Athi N. Naganathan

Hashi: Bridging Statistical Model Derived 1D Microstate Encodings and Protein 3D Structural Ensembles

Hashi generates realistic protein structural ensembles from WSME model outputs, enabling rapid analysis of conformational states and functional insights.

Switching Functional DNA-Binding Modes by Tuning Protein Order-Disorder Equilibria

This study shows how phosphorylation tuning affects Nhp6A's conformational equilibria and DNA binding modes, revealing a conserved mechanism for chromatin regulation.

A Structural Domain in the genomic RNA of SARS-CoV-2 Folds into a Compact Granular Structure without the N protein: A Single-Molecule Fluorescence Spectroscopic Investigation

This study shows a specific SARS-CoV-2 genomic RNA region forms compact granular structures autonomously without the N protein, and the N protein melts these structures, suggesting it acts as an RNA chaperone.

Diverse Conformational Ensembles Define the Shared Folding-Allosteric Landscapes of Protein Kinases

The paper analyzes sequence variation in eukaryotic protein kinases to uncover how it affects their folding and allostery, revealing conserved unfolding mechanisms and sequence-dependent ensemble behaviors.

Polyphosphate Discriminates Protein Conformational Ensembles More Efficiently than DNA Promoting Diverse Assembly and Maturation Behaviors

This study compares how polyphosphate and DNA influence the assembly of disordered proteins, showing polyP's superior ability to distinguish protein conformations and drive diverse assembly behaviors.

Oligomerization-Mediated Phase-Separation in the Nucleoid-Associated Sensory Protein H-NS is Controlled by Ambient Cues

This paper shows H-NS forms liquid-like condensates with DNA, regulated by temperature and ionic strength, and demonstrates that oligomerization and phase separation are linked to DNA binding and environmental cues.

The lack of trade-off between conformational stability and binding affinity in a nanobody with therapeutic potential for a misfolding disease

This study shows that reducing the stability of a nanobody does not affect its binding affinity, suggesting stability and affinity can be decoupled in therapeutic proteins.