Biology subjects

Potoyan, D.

Publications and source records attributed to Potoyan, D..

4 recordsLinked to original sources

bioRxiv2025

Thermal Adaptation of Extremozymes: Temperature-Sensitive Contact Analysis of Serine Proteases

Enzyme thermal adaptation reflects a delicate interplay between sequence, structure, and dynamics of proteins, fine-tuning the catalytic activity to environmental demands. Understanding these evolutionary relationships can drive bioengineering advances, including industrial enzyme design, biocatalysts for extreme conditions, and novel therapeutics. This work explores sequence-dynamics connections in subtilisin-like serine protease homologs using a recently developed computational methodology that uses expanded ensemble simulations and temperature-sensitive contact analysis. We reveal that thermophilic enzymes achieve thermal stability through extensive salt bridges and hydrophobic networks, while psychrophilic enzymes rely on targeted interaction stability for cold adaptation. An unsupervised cluster analysis of residue conservation, flexibility, and hydrophobic interactions provides a comprehensive view of residue-specific contributions to thermal adaptation. These findings underscore the coordinated roles of conserved and variable regions in enzyme stability and offer a framework for tailoring enzymes to specific thermal properties for biotechnological applications. SIGNIFICANCEThis study reveals how subtilisin-like serine proteases adapt to extreme temperatures by balancing sequence, structure, and dynamics. Through multi-ensemble simulations, we demonstrate that conserved catalytic regions and specific residue variations allow fine-tuned thermal adaptation. The analysis of simulations reveals the importance of salt bridges and hydrophobic interactions in enhancing thermophilic enzyme stability. We find that psychrophilic enzymes exhibit unique stability mechanisms for cold environments. The approach used in this study provides a comprehensive framework for understanding enzyme thermal adaptation and offers valuable insights for bioengineering enzymes with tailored properties for industrial and medical applications.

biophysics↗

bioRxiv2023

4D Mesoscale liquid model of nucleus resolves chromatin's radial organization

Recent chromatin capture, imaging techniques, and polymer modeling advancements have dramatically enhanced our quantitative understanding of chromosomal folding. However, the dynamism inherent in genome architectures due to physical and biochemical forces and their impact on nuclear architecture and cellular functions remains elusive. While imaging techniques capable of probing the physical properties of chromatin in 4D are growing, there is a conspicuous lack of physics-based computational tools appropriate for revealing the underlying forces that shape nuclear architecture and dynamics. To this end, we have developed a multi-phase liquid model of the nucleus, which can resolve chromosomal territories, compartments, and nuclear lamina using a physics-based and data-informed free energy function. The model enables rapid hypothesis-driven prototyping of nuclear dynamics in 4D, thereby facilitating comparison with whole nucleus imaging experiments. As an application, we model the Drosophila nucleus spanning the interphase and map phase diagram of nuclear morphologies. We shed light on the interplay of adhesive and cohesive interactions within the nucleus, giving rise to distinct radial organization seen in conventional, inverted, and senescent nuclear architectures. The results also show the highly dynamic nature of the radial organization, the disruption of which leads to significant variability in domain coarsening dynamics and, consequently, variability of chromatin architecture. The model also highlights the impact of oblate nuclear geometry and heterochromatin sub-type interactions on the global chromatin architecture and local asymmetry of chromatin compartments.

biophysics↗

bioRxiv2023

Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions

The functional properties of RNA-binding proteins (RBPs) require allosteric regulation through inter-domain communication. Despite the foundational importance of allostery to biological regulation, almost no studies have been conducted to describe the biophysical nature by which inter-domain communication manifests in RBPs. Here, we show through high-pressure studies with hnRNP A1 that inter-domain communication is vital for the unique stability of its N- terminal domain containing a tandem of RNA Recognition Motifs (RRMs). Despite high sequence similarity and nearly identical tertiary structures, the two RRMs exhibit drastically different stability under pressure. RRM2 unfolds completely under high-pressure as an individual domain, but when appended to RRM1, it remains stable. Variants in which inter-domain communication is disrupted between the tandem RRMs show a large decrease in stability under pressure. Carrying these mutations over to the full-length protein for in vivo experiments revealed that the mutations affected the ability of the disordered C-terminus to engage in protein-protein interactions and more importantly, they also influenced the RNA binding capacity. Collectively, this work reveals that thermodynamic coupling between the tandem RRMs of hnRNP A1 accounts for its allosteric regulatory functions.

biochemistry↗

bioRxiv2023

Conformational landscape of the transcription factor ATF4 is dominated by disordered-mediated inter-domain coupling

Transient intramolecular interactions between transactivation domain and DNA binding domain of transcription factors are known to play important functional roles, including modulation of DNA binding affinity and specificity. Similar type of inter-domain interactions has recently been reported for the transcription factor ATF4/CREB-2, a key regulator of the Integral Stress Response. In the case of ATF4, transient coupling between the transactivation and basic-leucine zipper (bZip) domains regulates the degree of phosphorylation of the disordered transactivation domain achievable by the casein kinase CK2. Despite the crucial importance of these inter-domain interactions, their structural and molecular basis remain ill-determined. In the present study, we use a combination of experimental and computational techniques to determine the precise nature of the long-range contacts established between the transactivation and bZip domains of ATF4 prior to its association with protein partners and DNA. Solution NMR spectroscopy experiments reveal that the isolated bZip domain of ATF4 is predominantly disordered and display evidence of conformational dynamics over a wide range of timescales. These experimental findings are supported by multi-microsecond timescale all-atom molecular simulations that unveil the molecular basis of the long-range interactions between the transactivation and bZip domains of ATF4. We found that inter-domain coupling is primarily driven by disorder-mediated interactions between a leucine-rich region of the transactivation domain and the leucine-zipper region of the bZip domain. This study uncovers the role played by structural disorder in facilitating the formation of long-range intramolecular interactions that shape the conformational ensemble of ATF4 in a critical manner.

biophysics↗