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List of works by Emad Tajkhorshid

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

scientific article published on 20 April 2020

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

scientific article published on 20 September 2019

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

scientific article published on 09 February 2022

A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane

A comparison of aqueous solvent models used in the calculation of the Raman and ROA spectra of l-alanine

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

scientific article

A highly tilted membrane configuration for the prefusion state of synaptobrevin

scientific article

A microscopic view of phospholipid insertion into biological membranes

scientific article published on 16 December 2013

A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl- channel ANO1 (TMEM16A)

scientific article published on 12 September 2019

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

scientific article published in May 2012

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

scientific article published on 28 February 2019

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

scientific article published on 06 February 2020

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

scientific article published on 05 November 2020

Arachidonic Acid Metabolism by Human Cardiovascular CYP2J2 Is Modulated by Doxorubicin.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 15 June 2020

Barrier to Rotation around the Csp2-Csp2Bond of the Ketoaldehyde Enol Ether MeC(O)CHCH−OEt As Determined by13C NMR and ab Initio Calculations

article

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

scientific article

Blood clotting reactions on nanoscale phospholipid bilayers

scientific article

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

scientific article published on 04 December 2018

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

scientific article

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

scientific article published on December 2010

Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide

scientific article published on 08 June 2015

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

scientific article

Changing the peptide specificity of a human T-cell receptor by directed evolution.

scientific article

Chapter 12 Gas Conduction of Lipid Bilayers and Membrane Channels

article

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

scientific article published on 12 April 2019

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

scientific article published on August 2013

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

scientific article published on 30 May 2013

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

scientific article published on 31 October 2017

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

scientific article published in October 2004

Clonidine-induced rhythmic activity in rabbit anococcygeus muscle

scientific article published in April 1996

Collective Diffusion Model for Water Permeation through Microscopic Channels

scientific article published in Physical Review Letters

Color Tuning in Rhodopsins:  The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II

scientific article

Complementarities and convergence of results in bacteriorhodopsin trimer simulations

scientific article published in August 2004

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

scientific article

Computational characterization of structural dynamics underlying function in active membrane transporters

scientific article published on 27 April 2015

Conformational Coupling of the Nucleotide-Binding and the Transmembrane Domains in ABC Transporters ⬇️

scientific article published on August 3, 2011

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

scientific article published on 07 November 2020

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

scientific article

Conformational dynamics at the inner gate of KcsA during activation

scientific article

Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

scientific article

Conformational heterogeneity of α-synuclein in membrane

scientific article

Confronting pitfalls of AI-augmented molecular dynamics using statistical physics

scientific article published on 01 December 2020

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

scientific article

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

scientific article

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

scientific article published on 07 January 2020

Cybershuttle: An End-to-End Cyberinfrastructure Continuum to Accelerate Discovery in Science and Engineering

scientific article published on 10 September 2023

Cytochrome aa3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O2 for Catalysis

scientific article published on 16 March 2018

Determination of structural and functional overlap/divergence of five proto-type galectins by analysis of the growth-regulatory interaction with ganglioside GM1 in silico and in vitro on human neuroblastoma cells

scientific article published on March 2005

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

scientific article

Different calcium dependencies of contractile activity of prostatic and epididymal portions of rat vas deferens

scientific article published on 01 May 1995

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

scientific article

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

scientific article published on 12 September 2008

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

scientific article published in Nature Communications

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

scientific article

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

scientific article published on 17 May 2013

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

scientific article

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

scientific article

Dynamics of K+ ion conduction through Kv1.2.

scientific article

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

scientific article published on 30 May 2008

Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution

scientific article published on 22 May 2015

Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels ⬇️

scientific article published on November 1, 2003

Electrostatic funneling of substrate in mitochondrial inner membrane carriers

scientific article

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

scientific article published on 19 July 2018

Endocannabinoid Virodhamine is an Endogenous Inhibitor of Human Cardiovascular CYP2J2 Epoxygenase

scientific article published on 06 November 2018

Energetics of glycerol conduction through aquaglyceroporin GlpF.

scientific article

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

scientific article

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

scientific article published on 2 February 2016

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

article

Exploring transmembrane diffusion pathways with molecular dynamics

scientific article published on June 2010

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

article

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

scientific article

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

scientific article published on 02 December 2020

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

scientific article

Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy

scientific article published on 16 March 2020

Incorporation of antimicrobial peptides into membranes: a combined liquid-state NMR and molecular dynamics study of alamethicin in DMPC/DHPC bicelles

scientific article

Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2-lipid bilayer interactions

scientific article

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

scientific article published on 21 March 2008

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

scientific article published on 11 October 2019

Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model

scientific article published in 2024

Interaction of the α2A domain of integrin with small collagen fragments

scientific article published on April 2010

Interplay of mechanical and binding properties of Fibronectin type I.

scientific article published on May 2010

Ion-releasing state of a secondary membrane transporter

scientific article published on December 2009

Large scale simulation of protein mechanics and function

scientific article published on January 2003

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

scientific article published on 7 August 2017

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

scientific article published on 16 September 2017

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

scientific article published on 20 December 2019

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

scientific article published in Nature Communications

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II.

scientific article published on 13 February 2017

Mechanics of force propagation in TonB-dependent outer membrane transport

scientific article

Mechanism of Gating and Ion Conductivity of a Possible Tetrameric Pore in Aquaporin-1

article by Jin Yu et al published September 2006 in Structure

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

scientific article published on 25 March 2015

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

scientific article published on 4 April 2008

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

scientific article

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

scientific article

Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail

scientific article published on 8 September 2015

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

scientific article published on 30 September 2020

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

scientific article

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

scientific article published on 02 March 2020

Methoxamine-induced rhythmic activity in rabbit anococcygeus muscle

scientific article published on 01 July 1993

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes

scientific article published on 25 November 2019

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

scientific article

Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter

scientific article

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

scientific article published on 12 February 2020

Molecular basis of proton blockage in aquaporins

scientific article published in January 2004

Molecular determinants of phospholipid synergy in blood clotting

scientific article

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

scientific article

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

scientific article published on January 2012

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

scientific article

Molecular dynamics simulations of membrane channels and transporters

scientific article published on April 2009

Molecular dynamics simulations of proteins in lipid bilayers

scientific article

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer

scientific article published in August 2001

Movement of NH₃ through the human urea transporter B: a new gas channel

scientific article published on 03 April 2013

Nanoscale studies of protein-membrane interactions in blood clotting.

scientific article published on July 2011

Nitric oxide conduction by the brain aquaporin AQP4.

scientific article

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

scientific article published on 08 May 2013

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

scientific article published on 01 October 2020

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

scientific article published on 30 January 2014

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

scientific article

Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules

article

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

scientific article

Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association

scientific article published on 10 September 2019

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

scientific article published on 12 September 2008

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

scientific article

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

scientific article published on 13 May 2019

Probing key elements of teixobactin-lipid II interactions in membranes

scientific article published on 20 July 2018

Protein-membrane interactions: blood clotting on nanoscale bilayers

scientific article

Protein-phospholipid interactions in blood clotting

scientific article published on 04 February 2010

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

scientific article published in February 2018

Rapid parameterization of small molecules using the Force Field Toolkit

scientific article published on 02 September 2013

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

scientific article published in Journal of Biological Chemistry

Residue-specific information about the dynamics of antimicrobial peptides from (1)H-(15)N and (2)H solid-state NMR spectroscopy

scientific article published in December 2009

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

scientific article published on 15 March 2008

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

scientific article published on 22 January 2016

Role of Water in Transient Cytochrome c2Docking

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis

scientific article published in September 2004

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

scientific article published on 01 July 2020

Scalable molecular dynamics with NAMD

scientific article (publication date: December 2005)

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

scientific article

Structural Determinants of Spectral Tuning in Retinal ProteinsBacteriorhodopsin vs Sensory Rhodopsin II#

article published in 2001

Structural Determinants of the Mechanical Stability of α-Catenin

scientific article published on 12 June 2015

Structural and functional analysis of SoPIP2;1 mutants adds insight into plant aquaporin gating

scientific article

Structural basis for iron piracy by pathogenic Neisseria

scientific article

Structural basis for the reaction cycle of DASS dicarboxylate transporters

scientific article published on 01 September 2020

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

scientific article published on September 2009

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

scientific article

Structural insights into photosystem II assembly

scientific article published on 12 April 2021

Structural mechanism of plant aquaporin gating

scientific article

Structure and permeation mechanism of a mammalian urea transporter

scientific article

Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions

scientific article

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

scientific article

Sugar binding and protein conformational changes in lactose permease

scientific article

Sugar transport across lactose permease probed by steered molecular dynamics

scientific article

The Mechanism of Glycerol Conduction in Aquaglyceroporins ⬇️

scientific article published on November 1, 2001

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

scientific article published on 29 November 2018

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

scientific article

The dielectric effect of the environment on the p K a of the retinal Schiff base and on the stabilization of the ion pair in bacteriorhodopsin

The mechanism of proton exclusion in aquaporin channels

scientific article published in May 2004

The role of calcium and alpha-adrenoceptors in contractile response of chick expansor secundariorum muscle to field stimulation

article

The structures of Secretory and dimeric Immunoglobulin A

scientific article published on 27 October 2020

Theory and simulation of water permeation in aquaporin-1.

scientific article

Thermodynamic insight into spontaneous hydration and rapid water permeation in aquaporins

scientific article

Tissue factor/factor VIIa complex: role of the membrane surface

scientific article

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

scientific article published on January 2006

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

scientific article published on January 2012

Transient formation of water-conducting states in membrane transporters

scientific article

Tribute to Klaus Schulten.

scientific article published in April 2017

Tuning symmetry breaking charge separation in perylene bichromophores by conformational control

scientific article published in 2019

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

scientific article published on 21 May 2020

Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria

scientific article

Unique conformer selection of human growth-regulatory lectin galectin-1 for ganglioside GM1 versus bacterial toxins

scientific article published on December 2003

Visualizing functional motions of membrane transporters with molecular dynamics simulations

scientific article

WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination

scientific article published in 2024

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

scientific article published on 30 December 2013

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

scientific article

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

scientific article

py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD

scientific article published on 27 May 2022

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