S. B. Ozkan

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

The paper integrates evolutionary predictions with protein dynamics to analyze molecular adaptations of SARS-CoV-2 Spike protein, revealing allosteric interactions and mutation effects on ACE2 binding and antibody escape.

RNA-induced allosteric coupling drives viral capsid assembly in bacteriophage MS2

This study shows RNA-induced allostery drives capsid assembly in bacteriophage MS2 by altering protein flexibility and dynamic coupling.

Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases

This paper compares the dynamic properties of SARS-CoV-1 and SARS-CoV-2 main proteases, finding that CoV-2 exhibits enhanced cross-chain coupling and dynamic allostery due to mutations.

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

The paper identifies a mechanism by which pathogenic missense variants disrupt dynamic coupling between protein residues and functional sites, explaining dysfunction in enzymes with distant mutations.

Design of novel Cyanovirin-N variants by modulation of binding dynamics through distal mutations

The paper introduces an ICDC approach to identify distal mutations that modulate protein function through dynamic allostery, validated on TEM-1 β-lactamase and applied to Cyanovirin-N.

Substitutions at Non-Conserved Rheostat Positions Modulate Function by Re-Wiring Long-Range, Dynamic Interactions

The paper shows that substitutions at nonconserved positions in the LacI protein alter DNA binding by re-wiring long-range dynamic interactions.

Ancient Thioredoxins Evolved to Modern Day Stability-Function Requirement by Altering Native State Ensemble

The paper compares ancient and modern Thioredoxins to show how their native state ensemble properties evolved, affecting stability and function.