S. Vemparala

Role of protein-protein interactions on model chromatin organization

This study uses a polymer-based model to show how protein-protein interactions and DNA sequence influence chromatin organization and compartmentalization.

Role of Tyrosine Phosphorylation in PTP-PEST

The paper investigates how tyrosine phosphorylation affects PTP-PEST's structure and function by identifying specific phosphorylation sites and their impact on substrate binding and catalytic conformation.

Correlation between antimicrobial structural classes and membrane partitioning: Role of emerging lipid packing defects

This study uses bioinformatics and molecular dynamics simulations to explore how antimicrobial peptide structures correlate with their membrane partitioning behavior and lipid defect interactions.

Role of lipid packing defects in determining membraneinteractions of antimicrobial polymers

This study investigates how antimicrobial polymers interact with bacterial membranes by inducing lipid packing defects, showing that ternary polymers with polar groups create different defect patterns compared to binary polymers.

In-silico identification of Tyr232 in AMPKα2 as a dephosphorylation site for the protein tyrosine phosphatase PTP-PEST

The paper identifies Tyr232 in AMPKα2 as a dephosphorylation site for PTP-PEST using bioinformatics and molecular dynamics simulations.

Phosphorylation of interfacial phosphosite leads to increased binding of Rap-Raf complex

The paper studies how phosphorylation of a serine residue in Rap protein affects the stability of the Rap-Raf complex through molecular dynamics simulations.

Kinetics of charged polymer collapse: effects of additional salt

This study uses molecular dynamics simulations to examine how additional salt affects the collapse kinetics of charged polymers, revealing distinct dynamics compared to neutral polymers.

Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14-3-3 ζ Protein

This study investigates how mutating D124 in 14-3-3ζ affects phosphopeptide binding through molecular dynamics simulations and limited proteolysis.

Role of Disulfide Bonds in Membrane Partitioning of a Viral Peptide

This study investigates how disulfide bonds affect the membrane partitioning of the HAV-2B viral peptide, showing reduced membrane remodeling due to conformational changes induced by SS bonds.

Effect of Cholesterol on Membrane Partitioning Dynamics of Hepatitis A Virus-2B peptide

This study investigates how cholesterol affects the partitioning of a viral peptide into host membranes by altering lipid packing defects.

Towards designing globular antimicrobial peptide mimics: role of polar functional groups in biomimetic ternary antimicrobial polymers

This study uses molecular dynamics simulations to show that ternary antimicrobial polymers with polar groups penetrate bacterial membranes more effectively than binary polymers by adopting folded conformations and avoiding amphiphilic structures.