Hung Nguyen Do

Anti-HIV-1 B cell antigen receptor signaling and structure

This study reports cryo-EM structures of full-length BCRs, revealing their dynamic conformation and antigen binding-induced signaling mechanisms.

Sequential HIV-1 fusion protein gates control the initiation of host cell entry

This study identifies two sequential conformational gates in HIV-1 Env that control fusion peptide release and host cell entry initiation.

Reconstructing a Missing Link of HIV-1 Assembly: HIV-1 Envelope-Matrix Interactions in a Native Viral Context

This study investigates HIV-1 Env-MA interactions using cryo-ET and simulations, revealing the Kennedy-sequence motif's role in Env incorporation and Gag maturation's effect on Env clustering.

Structure of HIV-1 Env glycoprotein on virions reveals an alternative fusion subunit organization and native membrane coupling

This study reveals conformational differences in HIV-1 Env glycoprotein on virions compared to soluble forms, highlighting the role of the viral membrane in maintaining native structure.

Structure-Based Optimization of Pathogen Signal Sequences for Enhanced Antigen Expression in Humans for Vaccine Designs

This paper introduces a structure-based workflow to optimize signal peptides for enhanced antigen expression in human cells, showing that structurally optimized SPs improve protein secretion for vaccine candidates.

SignalGen: A Protein Language Model Based AI Agent For Optimal Signal Peptide Prediction

SignalGen predicts optimal signal peptides for protein expression by integrating mature protein sequences, organism, and localization using a Latent Residual Transformer.

Diverse toxins exhibit a common binding mode to the Nicotinic Acetylcholine Receptors revealing a new molecular determinant

This study identifies two common binding and dissociation pathways for diverse toxins interacting with nAChRs, revealing electrostatic interactions as a key determinant for toxicity.

Iterative Multiscale Molecular Dynamics: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Molecular Dynamics Simulations

This paper introduces iMMD, an iterative multiscale MD workflow combining all-atom and coarse-grained simulations to accelerate conformational sampling of biomolecules.

Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly

This study uses molecular dynamics simulations to identify two dynamical events in B-cell receptor activation upon antigen binding.

Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell

This study uses molecular dynamics simulations to investigate how the HIV-1 fusion peptide inserts and anchors into a T-cell membrane mimic, identifying a critical motif for fusion.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

This study uses deep learning and simulations to reveal dynamic allostery mechanisms in GPCRs, showing modulators restrict conformational space and enhance selectivity.

Alzheimer mutations stabilize synaptotoxic γ-secretase-substrate complexes

This study shows that Alzheimer's mutations stabilize harmful enzyme-substrate complexes in gamma-secretase, leading to synaptic loss rather than the released Aβ peptides being the primary cause.

Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network

DBMD accelerates molecular simulations by using Bayesian neural networks to generate Gaussian boost potentials, improving sampling efficiency and accuracy in alanine dipeptide, chignolin, and RNA folding simulations.

Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis

The paper uses sequence coevolutionary analysis and structural contacts to reveal distinct residue interactions in GPCR classes A and B, providing insights for drug design.