W. Im

CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems

The paper introduces a tool for automated molecular assembly under periodic boundary conditions, demonstrating its application on six complex systems.

Click-Based Determination of Accumulation of Molecules in Escherichia coli

The paper develops CHAMP, a method to measure cytosolic accumulation of azide-tagged molecules in Gram-negative bacteria, enabling high-throughput screening of over 1,000 compounds.

Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer

The paper uses AlphaFold Multimer to model cytokine-receptor-JAK2 signaling complexes, revealing activation mechanisms and oncogenic mutation impacts.

Molecular basis of polyspecific drug binding and transport by OCT1 and OCT2

The paper presents cryo-EM structures of OCT1 and OCT2 in different states and combines them with functional experiments to reveal principles of organic cation recognition and the alternating access mechanism.

Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study

This study simulates Mid1's membrane binding mechanisms, showing multiple binding modes involving its PH and C2 domains, and how these contribute to its role in cytokinetic ring anchoring.

Lipoprotein sorting to the cell surface via a crosstalk between the Lpt and Lol pathways during outer membrane biogenesis

The paper identifies lipoproteins transported to the cell surface via LptDE and reveals a crosstalk between Lpt and Lol pathways in Gram-negative bacteria.

From Molecular Dynamics to Supramolecular Organization: The Role of PIM Lipids in the Originality of the Mycobacterial Plasma Membrane

This paper uses molecular dynamics simulations to study the role of PIM lipids in the structure and organization of the Mycobacterial plasma membrane and validates findings with drug testing.

Binding Free Energies of Piezo1 Channel Agonists at Protein-Membrane Interface

This study computes binding free energies of Yoda1 and its analogs at Piezo1 channels using molecular dynamics to predict agonist/inhibitor effects and guide drug design.

Calcium-induced environmental adaptability of the blood protein vitronectin

This study reveals how calcium binding enables vitronectin to adapt its structure to environmental changes like temperature and shear stress.

Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern

This study quantifies how Omicron variant's RBD mutations enhance binding affinity to ACE2 compared to the original SARS-CoV-2 strain.

All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed state

The paper uses molecular dynamics simulations to study the primed state of synaptic vesicles, revealing a spring-loaded configuration of trans-SNARE complexes bound to synaptotagmin-1 and complexin-1.

Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

This study uses molecular dynamics and experiments to analyze how mutations in SARS-CoV-2 variants affect their binding to ACE2, identifying which variants are more contagious.

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids

The paper extends CHARMM-GUI Membrane Builder to model and simulate lipid nanoparticles with ionizable cationic lipids and PEGylated lipids, showing how PEG-lipids affect membrane structure and dynamics.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

This study uses molecular dynamics simulations to analyze SARS-CoV-2 spike protein interactions with antibodies, revealing structural dynamics and mutation impacts on neutralization.

Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids

This study determines the atomic structure of PLEKHA7's PH domain and reveals its multivalent interaction mechanism with membrane-bound PIPs, providing insights for inhibitor design.

Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

This study uses molecular dynamics simulations to analyze the structure, dynamics, and antibody binding of the fully-glycosylated SARS-CoV-2 spike protein, revealing key roles of glycans in stabilizing RBD conformations and antibody epitope exposure.

Site-specific lipidation enhances IFITM3 membrane interactions and antiviral activity

This study shows site-specific S-palmitoylation of IFITM3 enhances its membrane interactions and antiviral activity by modulating its conformation and lipid membrane binding.

Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction

This study quantifies the biophysical differences in SARS-CoV-2 and SARS-CoV-1 RBD-ACE2 interactions using single-molecule force spectroscopy and SMD simulations, revealing a key N-glycan interaction in SARS-CoV-2 that enhances binding affinity.

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

The paper models and simulates a fully-glycosylated SARS-CoV-2 spike protein in a viral membrane using computational methods and provides the structures for research on COVID-19 prevention and treatment.

Conformational states of the cytoprotective protein Bcl-xL

This study investigates the conformational states of full-length Bcl-xL in soluble and membrane-anchored forms using NMR, MD simulations, and ITC to understand its structure and ligand binding.