Biology subjects

Bheemireddy, S.

Publications and source records attributed to Bheemireddy, S..

4 recordsLinked to original sources

bioRxiv2025

Stoichiometric Insights into SARS-CoV-2 Spike-ACE2 Binding Across Variants

The SARS-CoV-2 spike protein binds to the angiotensin-converting enzyme 2 (ACE2) receptor to mediate viral entry, with mutations in different variants influencing binding affinity and conformational dynamics. Using large-scale molecular dynamics simulations, we analyzed the Spike-ACE2 complex in the wild-type (WT), Beta, and Delta variants. Our findings reveal significant conformational rearrangements at the inter-face in Beta and Delta compared to WT, leading to distinct interaction networks and changes in complex stability. Binding free energy analysis further highlights variant-specific differences in ACE2 affinity, with alternative binding modes emerging over the simulation. The results enhance our understanding of spike-ACE2 stoichiometry across variants, providing implications for viral infectivity and therapeutic targeting.

bioinformatics↗

bioRxiv2025

Structural conformations of intrinsically disordered proteins of podocyte slit-diaphragm

The slit-diaphragm (SD), a specialized junction between the foot processes of neighboring podocytes, regulates the permselectivity of glomerular filtration. It functions as a size- and charge-selective molecular sieve, ensuing protein-free urine. SD comprises several proteins such as nephrin, NEPH1, podocin, CD2AP, and TRPC6. Nephrin and NEPH1 are extracellular proteins that bridge the gap between foot processes, whereas podocin and CD2AP are adapter proteins. The intrinsically disordered regions (IDRs) of SD proteins play a crucial role in assembling these proteins as a macromolecular complex. Mutations in these proteins disrupt SD integrity, leading to a nephrotic syndrome characterized by heavy proteinuria. The structural details of each protein of this macromolecular complex are poorly detailed. We employed molecular docking and molecular dynamics simulations to investigate the structural dynamics of SD proteins. Our findings reveal that SD proteins exhibit partner-specific conformational adaptations driven by short linear motifs and molecular recognition features. CD2AP interacts transiently with nephrin but forms a more stable complex with podocin. NEPH1 and nephrin interact via extracellular immunoglobulin domains while maintaining dynamic intracellular contacts. Podocin preferentially interacts with nephrin over NEPH1, and distinct subunit-sharing mechanisms emerge, where CD2AP and TRPC6 may simultaneously associate with a single podocin subunit. Mutational analysis reveals that disease-associated variants, including CD2AP (P532S), podocin (R138Q), and nephrin (G1161V), enhance local stability but restrict the flexibility of IDR and impair SD assembly. Our study provides evidence of dynamic subunit sharing within the SD complex, offering new insights into the assembly of SD in health and disease.

bioinformatics↗

bioRxiv2025

Communication pathway analysis within protein-nucleic acid complexes

Inter-residue communication forms a vast and intricate network that underpins essential biological processes such as catalysis, gene expression, and cell signaling. Allostery, a crucial phenomenon where distant regions of a macromolecule are energetically coupled to elicit functional responses, operates through these intricate communication networks within macromolecular complexes. Despite the pivotal role of nucleic acids in these networks, their contributions to allostery remain largely overlooked. To address this gap, we developed ComPASS, a large-scale computational method designed to study communication networks in protein-protein and protein-nucleic acid complexes. Recognizing the significance of dynamics in the communication of macromolecules, our approach leverages molecular dynamics (MD) simulation data to extract inter-residue key properties, including dynamical correlations, interactions, and distances. These properties are integrated to construct a weighted communication network that comprehensively represents dependencies among amino acids and nucleotides. Using ComPASS, we uncovered distinct mechanisms of signal transmission in diverse macromolecular systems. In Cysteinyl-tRNA synthetase, the central domain was found to mediate the coordination between substrate recognition and enzymatic activity, ensuring functional precision. In the LacI repressor, allosteric communication occurs through interface pathways within the dimer, effectively linking ligand sensing to DNA binding. For the Type IIF restriction endonuclease Bse634I, structural communication across dimer and tetramer interfaces was crucial for specific DNA recognition. In the liver X receptor, a key helical region was identified as a bridge connecting ligand-binding events to DNA interactions. Finally, our analysis with ComPASS aligned with previous literature, confirmed the role of H2A L1 loops in mediating communication across histone interfaces and coordinating interactions between structural domains in nucleosome complexes. ComPASS is available as an open-source tool, maintained at https://github.com/yasamankarami/compass. By offering an integrated framework for studying communication networks, ComPASS advances our understanding of conformational dynamics, particularly within protein-nucleic acid complexes.

bioinformatics↗

bioRxiv2024

Computational analysis of the effect of a binding protein (RbpA) on the dynamics of Mycobacterium tuberculosis RNA polymerase assembly

RNA polymerase-binding protein A (RbpA) is an actinomycetes-specific protein crucial for the growth and survival of the pathogen Mycobacterium tuberculosis. Its role is essential and influences the transcription and antibiotic responses. However, the regulatory mechanisms underlying RbpA-mediated transcription remain unknown. In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex. Our analysis reveals significant structural rearrangements in RNA polymerase happen upon interaction with RbpA. Hotspot residues, crucial amino acids in the RbpA-mediated transcriptional regulation, were identified through our examination. The study elucidates the dynamic behavior within the complex, providing insights into the flexibility and functional dynamics of the RbpA-RNA polymerase interaction. Notably, potential allosteric mechanisms, involving the interface of subunits 1 and 2 were uncovered, shedding light on how RbpA modulates transcriptional activity. Finally, potential ligands meant for the 1-2 binding site were identified through virtual screening. The outcomes of our computational study serve as a foundation for experimental investigations into inhibitors targeting the RbpA-regulated dynamics in RNA polymerase. Overall, this research contributes valuable information for understanding the intricate regulatory networks of RbpA in the context of transcription and suggests potential avenues for the development of RbpA-targeted therapeutics. Author SummaryInfection studies by Mycobacterium tuberculosis (Mtb) acquires primary importance due to its severe infection and antibiotic resistance. There is an open need for highly effective drugs and one needs to employ novel approaches such as detailed structural analysis and the possibility to focus on allosteric inhibitors. We have exploited the availability of cryo-EM structures of RNA polymerase of Mtb, with and without its transcription-activator protein namely RNA polymerase-binding protein A (RbpA). In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex. The assemblies were subject to molecular dynamics and perturbation scanning, followed by structural comparisons and measurement of subunit interface strength. These analyses could clearly show that subunits, which are far away from the RbpA binding site, undergo differential structural changes. Hence, we focused on the site to recognize potential small molecule inhibitors using virtual screening. These analyses demonstrate that it is possible to perform comparative structural analysis of different forms of assemblies, which can be useful towards drug design.

bioinformatics↗