Emad Tajkhorshid Department of Biochemistry University of Illinois at Urbana-Champaign Biography Publications Institution JoVE Articles Emad Tajkhorshid has not added a biography. If you are Emad Tajkhorshid and would like to personalize this page please email our Author Liaison for assistance. Publications 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 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 Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes Journal of Chemical Information and Modeling. Feb, 2022 | Pubmed ID: 35104125 Anionic Lipids Confine Cytochrome to the Surface of Bioenergetic Membranes Without Compromising Its Interaction with Redox Partners Biochemistry. Jan, 2022 | Pubmed ID: 35025510 Assembly and Analysis of Cell-Scale Membrane Envelopes Journal of Chemical Information and Modeling. Dec, 2021 | Pubmed ID: 34910495 Rationalizing the Generation of Broad Spectrum Antibiotics with the Addition of a Positive Charge Chemical Science. Nov, 2021 | Pubmed ID: 34909143 PIP-dependent Coupling of Voltage Sensor and Pore Domains in K7.2 Channel Communications Biology. 10, 2021 | Pubmed ID: 34650221 Editorial: Mitochondrial Exchangers and Transporters in Cell Survival and Death Frontiers in Physiology. 2021 | Pubmed ID: 34566705 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 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 Prestin Electromotive Signal Amplification Cell. 09, 2021 | Pubmed ID: 34390643 Calmodulin Complexes with Brain and Muscle Creatine Kinase Peptides Current Research in Structural Biology. 2021 | Pubmed ID: 34235492 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 Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-glycoprotein Chemical Science. Apr, 2021 | Pubmed ID: 34084427 Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II Communications Biology. 06, 2021 | Pubmed ID: 34083717 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 Cation-π Interactions and Their Functional Roles in Membrane Proteins Journal of Molecular Biology. 08, 2021 | Pubmed ID: 33957146 Structural Insights into Photosystem II Assembly Nature Plants. 04, 2021 | Pubmed ID: 33846594 Classical Molecular Dynamics The Journal of Chemical Physics. Mar, 2021 | Pubmed ID: 33722022 Binding Mode of SARS-CoV-2 Fusion Peptide to Human Cellular Membrane Biophysical Journal. 07, 2021 | Pubmed ID: 33675757 Carbon Dioxide Transport Across Membranes Interface Focus. Apr, 2021 | Pubmed ID: 33633837 Glutamate Transporters Have a Chloride Channel with Two Hydrophobic Gates Nature. 03, 2021 | Pubmed ID: 33597752 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 Conformational Changes in the Nucleotide-binding Domains of P-glycoprotein Induced by ATP Hydrolysis FEBS Letters. 03, 2021 | Pubmed ID: 33159693 Confronting Pitfalls of AI-augmented Molecular Dynamics Using Statistical Physics The Journal of Chemical Physics. Dec, 2020 | Pubmed ID: 33353347 Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers ACS Applied Bio Materials. Mar, 2020 | Pubmed ID: 33313482 Hydrogen-deuterium Exchange Mass Spectrometry Captures Distinct Dynamics Upon Substrate and Inhibitor Binding to a Transporter Nature Communications. 12, 2020 | Pubmed ID: 33268777 An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes Biochemistry. 11, 2020 | Pubmed ID: 33153264 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 The Structures of Secretory and Dimeric Immunoglobulin A ELife. 10, 2020 | Pubmed ID: 33107820 Membrane Surface Recognition by the ASAP1 PH Domain and Consequences for Interactions with the Small GTPase Arf1 Science Advances. Sep, 2020 | Pubmed ID: 32998886 Structural and Functional Diversity Calls for a New Classification of ABC Transporters FEBS Letters. 12, 2020 | Pubmed ID: 32978974 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 Basis for the Reaction Cycle of DASS Dicarboxylate Transporters ELife. 09, 2020 | Pubmed ID: 32869741 Twisting and Tilting of a Mechanosensitive Molecular Probe Detects Order in Membranes Chemical Science. Jun, 2020 | Pubmed ID: 32864081 Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD Journal of Chemical Information and Modeling. 11, 2020 | Pubmed ID: 32805108 Scalable Molecular Dynamics on CPU and GPU Architectures with NAMD The Journal of Chemical Physics. Jul, 2020 | Pubmed ID: 32752662 Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF Frontiers in Physiology. 2020 | Pubmed ID: 32695023 Aβ(1-42) Tetramer and Octamer Structures Reveal Edge Conductivity Pores As a Mechanism for Membrane Damage Nature Communications. 06, 2020 | Pubmed ID: 32541820 Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics Biophysical Journal. 07, 2020 | Pubmed ID: 32533943 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 Identifying Mutation Hotspots Reveals Pathogenetic Mechanisms of KCNQ2 Epileptic Encephalopathy Scientific Reports. 03, 2020 | Pubmed ID: 32179837 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 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 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 Computational Dissection of Membrane Transport at a Microscopic Level Trends in Biochemical Sciences. 03, 2020 | Pubmed ID: 31813734 Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes Journal of Computational Chemistry. 03, 2020 | Pubmed ID: 31762060 Probing Cholesterol Binding and Translocation in P-glycoprotein Biochimica Et Biophysica Acta. Biomembranes. 01, 2020 | Pubmed ID: 31676371 Tuning Symmetry Breaking Charge Separation in Perylene Bichromophores by Conformational Control Chemical Science. Sep, 2019 | Pubmed ID: 34040711 Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation ACS Macro Letters. Oct, 2019 | Pubmed ID: 32149017 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 Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures Structure (London, England : 1993). 12, 2019 | Pubmed ID: 31780431 Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism Cell. 11, 2019 | Pubmed ID: 31730852 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 A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes Angewandte Chemie (International Ed. in English). 10, 2019 | Pubmed ID: 31539191 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 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 Structural Insights into the Lipid A Transport Pathway in MsbA Structure (London, England : 1993). 07, 2019 | Pubmed ID: 31130486 Serotonin Transporter-ibogaine Complexes Illuminate Mechanisms of Inhibition and Transport Nature. 05, 2019 | Pubmed ID: 31019304 Pro-Nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-cancer Therapy ACS Applied Materials & Interfaces. May, 2019 | Pubmed ID: 31013055 Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213 Biochemistry. 03, 2019 | Pubmed ID: 30785734 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 Main-chain Mutagenesis Reveals Intrahelical Coupling in an Ion Channel Voltage-sensor Nature Communications. 11, 2018 | Pubmed ID: 30498243 The SERM/SERD Bazedoxifene Disrupts ESR1 Helix 12 to Overcome Acquired Hormone Resistance in Breast Cancer Cells ELife. 11, 2018 | Pubmed ID: 30489256 Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane Biochemistry. 12, 2018 | Pubmed ID: 30456950 Direct Protein-lipid Interactions Shape the Conformational Landscape of Secondary Transporters Nature Communications. Oct, 2018 | Pubmed ID: 30297844 Probing Key Elements of Teixobactin-lipid II Interactions in Membranes Chemical Science. Sep, 2018 | Pubmed ID: 30210775 Selective Permeability of Carboxysome Shell Pores to Anionic Molecules The Journal of Physical Chemistry. B. 10, 2018 | Pubmed ID: 30193460 Constructing Atomic Structural Models into Cryo-EM Densities Using Molecular Dynamics - Pros and Cons Journal of Structural Biology. 11, 2018 | Pubmed ID: 30092279 Microscopic View of Lipids and Their Diverse Biological Functions Current Opinion in Structural Biology. 08, 2018 | Pubmed ID: 30048836 Reconstitution and Substrate Specificity for Isopentenyl Pyrophosphate of the Antiviral Radical SAM Enzyme Viperin The Journal of Biological Chemistry. 09, 2018 | Pubmed ID: 30030381 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 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 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 A "cross-stitched" Peptide with Improved Helicity and Proteolytic Stability Organic & Biomolecular Chemistry. 05, 2018 | Pubmed ID: 29725689 Structure of the Alternative Complex III in a Supercomplex with Cytochrome Oxidase Nature. 05, 2018 | Pubmed ID: 29695868 Cytochrome Aa Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O for Catalysis Biochemistry. 04, 2018 | Pubmed ID: 29546752 Molecular Insight into Drug Exporters Within the Cellular Membrane Pharmacological Research. 07, 2018 | Pubmed ID: 29535020 PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations Biophysical Journal. 02, 2018 | Pubmed ID: 29414703 Drug-Drug Interactions Between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4 Biochemistry. 02, 2018 | Pubmed ID: 29200287 Chasing the Open-state Structure of Pentameric Ligand-gated Ion Channels The Journal of General Physiology. Dec, 2017 | Pubmed ID: 29089419 Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1 Biophysical Journal. Oct, 2017 | Pubmed ID: 28978444 Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the NhTMEM16 Scramblase ELife. 09, 2017 | Pubmed ID: 28917060 Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM Cell. Sep, 2017 | Pubmed ID: 28823560 Lipid Specificity of the Membrane Binding Domain of Coagulation Factor X Journal of Thrombosis and Haemostasis : JTH. 10, 2017 | Pubmed ID: 28782177 Dimeric Structure of the Uracil:proton Symporter UraA Provides Mechanistic Insights into the SLC4/23/26 Transporters Cell Research. Aug, 2017 | Pubmed ID: 28621327 Tribute to Klaus Schulten The Journal of Physical Chemistry. B. 04, 2017 | Pubmed ID: 28423902 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 Energy Transduction and Alternating Access of the Mammalian ABC Transporter P-glycoprotein Nature. 03, 2017 | Pubmed ID: 28289287 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 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 Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome Nature. 01, 2017 | Pubmed ID: 28077875 Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail Biochemistry. Jan, 2017 | Pubmed ID: 27997124 Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase Biochemistry. Dec, 2016 | Pubmed ID: 27992998 X-ray Structures Define Human P2X3 Receptor Gating Cycle and Antagonist Action Nature. Sep, 2016 | Pubmed ID: 27626375 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 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 Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation Methods in Enzymology. 2016 | Pubmed ID: 27497175 TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS Within VMD Journal of Chemical Information and Modeling. 06, 2016 | Pubmed ID: 27196035 The Cellular Membrane As a Mediator for Small Molecule Interaction with Membrane Proteins Biochimica Et Biophysica Acta. 10, 2016 | Pubmed ID: 27163493 Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form Biochemistry. Apr, 2016 | Pubmed ID: 26953503 Atomic-level Description of Protein-lipid Interactions Using an Accelerated Membrane Model Biochimica Et Biophysica Acta. Jul, 2016 | Pubmed ID: 26940626 Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction Angewandte Chemie (International Ed. in English). Mar, 2016 | Pubmed ID: 26928945 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 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 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 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 Revealing an Outward-facing Open Conformational State in a CLC Cl(-)/H(+) Exchange Transporter ELife. Jan, 2016 | Pubmed ID: 26799336 CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model Biophysical Journal. Nov, 2015 | Pubmed ID: 26588561 Atomic-level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-phosphate:phosphate Antiporter Nature Communications. Sep, 2015 | Pubmed ID: 26417850 Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail Biochemistry. Oct, 2015 | Pubmed ID: 26346528 Structural Determinants of the Mechanical Stability of α-Catenin The Journal of Biological Chemistry. Jul, 2015 | Pubmed ID: 26070562 Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution The Journal of Membrane Biology. Jun, 2015 | Pubmed ID: 25998378 Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide The Journal of Physical Chemistry. B. Jun, 2015 | Pubmed ID: 25996559 Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters Current Opinion in Structural Biology. Apr, 2015 | Pubmed ID: 25913536 Mechanism of Drug-drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer Biochemistry. Apr, 2015 | Pubmed ID: 25777547 Redox Potential Tuning Through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter Sphaeroides Biochemistry. Mar, 2015 | Pubmed ID: 25734689 A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin Biophysical Journal. Nov, 2014 | Pubmed ID: 25418096 Membrane-induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3 Biophysical Journal. Nov, 2014 | Pubmed ID: 25418091 Atomistic Models of General Anesthetics for Use in in Silico Biological Studies The Journal of Physical Chemistry. B. Oct, 2014 | Pubmed ID: 25303275 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 Conformational Heterogeneity of α-synuclein in Membrane Biochimica Et Biophysica Acta. Dec, 2014 | Pubmed ID: 25135664 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 Dynamics at the Inner Gate of KcsA During Activation Biochemistry. Apr, 2014 | Pubmed ID: 24621378 Partitioning of Amino Acids into a Model Membrane: Capturing the Interface The Journal of Physical Chemistry. B. Feb, 2014 | Pubmed ID: 24451004 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 A Microscopic View of Phospholipid Insertion into Biological Membranes The Journal of Physical Chemistry. B. Feb, 2014 | Pubmed ID: 24313792 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 Rapid Parameterization of Small Molecules Using the Force Field Toolkit Journal of Computational Chemistry. Dec, 2013 | Pubmed ID: 24000174 Characterizing a Histidine Switch Controlling PH-dependent Conformational Changes of the Influenza Virus Hemagglutinin Biophysical Journal. Aug, 2013 | Pubmed ID: 23972851 Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations The Journal of Physical Chemistry Letters. Jun, 2013 | Pubmed ID: 23795244 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 On the Origin of Large Flexibility of P-glycoprotein in the Inward-facing State The Journal of Biological Chemistry. Jun, 2013 | Pubmed ID: 23658020 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 Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations Biochemistry. Jan, 2013 | Pubmed ID: 23298176 Simulation Studies of the Mechanism of Membrane Transporters Methods in Molecular Biology (Clifton, N.J.). 2013 | Pubmed ID: 23034756 Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model Biophysical Journal. May, 2012 | Pubmed ID: 22824277 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 Tracing Cytoplasmic Ca(2+) Ion and Water Access Points in the Ca(2+)-ATPase Biophysical Journal. Jan, 2012 | Pubmed ID: 22339863 Molecular Dynamics Investigation of the ω-current in the Kv1.2 Voltage Sensor Domains Biophysical Journal. Jan, 2012 | Pubmed ID: 22339862 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 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 Conformational Coupling of the Nucleotide-binding and the Transmembrane Domains in ABC Transporters Biophysical Journal. Aug, 2011 | Pubmed ID: 21806936 Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-mimetic Model The Journal of Physical Chemistry. B. Jun, 2011 | Pubmed ID: 21561114 Atomic View of Calcium-induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers Biochemistry. Mar, 2011 | Pubmed ID: 21294564 Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation Journal of Computational and Theoretical Nanoscience. Dec, 2010 | Pubmed ID: 23710155 Interaction of the α2A Domain of Integrin with Small Collagen Fragments Protein & Cell. Apr, 2010 | Pubmed ID: 21203951 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 Modeling and Dynamics of the Inward-facing State of a Na+/Cl- Dependent Neurotransmitter Transporter Homologue PLoS Computational Biology. Aug, 2010 | Pubmed ID: 20865057 Interplay of Mechanical and Binding Properties of Fibronectin Type I Theoretical Chemistry Accounts. May, 2010 | Pubmed ID: 20824113 Identification of the Third Na+ Site and the Sequence of Extracellular Binding Events in the Glutamate Transporter Biophysical Journal. Sep, 2010 | Pubmed ID: 20816053 Exploring Transmembrane Diffusion Pathways with Molecular Dynamics Physiology (Bethesda, Md.). Jun, 2010 | Pubmed ID: 20551228 Calculation of the Gating Charge for the Kv1.2 Voltage-activated Potassium Channel Biophysical Journal. May, 2010 | Pubmed ID: 20483327 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 Functional Interplay Between Acetylation and Methylation of the RelA Subunit of NF-kappaB Molecular and Cellular Biology. May, 2010 | Pubmed ID: 20160011 Protein-phospholipid Interactions in Blood Clotting Thrombosis Research. Apr, 2010 | Pubmed ID: 20129649 Simulation of Spontaneous Substrate Binding Revealing the Binding Pathway and Mechanism and Initial Conformational Response of GlpT Biochemistry. Feb, 2010 | Pubmed ID: 20058936 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 Coupling of Calcium and Substrate Binding Through Loop Alignment in the Outer-membrane Transporter BtuB Journal of Molecular Biology. Nov, 2009 | Pubmed ID: 19747487 Structural Basis of Substrate Selectivity in the Glycerol-3-phosphate: Phosphate Antiporter GlpT Biophysical Journal. Sep, 2009 | Pubmed ID: 19720022 Molecular Dynamics Simulations of Membrane Channels and Transporters Current Opinion in Structural Biology. Apr, 2009 | Pubmed ID: 19345092 Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation Biophysical Journal. Jan, 2009 | Pubmed ID: 19167292 Dimer Opening of the Nucleotide Binding Domains of ABC Transporters After ATP Hydrolysis Biophysical Journal. Dec, 2008 | Pubmed ID: 18790847 Potential Cation and H+ Binding Sites in Acid Sensing Ion Channel-1 Biophysical Journal. Dec, 2008 | Pubmed ID: 18790845 Blood Clotting Reactions on Nanoscale Phospholipid Bilayers Thrombosis Research. 2008 | Pubmed ID: 18691494 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 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 Dynamics of the Extracellular Gate and Ion-substrate Coupling in the Glutamate Transporter Biophysical Journal. Sep, 2008 | Pubmed ID: 18515371 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 Indirect Role of Ca2+ in the Assembly of Extracellular Matrix Proteins Biophysical Journal. Jul, 2008 | Pubmed ID: 18359797 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 Distinct Structural and Adhesive Roles of Ca2+ in Membrane Binding of Blood Coagulation Factors Structure (London, England : 1993). Jan, 2008 | Pubmed ID: 18184585 Substrate Binding and Formation of an Occluded State in the Leucine Transporter Biophysical Journal. Mar, 2008 | Pubmed ID: 18024499 Diffusion of Glycerol Through Escherichia Coli Aquaglyceroporin GlpF Biophysical Journal. Feb, 2008 | Pubmed ID: 17921212 Molecular Mechanisms of Conduction and Selectivity in Aquaporin Water Channels The Journal of Nutrition. 06, 2007 | Pubmed ID: 17513417 Mechanics of Force Propagation in TonB-dependent Outer Membrane Transport Biophysical Journal. Jul, 2007 | Pubmed ID: 17449669 Sugar Transport Across Lactose Permease Probed by Steered Molecular Dynamics Biophysical Journal. Jul, 2007 | Pubmed ID: 17434947 Exploring Gas Permeability of Cellular Membranes and Membrane Channels with Molecular Dynamics Journal of Structural Biology. Mar, 2007 | Pubmed ID: 17306562 Sugar Binding and Protein Conformational Changes in Lactose Permease Biophysical Journal. Dec, 2006 | Pubmed ID: 16963502 Mechanism of Gating and Ion Conductivity of a Possible Tetrameric Pore in Aquaporin-1 Structure (London, England : 1993). Sep, 2006 | Pubmed ID: 16962972 Dynamics of K+ Ion Conduction Through Kv1.2 Biophysical Journal. Sep, 2006 | Pubmed ID: 16844753 Scalable Molecular Dynamics with NAMD Journal of Computational Chemistry. Dec, 2005 | Pubmed ID: 16222654 What Makes an Aquaporin a Glycerol Channel? A Comparative Study of AqpZ and GlpF Structure (London, England : 1993). Aug, 2005 | Pubmed ID: 16084383 Molecular Dynamics Simulations of Proteins in Lipid Bilayers Current Opinion in Structural Biology. Aug, 2005 | Pubmed ID: 16043343 Collective Diffusion Model for Water Permeation Through Microscopic Channels Physical Review Letters. Nov, 2004 | Pubmed ID: 15601094 Classical Force Field Parameters for the Heme Prosthetic Group of Cytochrome C Journal of Computational Chemistry. Oct, 2004 | Pubmed ID: 15264255 Theory and Simulation of Water Permeation in Aquaporin-1 Biophysical Journal. Jan, 2004 | Pubmed ID: 14695248 Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels Biophysical Journal. Nov, 2003 | Pubmed ID: 14581193 Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore Biophysical Journal. Sep, 2003 | Pubmed ID: 12944261 Mechanisms of Selectivity in Channels and Enzymes Studied with Interactive Molecular Dynamics Biophysical Journal. Jul, 2003 | Pubmed ID: 12829462 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 Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin Biophysical Journal. Dec, 2002 | Pubmed ID: 12496081 Structural Changes During the Formation of Early Intermediates in the Bacteriorhodopsin Photocycle Biophysical Journal. Sep, 2002 | Pubmed ID: 12202355 Pressure-induced Water Transport in Membrane Channels Studied by Molecular Dynamics Biophysical Journal. Jul, 2002 | Pubmed ID: 12080108 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 Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning Science (New York, N.Y.). Apr, 2002 | Pubmed ID: 11964478 Protein-Lipid Etkileşimlerini Ölçmek için Mikro Ölçekli Termoforez Kullanımı 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 JoVE 60607 Biochimica
Protein-Lipid Etkileşimlerini Ölçmek için Mikro Ölçekli Termoforez Kullanımı 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 JoVE 60607 Biochimica