Emad Tajkhorshid

Control of the selectivity of the aquaporin water channel family by global orientational tuning.

Energetics of glycerol conduction through aquaglyceroporin GlpF.

Pressure-induced water transport in membrane channels studied by molecular dynamics.

Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle.

Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin.

Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.

Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics.

Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore.

Electrostatic tuning of permeation and selectivity in aquaporin water channels.

Theory and simulation of water permeation in aquaporin-1.

Classical force field parameters for the heme prosthetic group of cytochrome c.

Collective diffusion model for water permeation through microscopic channels.

Molecular dynamics simulations of proteins in lipid bilayers.

What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF.

Scalable molecular dynamics with NAMD.

Dynamics of K+ ion conduction through Kv1.2.

Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1.

Sugar binding and protein conformational changes in lactose permease.

Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics.

Sugar transport across lactose permease probed by steered molecular dynamics.

Mechanics of force propagation in TonB-dependent outer membrane transport.

Molecular mechanisms of conduction and selectivity in aquaporin water channels.

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

Substrate binding and formation of an occluded state in the leucine transporter.

Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors.

Resolution enhancement in solid-state NMR of oriented membrane proteins by anisotropic differential linebroadening.

Indirect role of Ca2+ in the assembly of extracellular matrix proteins.

Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.

Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter.

Electrostatic funneling of substrate in mitochondrial inner membrane carriers.

Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study.

Blood clotting reactions on nanoscale phospholipid bilayers.

Potential cation and H+ binding sites in acid sensing ion channel-1.

Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.

Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation.

Molecular dynamics simulations of membrane channels and transporters.

Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT.

Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.

Nitric oxide conduction by the brain aquaporin AQP4.

Ion-releasing state of a secondary membrane transporter.

Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT.

Protein-phospholipid interactions in blood clotting.

Functional interplay between acetylation and methylation of the RelA subunit of NF-kappaB.

Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor.

Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel.

Exploring transmembrane diffusion pathways with molecular dynamics.

Identification of the third Na+ site and the sequence of extracellular binding events in the glutamate transporter.

Interplay of mechanical and binding properties of Fibronectin type I.

Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.

The binding interface of cytochrome c and cytochrome c₁ in the bc₁ complex: rationalizing the role of key residues.

Interaction of the α2A domain of integrin with small collagen fragments.

Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers.

Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model.

Conformational coupling of the nucleotide-binding and the transmembrane domains in ABC transporters.

A gate-free pathway for substrate release from the inward-facing state of the Na⁺-galactose transporter.

Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.

Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains.

Tracing cytoplasmic Ca(2+) ion and water access points in the Ca(2+)-ATPase.

Structure and permeation mechanism of a mammalian urea transporter.

Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model.

Simulation studies of the mechanism of membrane transporters.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Transient formation of water-conducting states in membrane transporters.

On the origin of large flexibility of P-glycoprotein in the inward-facing state.

Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation.

Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation.

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.

Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin.

Rapid parameterization of small molecules using the Force Field Toolkit.

Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.

A microscopic view of phospholipid insertion into biological membranes.

Water access points and hydration pathways in CLC H+/Cl- transporters.

Partitioning of amino acids into a model membrane: capturing the interface.

Conformational dynamics at the inner gate of KcsA during activation.

Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

Conformational heterogeneity of α-synuclein in membrane.

Conformational coupling between the active site and residues within the K(C)-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase.

Atomistic models of general anesthetics for use in in silico biological studies.

Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3.

A highly tilted membrane configuration for the prefusion state of synaptobrevin.

Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides.

Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer.

Computational characterization of structural dynamics underlying function in active membrane transporters.

Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide.

Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution.

Structural Determinants of the Mechanical Stability of α-Catenin.

Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail.

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

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.

Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter.

Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation.

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.

Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl(-)/H(+) Exchanger ClC-ec1.

Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions.

Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.

Atomic-level description of protein-lipid interactions using an accelerated membrane model.

Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form.

The cellular membrane as a mediator for small molecule interaction with membrane proteins.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo from Escherichia coli.

X-ray structures define human P2X3 receptor gating cycle and antagonist action.

Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase.

Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail.

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome in Photosystem II.

Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.

Energy transduction and alternating access of the mammalian ABC transporter P-glycoprotein.

A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the ion channel.

Tribute to Klaus Schulten.

Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters.

Lipid specificity of the membrane binding domain of coagulation factor X.

Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM.

Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase.

Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1.

Chasing the open-state structure of pentameric ligand-gated ion channels.

Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4.

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

Molecular insight into drug exporters within the cellular membrane.

Cytochrome aa Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O for Catalysis.

Structure of the alternative complex III in a supercomplex with cytochrome oxidase.

A "cross-stitched" peptide with improved helicity and proteolytic stability.

Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates.

Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins.

Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE.

Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin.

Microscopic view of lipids and their diverse biological functions.

Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.

Selective Permeability of Carboxysome Shell Pores to Anionic Molecules.

Probing key elements of teixobactin-lipid II interactions in membranes.

Direct protein-lipid interactions shape the conformational landscape of secondary transporters.

Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane.

The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells.

Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor.

Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming.

Menthol Stereoisomers Exhibit Different Effects on α4β2 nAChR Upregulation and Dopamine Neuron Spontaneous Firing.

Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213.

Pro-Nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-cancer Therapy.

Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport.

Structural Insights into the Lipid A Transport Pathway in MsbA.

A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion.

A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca-activated Cl channel ANO1 (TMEM16A).

A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes.

Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins.

Probing cholesterol binding and translocation in P-glycoprotein.

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes.

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Computational Dissection of Membrane Transport at a Microscopic Level.

An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells.

Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter.

Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer.

Menthol Binding to the Human α4β2 Nicotinic Acetylcholine Receptor Facilitated by Its Strong Partitioning in the Membrane.

Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation.

Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy.

A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl/H transport cycle.

Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics.

Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage.

Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF.

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.

Twisting and tilting of a mechanosensitive molecular probe detects order in membranes.

Structural basis for the reaction cycle of DASS dicarboxylate transporters.

Knockout of VDAC1 in H9c2 Cells Promotes Oxidative Stress-Induced Cell Apoptosis through Decreased Mitochondrial Hexokinase II Binding and Enhanced Glycolytic Stress.

Structural and functional diversity calls for a new classification of ABC transporters.

Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1.

The structures of secretory and dimeric immunoglobulin A.

Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison.

An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes.

Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis.

Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter.

Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers.

Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.

Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study.

Glutamate transporters have a chloride channel with two hydrophobic gates.

Carbon dioxide transport across membranes.

Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane.

Classical molecular dynamics.

Structural insights into photosystem II assembly.

Cation-π Interactions and their Functional Roles in Membrane Proteins.

Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer.

Tuning symmetry breaking charge separation in perylene bichromophores by conformational control.

Structural basis of complex formation between mitochondrial anion channel VDAC1 and Hexokinase-II.

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein.

Amphiphilic Distyrylbenzene Derivatives as Potential Therapeutic and Imaging Agents for Soluble and Insoluble Amyloid β Aggregates in Alzheimer's Disease.

Calmodulin complexes with brain and muscle creatine kinase peptides.

Molecular mechanism of prestin electromotive signal amplification.

Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.

Molecular mechanism of capsid disassembly in hepatitis B virus.

Editorial: Mitochondrial Exchangers and Transporters in Cell Survival and Death.

PIP-dependent coupling of voltage sensor and pore domains in K7.2 channel.

Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge.

Assembly and Analysis of Cell-Scale Membrane Envelopes.

Anionic Lipids Confine Cytochrome to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners.

Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes.

Identification of Structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.