E. Tajkhorshid

Secondary structure determines electron transport in peptides

This study investigates how secondary structure influences electron transport in peptides using a combination of experiments and computational methods, revealing a two-state conductance behavior linked to conformational flexibility.

Atomistic Characterization of Beta-2-Glycoprotein I Domain V Interaction with Anionic Membranes

This study identifies key regions and binding modes of beta-2-glycoprotein I domain V interacting with anionic membranes, important for antiphospholipid syndrome pathogenesis.

Topological Learning Approach to Characterizing Biological Membranes

The paper introduces a topological learning method to predict lipid effective temperatures from static coordinates using persistent homology and machine learning.

Structure Reveals Homology in Elevator Transporters

The paper identifies a conserved architecture in elevator transporters across 18 families and constructs a phylogenetic tree to reveal their homology.

Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter

This study uses cryo-EM, DEER, and MD simulations to analyze the conformational dynamics of BmrCD, revealing asymmetric ATP and substrate interactions that drive its transport cycle.

Molecular mechanisms of functional impairment for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease.

This study identifies atomic interactions and energetic perturbations in G6PC1 active site mutations linked to glycogen storage disease type 1a using computational models and experimental validation.

Backbone amides are key determinants of Cl- selectivity in CLC ion channels

The paper shows that backbone amides in CLC channels are critical for Cl- selectivity, as replacing them with ester groups reduces ion discrimination.

Lipid-mediated organization of prestin in the outer hair cell membrane and its implications in sound amplification

The paper uses molecular dynamics simulations to show how prestin's lipid interactions influence membrane deformation and sound amplification in outer hair cells.

Structure of C. elegans TMC-1 complex illuminates auditory mechanosensory transduction

The paper determines the structure of the C. elegans TMC-1 complex using cryo-EM, revealing its composition and mechanism of mechanosensory transduction.

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

This study uses single-molecule experiments to show that VcINDY, a sodium-coupled dicarboxylate transporter, uses stochastic elevator-like motions for substrate translocation, with non-cooperative protomer movements and cooperative binding.

Tuning aromatic contributions by site-specific encoding of fluorinated phenylalanine residues in bacterial and mammalian cells

This paper introduces new pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs to site-specifically encode fluorinated phenylalanine residues in bacterial and mammalian cells, enabling experimental assessment of aromatic-pi interactions.

Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity efflux pumps

This study identifies conformational states and proton-coupled dynamics of a bacterial Spns transporter, revealing its role in multidrug resistance and substrate specificity.

Post-Translational Modifications Optimize the Ability of SARS-CoV-2 Spike for Effective Interaction with Host Cell Receptors

This paper develops a full-length, membrane-bound SARS-CoV-2 spike model with post-translational modifications, revealing how glycosylation and palmitoylation enhance its conformational dynamics and interaction with host cell receptors.

Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1 (EAAT1)

This study identifies a chloride-conducting conformation in human EAAT1 using MD simulations and mutagenesis, revealing a conserved mechanism across SLC1A family transporters.

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

This study develops an AI-driven multi-resolution simulation workflow to study SARS-CoV-2 RTC dynamics, combining cryo-EM with mesoscale simulations and AI methods.

Structural transitions permitting ligand entry and exit in bacterial fatty acid binding proteins.

This study reveals how FakB1 transitions between closed and open states to facilitate fatty acid exchange with the membrane.

Investigation of gating in outer membrane porins provides new perspectives on antibiotic resistance mechanisms

This study uses molecular dynamics simulations and experiments to show that dynamic gating of E. coli outer membrane porin OmpF, mediated by conserved acidic residues, regulates antibiotic permeability and contributes to antibiotic resistance.

Rationalizing generation of broad spectrum antibiotics with the addition of a primary amine

This study uses molecular dynamics simulations and experimental validation to show that adding a primary amine to antibiotics enhances their permeation through the outer membrane of Gram-negative bacteria by aligning dipole moments and forming electrostatic interactions.

PIP2-dependent coupling of voltage sensor and pore domains in Kv7.2

This study identifies PIP2 binding sites in Kv7.2 channels using simulations and electrophysiology, showing how PIP2 couples voltage sensor and pore domains during activation.

Extended-Ensemble Docking to Probe Evolution of Ligand Binding Sites in Proteins Undergoing Large-Scale Structural Changes for Their Function

This paper introduces extended-ensemble docking to study ligand binding in P-glycoprotein, showing better agreement with experiments by considering multiple conformational states.

Capturing the interplay of membrane lipids and structural transitions in human ABCA7

This study presents cryo-EM structures of human ABCA7 in open and closed states, revealing lipid interactions and conformational changes, supported by functional analysis and MD simulations.

Glutamate transporters contain a conserved chloride channel with two hydrophobic gates

The paper reports the cryo-EM structure of a glutamate transporter homologue, revealing a conserved chloride channel with two hydrophobic gates that facilitates dual-function transport.

Molecular Mechanism of Capsid Disassembly in Hepatitis B Virus

This study uses molecular dynamics simulations to reveal how mechanical stress and thermal fluctuations cause HBV capsid disassembly by targeting specific residues in hexameric regions.

Confronting pitfalls of AI-augmented molecular dynamics using statistical physics

This paper introduces an automated algorithm to improve AI-augmented molecular dynamics by maximizing time-scale separation, tested on three benchmark problems.

Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II

This study investigates the structural basis of the HKII/VDAC1 complex formation using simulations and electrophysiological measurements, revealing partial blockade of VDAC1 and phosphorylation-dependent disruption of binding.

Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein

This study uses molecular dynamics simulations to show that tariquidar, a P-glycoprotein inhibitor, recruits lipids into the transporter's lumen, enhancing conformational restriction and inhibiting drug efflux.

Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane

This study uses molecular dynamics simulations to analyze how the SARS-CoV2 fusion peptide binds to human cell membranes, identifying three binding modes with the deepest penetration being the most biologically relevant.

How to build a water-splitting machine: structural insights into photosystem II assembly

The paper solves the structure of a PSII assembly intermediate using cryo-EM, revealing how assembly factors protect PSII during biogenesis and prepare it for water splitting.

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

CryoFold determines protein structures from electron density maps using molecular dynamics and physical knowledge, producing ensembles of low-energy conformations validated experimentally.

Anti-inflammatory dopamine- and serotonin-based endocannabinoid epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel

This paper identifies novel endocannabinoid epoxides that modulate TRPV1 and cannabinoid receptors, reducing inflammation and offering potential for new therapeutics.