ID: 20483327
Exploring transmembrane diffusion pathways with molecular dynamics.
Physiology (Bethesda, Md.) Jun, 2010 | Pubmed ID: 20551228
Identification of the third Na+ site and the sequence of extracellular binding events in the glutamate transporter.
Biophysical journal Sep, 2010 | Pubmed ID: 20816053
Interplay of mechanical and binding properties of Fibronectin type I.
Theoretical chemistry accounts May, 2010 | Pubmed ID: 20824113
Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
PLoS computational biology Aug, 2010 | Pubmed ID: 20865057
The binding interface of cytochrome c and cytochrome c₁ in the bc₁ complex: rationalizing the role of key residues.
Biophysical journal Oct, 2010 | Pubmed ID: 20959106
Interaction of the α2A domain of integrin with small collagen fragments.
Protein & cell Apr, 2010 | Pubmed ID: 21203951
Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers.
Biochemistry Mar, 2011 | Pubmed ID: 21294564
Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model.
The journal of physical chemistry. B Jun, 2011 | Pubmed ID: 21561114
Conformational coupling of the nucleotide-binding and the transmembrane domains in ABC transporters.
Biophysical journal Aug, 2011 | Pubmed ID: 21806936
A gate-free pathway for substrate release from the inward-facing state of the Na⁺-galactose transporter.
Biochimica et biophysica acta Feb, 2012 | Pubmed ID: 21978597
Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.
Journal of molecular biology Jan, 2012 | Pubmed ID: 22094314
Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains.
Biophysical journal Jan, 2012 | Pubmed ID: 22339862
Tracing cytoplasmic Ca(2+) ion and water access points in the Ca(2+)-ATPase.
Biophysical journal Jan, 2012 | Pubmed ID: 22339863
Structure and permeation mechanism of a mammalian urea transporter.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2012 | Pubmed ID: 22733730
Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model.
Biophysical journal May, 2012 | Pubmed ID: 22824277
Simulation studies of the mechanism of membrane transporters.
Methods in molecular biology (Clifton, N.J.) , 2013 | Pubmed ID: 23034756
Visualizing functional motions of membrane transporters with molecular dynamics simulations.
Biochemistry Jan, 2013 | Pubmed ID: 23298176
Transient formation of water-conducting states in membrane transporters.
Proceedings of the National Academy of Sciences of the United States of America May, 2013 | Pubmed ID: 23610412
On the origin of large flexibility of P-glycoprotein in the inward-facing state.
The Journal of biological chemistry Jun, 2013 | Pubmed ID: 23658020
Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation.
Journal of the American Chemical Society Jun, 2013 | Pubmed ID: 23697766
Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation.
Journal of computational and theoretical nanoscience Dec, 2010 | Pubmed ID: 23710155
Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.
The journal of physical chemistry letters Jun, 2013 | Pubmed ID: 23795244
Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin.
Biophysical journal Aug, 2013 | Pubmed ID: 23972851
Rapid parameterization of small molecules using the Force Field Toolkit.
Journal of computational chemistry Dec, 2013 | Pubmed ID: 24000174
Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.
Proceedings of the National Academy of Sciences of the United States of America Nov, 2013 | Pubmed ID: 24191018
A microscopic view of phospholipid insertion into biological membranes.
The journal of physical chemistry. B Feb, 2014 | Pubmed ID: 24313792
Water access points and hydration pathways in CLC H+/Cl- transporters.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2014 | Pubmed ID: 24379362
Partitioning of amino acids into a model membrane: capturing the interface.
The journal of physical chemistry. B Feb, 2014 | Pubmed ID: 24451004
Conformational dynamics at the inner gate of KcsA during activation.
Biochemistry Apr, 2014 | Pubmed ID: 24621378
Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.
Journal of chemical theory and computation Jul, 2014 | Pubmed ID: 25018675
Conformational heterogeneity of α-synuclein in membrane.
Biochimica et biophysica acta Dec, 2014 | Pubmed ID: 25135664
Conformational coupling between the active site and residues within the K(C)-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2014 | Pubmed ID: 25288772
Atomistic models of general anesthetics for use in in silico biological studies.
The journal of physical chemistry. B Oct, 2014 | Pubmed ID: 25303275
Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3.
Biophysical journal Nov, 2014 | Pubmed ID: 25418091
A highly tilted membrane configuration for the prefusion state of synaptobrevin.
Biophysical journal Nov, 2014 | Pubmed ID: 25418096
Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides.
Biochemistry Mar, 2015 | Pubmed ID: 25734689
Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer.
Biochemistry Apr, 2015 | Pubmed ID: 25777547
Computational characterization of structural dynamics underlying function in active membrane transporters.
Current opinion in structural biology Apr, 2015 | Pubmed ID: 25913536
Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide.
The journal of physical chemistry. B Jun, 2015 | Pubmed ID: 25996559
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution.
The Journal of membrane biology Jun, 2015 | Pubmed ID: 25998378
Structural Determinants of the Mechanical Stability of α-Catenin.
The Journal of biological chemistry Jul, 2015 | Pubmed ID: 26070562
Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail.
Biochemistry Oct, 2015 | Pubmed ID: 26346528
Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter.
Nature communications Sep, 2015 | Pubmed ID: 26417850
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
Biophysical journal Nov, 2015 | Pubmed ID: 26588561
Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter.
eLife Jan, 2016 | Pubmed ID: 26799336
Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation.
eLife Feb, 2016 | Pubmed ID: 26836308
All the O2 Consumed by Thermus thermophilus Cytochrome ba3 Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer.
Biochemistry Mar, 2016 | Pubmed ID: 26845082
Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl(-)/H(+) Exchanger ClC-ec1.
Journal of the American Chemical Society Mar, 2016 | Pubmed ID: 26880377
Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions.
Biochemistry Mar, 2016 | Pubmed ID: 26885726
Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.
Angewandte Chemie (International ed. in English) Mar, 2016 | Pubmed ID: 26928945
Atomic-level description of protein-lipid interactions using an accelerated membrane model.
Biochimica et biophysica acta Jul, 2016 | Pubmed ID: 26940626
Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form.
Biochemistry Apr, 2016 | Pubmed ID: 26953503
The cellular membrane as a mediator for small molecule interaction with membrane proteins.
Biochimica et biophysica acta 10, 2016 | Pubmed ID: 27163493
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.
Journal of chemical information and modeling 06, 2016 | Pubmed ID: 27196035
Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.
Methods in enzymology , 2016 | Pubmed ID: 27497175
Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2.
Journal of the American Chemical Society 09, 2016 | Pubmed ID: 27508459
Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo from Escherichia coli.
Biochemistry Oct, 2016 | Pubmed ID: 27622672
X-ray structures define human P2X3 receptor gating cycle and antagonist action.
Nature Sep, 2016 | Pubmed ID: 27626375
Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase.
Biochemistry Dec, 2016 | Pubmed ID: 27992998
Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail.
Biochemistry Jan, 2017 | Pubmed ID: 27997124
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.
Nature 01, 2017 | Pubmed ID: 28077875
Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome in Photosystem II.
Proceedings of the National Academy of Sciences of the United States of America 02, 2017 | Pubmed ID: 28193857
Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.
The journal of physical chemistry. B 04, 2017 | Pubmed ID: 28241729
Energy transduction and alternating access of the mammalian ABC transporter P-glycoprotein.
Nature 03, 2017 | Pubmed ID: 28289287
A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the ion channel.
The Journal of biological chemistry 06, 2017 | Pubmed ID: 28420728
Tribute to Klaus Schulten.
The journal of physical chemistry. B 04, 2017 | Pubmed ID: 28423902
Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters.
Cell research Aug, 2017 | Pubmed ID: 28621327
Lipid specificity of the membrane binding domain of coagulation factor X.
Journal of thrombosis and haemostasis : JTH 10, 2017 | Pubmed ID: 28782177
Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM.
Cell Sep, 2017 | Pubmed ID: 28823560
Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase.
eLife 09, 2017 | Pubmed ID: 28917060
Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1.
Biophysical journal Oct, 2017 | Pubmed ID: 28978444
Chasing the open-state structure of pentameric ligand-gated ion channels.
The Journal of general physiology Dec, 2017 | Pubmed ID: 29089419
Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4.
Biochemistry 02, 2018 | Pubmed ID: 29200287
PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.
Biophysical journal 02, 2018 | Pubmed ID: 29414703
Molecular insight into drug exporters within the cellular membrane.
Pharmacological research 07, 2018 | Pubmed ID: 29535020
Cytochrome aa Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O for Catalysis.
Biochemistry 04, 2018 | Pubmed ID: 29546752
Structure of the alternative complex III in a supercomplex with cytochrome oxidase.
Nature 05, 2018 | Pubmed ID: 29695868
A "cross-stitched" peptide with improved helicity and proteolytic stability.
Organic & biomolecular chemistry 05, 2018 | Pubmed ID: 29725689
Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates.
Biochimica et biophysica acta. Bioenergetics 09, 2018 | Pubmed ID: 29883591
Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins.
Biochimica et biophysica acta. Biomembranes 10, 2018 | Pubmed ID: 29920237
Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE.
Proceedings of the National Academy of Sciences of the United States of America 08, 2018 | Pubmed ID: 30026196
Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin.
The Journal of biological chemistry 09, 2018 | Pubmed ID: 30030381
Microscopic view of lipids and their diverse biological functions.
Current opinion in structural biology 08, 2018 | Pubmed ID: 30048836
Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.
Journal of structural biology 11, 2018 | Pubmed ID: 30092279
Selective Permeability of Carboxysome Shell Pores to Anionic Molecules.
The journal of physical chemistry. B 10, 2018 | Pubmed ID: 30193460
Probing key elements of teixobactin-lipid II interactions in membranes.
Chemical science Sep, 2018 | Pubmed ID: 30210775
Direct protein-lipid interactions shape the conformational landscape of secondary transporters.
Nature communications Oct, 2018 | Pubmed ID: 30297844
Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane.
Biochemistry 12, 2018 | Pubmed ID: 30456950
The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells.
eLife 11, 2018 | Pubmed ID: 30489256
Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor.
Nature communications 11, 2018 | Pubmed ID: 30498243
Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming.
The Journal of biological chemistry 03, 2019 | Pubmed ID: 30617180
Menthol Stereoisomers Exhibit Different Effects on α4β2 nAChR Upregulation and Dopamine Neuron Spontaneous Firing.
eNeuro Nov-Dec, 2018 | Pubmed ID: 30627659
Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213.
Biochemistry 03, 2019 | Pubmed ID: 30785734
Pro-Nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-cancer Therapy.
ACS applied materials & interfaces May, 2019 | Pubmed ID: 31013055
Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport.
Nature 05, 2019 | Pubmed ID: 31019304
Structural Insights into the Lipid A Transport Pathway in MsbA.
Structure (London, England : 1993) 07, 2019 | Pubmed ID: 31130486
A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion.
The Journal of biological chemistry 11, 2019 | Pubmed ID: 31515268
A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca-activated Cl channel ANO1 (TMEM16A).
Proceedings of the National Academy of Sciences of the United States of America 10, 2019 | Pubmed ID: 31515451
A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes.
Angewandte Chemie (International ed. in English) 10, 2019 | Pubmed ID: 31539191
Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins.
Nature protocols 11, 2019 | Pubmed ID: 31605097
Probing cholesterol binding and translocation in P-glycoprotein.
Biochimica et biophysica acta. Biomembranes 01, 2020 | Pubmed ID: 31676371
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.
Cell 11, 2019 | Pubmed ID: 31730852
Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes.
Journal of computational chemistry 03, 2020 | Pubmed ID: 31762060
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Structure (London, England : 1993) 12, 2019 | Pubmed ID: 31780431
Computational Dissection of Membrane Transport at a Microscopic Level.
Trends in biochemical sciences 03, 2020 | Pubmed ID: 31813734
An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells.
Angewandte Chemie (International ed. in English) 02, 2020 | Pubmed ID: 31854058
Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter.
Scientific reports 12, 2019 | Pubmed ID: 31862903
Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer.
Proceedings of the National Academy of Sciences of the United States of America 01, 2020 | Pubmed ID: 31911476
Menthol Binding to the Human α4β2 Nicotinic Acetylcholine Receptor Facilitated by Its Strong Partitioning in the Membrane.
The journal of physical chemistry. B 03, 2020 | Pubmed ID: 32048843
Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation.
ACS macro letters Oct, 2019 | Pubmed ID: 32149017
Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy.
Scientific reports 03, 2020 | Pubmed ID: 32179837
A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl/H transport cycle.
eLife 04, 2020 | Pubmed ID: 32310757
Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics.
Biophysical journal 07, 2020 | Pubmed ID: 32533943
Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage.
Nature communications 06, 2020 | Pubmed ID: 32541820
Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF.
Frontiers in physiology , 2020 | Pubmed ID: 32695023
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
The Journal of chemical physics Jul, 2020 | Pubmed ID: 32752662
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.
Journal of chemical information and modeling 11, 2020 | Pubmed ID: 32805108
Twisting and tilting of a mechanosensitive molecular probe detects order in membranes.
Chemical science Jun, 2020 | Pubmed ID: 32864081
Structural basis for the reaction cycle of DASS dicarboxylate transporters.
eLife 09, 2020 | Pubmed ID: 32869741
Knockout of VDAC1 in H9c2 Cells Promotes Oxidative Stress-Induced Cell Apoptosis through Decreased Mitochondrial Hexokinase II Binding and Enhanced Glycolytic Stress.
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology Sep, 2020 | Pubmed ID: 32901466
Structural and functional diversity calls for a new classification of ABC transporters.
FEBS letters 12, 2020 | Pubmed ID: 32978974
Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1.
Science advances Sep, 2020 | Pubmed ID: 32998886
The structures of secretory and dimeric immunoglobulin A.
eLife 10, 2020 | Pubmed ID: 33107820
Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison.
The Journal of chemical physics Oct, 2020 | Pubmed ID: 33138412
An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes.
Biochemistry 11, 2020 | Pubmed ID: 33153264
Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis.
FEBS letters 03, 2021 | Pubmed ID: 33159693
Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter.
Nature communications 12, 2020 | Pubmed ID: 33268777
Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers.
ACS applied bio materials Mar, 2020 | Pubmed ID: 33313482
Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.
The Journal of chemical physics Dec, 2020 | Pubmed ID: 33353347
Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study.
Journal of the mechanical behavior of biomedical materials 05, 2021 | Pubmed ID: 33588213
Glutamate transporters have a chloride channel with two hydrophobic gates.
Nature 03, 2021 | Pubmed ID: 33597752
Carbon dioxide transport across membranes.
Interface focus Apr, 2021 | Pubmed ID: 33633837
Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane.
Biophysical journal 07, 2021 | Pubmed ID: 33675757
Classical molecular dynamics.
The Journal of chemical physics Mar, 2021 | Pubmed ID: 33722022
Structural insights into photosystem II assembly.
Nature plants 04, 2021 | Pubmed ID: 33846594
Cation-π Interactions and their Functional Roles in Membrane Proteins.
Journal of molecular biology 08, 2021 | Pubmed ID: 33957146
Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer.
Molecular cancer research : MCR 09, 2021 | Pubmed ID: 34021071
Tuning symmetry breaking charge separation in perylene bichromophores by conformational control.
Chemical science Sep, 2019 | Pubmed ID: 34040711
Structural basis of complex formation between mitochondrial anion channel VDAC1 and Hexokinase-II.
Communications biology 06, 2021 | Pubmed ID: 34083717
Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein.
Chemical science Apr, 2021 | Pubmed ID: 34084427
Amphiphilic Distyrylbenzene Derivatives as Potential Therapeutic and Imaging Agents for Soluble and Insoluble Amyloid β Aggregates in Alzheimer's Disease.
Journal of the American Chemical Society 07, 2021 | Pubmed ID: 34213901
Calmodulin complexes with brain and muscle creatine kinase peptides.
Current research in structural biology , 2021 | Pubmed ID: 34235492
Molecular mechanism of prestin electromotive signal amplification.
Cell 09, 2021 | Pubmed ID: 34390643
Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Proceedings of the National Academy of Sciences of the United States of America 08, 2021 | Pubmed ID: 34417297
Molecular mechanism of capsid disassembly in hepatitis B virus.
Proceedings of the National Academy of Sciences of the United States of America 09, 2021 | Pubmed ID: 34465620
Editorial: Mitochondrial Exchangers and Transporters in Cell Survival and Death.
Frontiers in physiology , 2021 | Pubmed ID: 34566705
PIP-dependent coupling of voltage sensor and pore domains in K7.2 channel.
Communications biology 10, 2021 | Pubmed ID: 34650221
Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge.
Chemical science Nov, 2021 | Pubmed ID: 34909143
Assembly and Analysis of Cell-Scale Membrane Envelopes.
Journal of chemical information and modeling Dec, 2021 | Pubmed ID: 34910495
Anionic Lipids Confine Cytochrome to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners.
Biochemistry Jan, 2022 | Pubmed ID: 35025510
Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes.
Journal of chemical information and modeling Feb, 2022 | Pubmed ID: 35104125
Identification of Structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.
The Journal of biological chemistry Feb, 2022 | Pubmed ID: 35122790
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.
Journal of chemical theory and computation Feb, 2022 | Pubmed ID: 35138832
Robert P. Sparks*,1,
William Lawless*,2,
Andres S. Arango*,1,3,4,
Emad Tajkhorshid1,3,4,
Rutilio A. Fratti1,3
1Department of Biochemistry, University of Illinois at Urbana-Champaign,
2Department of Chemistry, University of South Florida,
3Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign,
4Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
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