Biology subjects

Prusty, S.

Publications and source records attributed to Prusty, S..

3 recordsLinked to original sources

bioRxiv2026

Bilayer thickness and transmembrane domain dynamics drive directional ER-Golgi traffic via Erv14/cornichon

Directionality of protein traffic during secretion is driven by sorting receptors that bind cargo in one compartment and release them in another. Erv14/cornichon family receptors mediate delivery from the endoplasmic reticulum (ER) to the Golgi. Erv14 traffics its client, Mid2, via a conserved interface formed by two transmembrane helices (TMHs). Molecular dynamics simulations of Erv14-Mid2 suggest that Erv14 TMHs undergo dynamic movement in response to both client binding and lipid bilayer thickness. Interaction between charged residues that flank the TMHs of Mid2 and Erv14 couple client binding to stabilization of the Erv14 export signal and thus engagement with the COPII coat. We term this mechanism Helix Engagement Induced Signal-mediated Traffic (HEIST) and suggest it as a general mechanism where changes in membrane biophysical properties drive directional transport.

cell biology↗

bioRxiv2025

Exploring the kinetics and mechanism of phase separation in ternary lipid mixtures containing APP C99 using atomistic vs coarse-grained MD simulations

The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter time exponential phase followed by a power law phase followed by a longer time plateau phase. Comparison of lipid, protein and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of dynamics of AA and CG simulation yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and the ongoing efforts to define the role of lipid rafts in the structure and function of cellular membrane.

biophysics↗

bioRxiv2021

Correlation in Domain Fluctuations Navigates Target Search of a Viral Peptide along RNA

Biological macromolecules often exhibit correlation in fluctuations involving distinct domains. This study decodes their functional implications in RNA-protein recognition and target-specific binding. The target search of a peptide along RNA in viral TAR-Tat complex is closely monitored using atomistic simulations, steered molecular dynamics simulations, free energy calculations, and a machine-learning-based clustering technique. An anti-correlated domain fluctuation is identified between the tetraloop and the bulge region in the apo form of TAR RNA that sets a hierarchy in the domain-specific fluctuations at each binding event and that directs succeeding binding footsteps. Thus, at each binding footstep, the dynamic partner selects an RNA location for binding where it senses higher fluctuation, which is conventionally reduced upon binding. This event stimulates an alternate domain-fluctuation which then dictates sequential binding footstep/s and thus, the search progresses. Our cross-correlation maps show that the fluctuations relay from one domain to another specific domain till the anti-correlation between that inter-domain fluctuations sustains. Artificial attenuation of that hierarchical domain fluctuation inhibits specific RNA binding. The binding is completed with the arrival of a few long-lived water molecules that mediate slightly distant RNA-protein sites and finally stabilizes the overall complex. The study underscores the functional importance of naturally designed fluctuating RNA motifs (bulge, tetraloop) and their interplay in dictating the directionality of the search in a highly dynamic environment.

biophysics↗