Sandrasegaram Gnanakaran

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.

Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence

This study analyzes structural changes in the SARS-CoV-2 Spike protein between D614G and Delta variants using molecular dynamics simulations to identify allosteric and glycan shielding adaptations affecting virulence and immune evasion.

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.

Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-Human interactions

The paper evaluates challenges in predicting arenavirus-human PPIs, revealing issues with model generalization and proposing a framework for more reliable evaluation.

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.

Quantification of heterogeneity in human CD8+ T cell responses to vaccine antigens: an HLA-guided perspective

The paper introduces metrics to quantify CD8+ T cell responses to vaccine antigens, considering HLA genetic variation and viral evolution, using Ebola, SARS-CoV-2, and Burkholderia pseudomallei as examples.

Network analysis outlines strengths and weaknesses of emerging SARS-CoV-2 Spike variants

The paper uses network analysis of SARS-CoV-2 Spike protein variants to identify critical residues and assess the impact of mutations on protein function and adaptation.

A Graph-Directed Approach for Creation of a Homology Modeling Library: Application to Venom Structure Prediction

The paper introduces a graph-based algorithm to generate a homology modeling library for venom structure prediction, expanding the conotoxin structure library by 300%.

Unsupervised Machine Learning for Analysis of Coexisting Lipid Phases and Domain Growth in Biological Membranes

This paper introduces NMFk, an unsupervised machine learning method, to analyze lipid phase separation in MD simulations, identifying roles of lipids, nano-domains, timescales, and physical features.