S. Gnanakaran

Predicting Permeation of Compounds across the Outer Membrane of P. aeruginosa Using Molecular Descriptors: Advantages and Limitations

This study identifies molecular descriptors predictive of compound permeation across P. aeruginosa outer membrane using physicochemical, docking, and MD simulation data.

Site-specific Effector Protein Functionalization to Create Bead-based Avidity Model Systems

This paper introduces a method to create bead-based avidity model systems using effector beads for measuring avidity effects in cell-cell interactions and drug potency assessment.

Inferring pathways of oxidative folding from pre-folding free energy landscapes of disulfide-rich toxin

This study uses diffusion maps to analyze the free energy landscapes of micro-conotoxins, revealing how sequence and length influence folding pathways and disulfide bond formation.

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

This study identifies nAbs against SIVmac239, reveals structural features of its Env trimer, and shows passive transfer of nAbs protects macaques from infection.

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

This study shows the D614G mutation in SARS-CoV-2 Spike protein increases open conformations, enhancing infectivity and neutralization sensitivity.

Exploring the role of glycans in the interaction of SARS-CoV-2 RBD and human receptor ACE2

This study uses molecular simulations to analyze how different glycan types on SARS-CoV-2 RBD and ACE2 affect their binding, finding that glycan presence does not alter the contact signature but influences binding affinity.

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines

This study shows that B.1.1.7 SARS-CoV-2 variant remains neutralizable by antibodies from ancestral Spike vaccines and convalescent sera, though with reduced efficacy.

Visualization of the HIV-1 Env Glycan Shield Across Scales

This study uses cryo-EM, computational modeling, and mass-spectrometry to analyze the HIV-1 Env glycan shield's structure and dynamics, revealing how heterogeneity and interactions affect epitope accessibility and trimer stability.

Quantification of the Resilience and Vulnerability of HIV-1 Native GlycanShield at Atomistic Detail

The paper quantifies the resilience and vulnerability of HIV-1's glycan shield using atomistic modeling and graph theory, revealing new insights into its structure and potential for immunogen design.

Multiscale Characterization of Complex Binding Interactions of Cellulolytic Enzymes Highlights Limitations of Classical Approaches

This study uses single-molecule assays and simulations to show how CBM1 binding affects cellulase activity on different cellulose allomorphs, highlighting limitations of classical binding models.

Molecular aspects of multivalent engagement between Syk and FcϵRIγ

The paper models and experimentally validates that cis binding of Syk to FcεRIγ is more effective for signaling than trans binding, with Y130 phosphorylation reducing cis binding.