M. Moradi

Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH

This study uses molecular dynamics simulations to investigate how protonation affects the conformational changes of influenza hemagglutinin at low pH, revealing structural shifts linked to receptor binding and immune evasion.

Lipid-dependent conformational dynamics of bacterial ATP-binding cassette transporter Sav1866

The paper investigates how lipid environments affect the conformational dynamics of the bacterial ABC transporter Sav1866 using molecular dynamics simulations.

Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1

This study uses molecular dynamics simulations to compare conformational dynamics of inactive and active states of CB1 receptor, identifying key structural differences and electrostatic interactions that influence its function.

Cholesterol Dependence on the Conformational Changes of Metabotropic Glutamate Receptor 1

This study uses molecular dynamics simulations to show that cholesterol modulates conformational changes in mGluR1 dimers, with 10% cholesterol causing the most significant effects.

Novel Pentafluorosulfanyl-containing Triclocarban Analogs selectively kill Gram-positive bacteria.

The paper evaluates novel pentafluorosulfanyl-containing triclocarban analogs, finding they effectively kill Gram-positive bacteria at low concentrations compared to common antibiotics.

Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins

This study uses molecular dynamics simulations to characterize conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins, revealing distinct pathways and free energy barriers between the two viruses.

Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase

This study uses molecular dynamics simulations to investigate the structure and function of YidC in gram-negative bacteria, revealing its role in protein insertion and highlighting domain interactions.

An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

This study uses molecular dynamics simulations to investigate the YidC-mediated insertion of Pf3 coat protein, revealing the role of YidC's hydrophilic groove in protein transport.

cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach

This study investigates the structural stability and flexibility of cpSRP43 using biophysical techniques and molecular dynamics simulations, revealing it is both highly stable and flexible.

Binding Affinity Estimation From Restrained Umbrella Sampling Simulations

The paper estimates protein-ligand binding affinity using restrained umbrella sampling simulations and compares results to experimental data.

Computational Elucidation of Recombinant Fusion Protein Effect on Peptide-Directed Nanoparticles

This study uses molecular dynamics simulations to analyze how peptide sequences and their binding to GFPuv affect nanoparticle properties and free energies.

Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

This paper uses molecular dynamics simulations to elucidate the atomic-level activation mechanism of an engineered MscL channel triggered by pH changes, identifying key structural changes and interactions involved.

Addressing the Embeddability Problem in Transition Rate Estimation

This paper addresses the embeddability problem in transition rate estimation by proposing eight methods, including a novel approach, tested on a one-dimensional toy model.

Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework

This paper introduces a Riemannian framework for molecular dynamics simulations to improve sampling, path-finding, and transition rate estimation in biomolecular systems.

Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics

The paper simulates freely-diffusing single-molecule FRET data with conformational dynamics using Langevin dynamics to test analysis techniques for flexible proteins.

Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2

This study uses molecular dynamics simulations to compare the dynamic behavior of prefusion spike proteins in SARS-CoV-1 and SARS-CoV-2, finding that SARS-CoV-2's spike is more stable with a higher energy barrier for activation.

Mechanistic picture for chemo-mechanical couplings in a bacterial proton-coupled oligopeptide transporter from Streptococcus thermophilus

The paper uses molecular dynamics simulations to investigate chemo-mechanical couplings in a bacterial proton-coupled oligopeptide transporter, identifying key residues involved in conformational changes and substrate transport.

Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding

This study uses molecular dynamics simulations to show how heparin stabilizes hFGF1 by altering its conformational dynamics and electrostatic interactions.

Chloroplast SRP43 Subunit Prevents Aggregation of Proteins

This study shows that chloroplast SRP43 can act as a generic chaperone for non-LHCP proteins, preventing heat-induced aggregation and preserving bioactivity in some cases.

The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2

The paper uses molecular dynamics simulations to show that the unresolved C2 loop in YidC2 stabilizes the protein structure and interacts with lipid head groups.

Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Diffusion Formalism

The paper develops a Riemannian diffusion formalism to characterize protein conformational dynamics, enabling invariant calculations of thermodynamic and kinetic quantities in molecular simulations.