Biology subjects

Chaurasiya, D. K.

Publications and source records attributed to Chaurasiya, D. K..

2 recordsLinked to original sources

bioRxiv2025

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

Sequence variation across members of an enzyme family contributes to diverse ensemble behaviors, which subtly influence substrate affinity, selectivity and regulation. A classic example is the family of eukaryotic protein kinases (EPKs), which regulate numerous cellular processes and serve as important drug targets. Here, we dissect the consequences of sequence variation on the folding-conformational landscapes by performing a meta-analysis of 274 EPKs through a structure-based statistical mechanical framework. We find that EPKs populate several partially structured states in their native ensemble with a hierarchy of structural order in the N-terminal lobe that is critical for catalysis and activation. Despite this, the unfolding mechanism is uniquely conserved across the majority of kinases, with the N-terminal lobe unfolding first. Kinase activation modulates the local stability and thermodynamic connectivity in a non-conserved manner and across the entire structure, due to the strong coupling between the active site residues to distant sites, including the established allosteric pockets. We further show how activation drives the Abl kinase ensemble towards a more folded and thermodynamically coupled system in a graded manner. Our work uncovers the thermodynamic design principles of kinases with insights into allostery, while shedding light on the extents to which ensemble behaviors are impacted by sequence variations in paralogs.

biophysics↗

bioRxiv2023

Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins

Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we resolve the underlying mechanism of promiscuous binding versus partial sub-functionalization in paralogs by studying structurally-identical Acyl-CoA Binding Proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR and simulations on two of the paralogs, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding-pocket volume, compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly more apparent in A749, hinting at conformational-selection-like mechanism of binding. The paralogs exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to Lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogs.

biophysics↗