Biology subjects

Kazan, I. C.

Publications and source records attributed to Kazan, I. C..

3 recordsLinked to original sources

bioRxiv2025

Long-range coupling regulates stator dynamics in the bacterial flagellar motor

The bacterial flagellar motor generates torque through MotAB stator complexes which couple ion flux to rotation. Stators anchor in the peptidoglycan cell wall and dynamically remodel in response to changes in external conditions such as the mechanical load, yet how stator anchoring is regulated remains unknown. Here, we show that long-range allosteric interactions within the MotB periplasmic domain tune stator binding in Escherichia coli. Using coarse-grained elastic-network modeling and co-evolutionary analyses, we identified residues mechanically coupled to peptidoglycan-interacting loops of MotB. Targeted mutagenesis at these coupled sites produced distinct motility phenotypes in some mutants, exhibiting altered swimming speeds compared to wild-type and characteristic expression-dependent swimming trends, indicating mutation-specific effects on stator dynamics or torque. Single-motor measurements distinguished mutants with altered torque from those with altered stator dynamics. Molecular dynamics simulations revealed that mutations at distal positions reshape loop flexibility in ways that quantitatively correlate with swimming speeds. These results demonstrate that allosteric communication within MotB propagates across length scales to modulate the performance of the entire motor, revealing how local molecular changes can tune large-scale bacterial motion.

biophysics↗

bioRxiv2023

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

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

biophysics↗

bioRxiv2020

Design of novel CV-N variants: Modulation of binding dynamics through distal mutations

We develop integrated coevolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 {beta}-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, Cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a general mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.

biophysics↗