Biology subjects

Laha, S.

Publications and source records attributed to Laha, S..

5 recordsLinked to original sources

bioRxiv2026

Theory for Biomolecular Catalysis in Phase-Separated Systems

Enzymatic reactions in biomolecular condensates are often assumed to be regulated through local enrichment of reactants. However, condensates also reshape molecular transport and reaction kinetics, making it unclear how phase separation controls catalysis in living cells. Here, we develop a quantitative theory of biomolecular catalysis in phase-separated systems and find that liquid condensates can act as tunable catalytic switches, transitioning between regimes of enhanced and suppressed enzymatic activity, exhibiting optimal responses at biologically relevant condensate sizes. We show that condensate-mediated catalysis cannot be understood from reactant enrichment alone, but instead emerges from the coupled interplay of molecular partitioning, diffusive transport, and phase-dependent reaction kinetics. The strongest regulatory effects occur under rapid interphase exchange, where the spatially heterogeneous catalytic network admits a system-level Michaelis-Menten description governed by system-averaged concentrations and reaction kinetics. Our framework predicts that micron-sized condensates can either enhance or suppress enzymatic activity by up to two orders of magnitude, and that optimal catalytic regulation can emerge at condensate sizes comparable to many biomolecular condensates. These results provide experimentally testable predictions for condensate-mediated catalysis and establish quantitative principles for understanding and engineering enzyme-catalysed reactions in biomolecular condensates.

biophysics↗

bioRxiv2026

Switching Functional DNA-Binding Modes by Tuning Protein Order-Disorder Equilibria

Physical remodeling of chromatin by non-histone architectural proteins of the High Mobility Group B (HMGB) family is central to eukaryotic transcriptional regulation. Nhp6A, the prototypical single-HMG-box protein from yeast, harbors both ordered and disordered regions enabling it to bind and bend DNA without sequence specificity. Here, we integrate ensemble experiments, single-molecule FRET, statistical mechanical modeling and atomistic simulations to dissect the structural and functional consequences of context-dependent phosphorylation in the ordered domain and its interplay with the intrinsically disordered region in Nhp6A. We find that Nhp6A occupies a narrow thermodynamic window, with a melting temperature close to the growth temperature of its host organism and high unfolding cooperativity, a feature conserved across the HMG-box family. Phosphorylation extents - mimicked by multisite phosphomimetic substitutions at residue positions conserved across fungal taxa - smoothly tuning the conformational equilibria between at least two different substates in the native ensemble, apart from the unfolded state. This intrinsic plasticity enables close packing of Nhp6A on DNA through two degenerate binding modes, accompanied by two distinct DNA bending geometries. DNA rescues a strongly destabilized mutant, T63D, through favorable intermolecular interactions, thus effectively acting as a chaperone driving folding. Our findings thus reveal a conserved sequence-ensemble-dynamics code in Nhp6A wherein not just stability, but also phosphorylation-induced conformational switching, disordered tail dynamics, and DNA binding-bending closely coordinate chromatin accessibility. The combination of marginal stability, large cooperativity and electrostatic frustration emerges as a design principle to encode charge sensitivity into proteins, and may represent a general strategy for multisite post-translational regulation.

biophysics↗

bioRxiv2026

A Structural Domain in the genomic RNA of SARS-CoV-2 Folds into a Compact Granular Structure without the N protein: A Single-Molecule Fluorescence Spectroscopic Investigation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) packages its single-stranded genomic RNA (gRNA) having about 30,000 nucleotides into virions by forming 35-40 granular ribonucleoprotein (RNP) units. Each RNP unit has a diameter of [~]15 nm. While it is generally assumed that the assembly of these RNPs is driven by the binding of the nucleocapsid (N) protein to the gRNA in the cytoplasm, the precise molecular mechanism remains to be fully elucidated. In this study, we develop an experimental strategy based on single-molecule fluorescence and fluorescence correlation spectroscopies to examine the formation of long-range base pairing within a candidate structural domain corresponding to nt 12230-12686 of the gRNA (gRNA12k). Our results demonstrate that the 5 and 3 regions of gRNA12k autonomously form long-range base pairing in near-physiological buffers containing mono- and divalent cations, independently of the N protein. This domain possesses an extensive secondary structure, is compact, and can unfold and refold reversibly upon heat treatment and cooling. Notably, the addition of the N protein melts the long-range base pairs, and causes the aggregation of multiple molecules of gRNA12k. Based on these observations, we propose a refined mechanism for the genome assembly in SARS-CoV-2: gRNA initially forms autonomous granular structures, which are subsequently reorganized and condensed by the N protein to chaperone the assembly of the entire gRNA. SignificanceSARS-CoV-2 organizes its exceptionally long genomic RNA (gRNA) having about 30,000 nt into 35-40 granular ribonucleoprotein (RNP) units for viral packaging. It has been assumed that the nucleocapsid (N) protein drives the formation of the RNP granules. In this study, we challenge this prevailing view by demonstrating that a specific region of the gRNA sequence inherently encodes the information to fold into a compact, granular architecture independently of any proteins. Unexpectedly, we found that the N protein partially melts the autonomous structures, suggesting that it acts as an RNA chaperone to facilitate flexible genome assembly. Our findings redefine the interplay between viral proteins and gRNA, offering a new perspective on the mechanism of coronavirus replication.

biophysics↗

bioRxiv2025

Melatonin-mediated methylglyoxal homeostasis and regulation of autophagy during seed germination under PEG-induced drought stress in upland cotton

Methylglyoxal (MGO), toxic byproduct of glycolysis, acts as a signaling molecule at low levels, but its over-accumulation during drought stress disrupts redox balance and accelerates cell death. Contrarily, melatonin maintains redox balance, particularly during stress. The redox status and MGO level might differ in drought-sensitive and drought-tolerant varieties, so shall the melatonins effect. The study evaluated the effect of melatonin-priming on MGO detoxification and autophagy during polyethylene glycol (PEG)-induced drought stress during seed germination in drought-sensitive (L-799) and drought-tolerant (Suraj) varieties of upland cotton. Melatonin-priming increased endogenous melatonin content, reduced MGO accumulation and advanced glycation end-products (AGEs), and downregulated the expression of MGO biosynthesis genes in L-799 under stress. The expression and activities of glyoxalases and non-glyoxalases were upregulated, showing melatonins effectiveness in MGO detoxification. Additionally, priming upregulated the expression of TPI1, PGK5, and PK1 and downregulated HK3 expression, allowing better conversion of glucose to pyruvate, leading to reduced MGO in L-799. The downregulation of necrosis-related genes with reduced cell death in L-799 shows the potential of priming in maintaining cell viability under stress. Furthermore, upregulated expression of SnRK1.1, SnRK2.6 genes and KIN10 protein levels, with enhanced autophagy markers (ATGs, MDC-stained bodies, lipidated-ATG8), confirmed improved autophagy in melatonin-primed L-799 under stress. Despite lowered ABA, melatonin-mediated MGO homeostasis likely activated MAPK6, inducing autophagy independent of ABA in stressed plants. Conversely, Suraj, with higher endogenous melatonin and inherent stress tolerance, showed limited response to priming. Thus, the study illustrates melatonins role in regulating MGO homeostasis and autophagy under drought stress in cotton.

plant biology↗

bioRxiv2020

Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission

The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has a capability of gaining rapid mutations as the virus spreads. Whole genome sequencing data offers a wide range of opportunities to study the mutation dynamics. The advantage of increasing amount of whole genome sequence data of SARS-CoV-2 intrigued us to explore the mutation profile across the genome, to check the genome diversity and to investigate the implications of those mutations in protein stability and viral transmission. Four proteins, surface glycoprotein, nucleocapsid, ORF1ab and ORF8 showed frequent mutations, while envelop, membrane, ORF6 and ORF7a proteins showed conservation in terms of amino acid substitutions. Some of the mutations across different proteins showed co-occurrence, suggesting their functional cooperation in stability, transmission and adaptability. Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis. Analysis of protein structure stability of surface glycoprotein mutants indicated viability of specific variants and are more prone to be temporally and spatially distributed across the globe. Similar empirical analysis of other proteins indicated existence of important functional implications of several variants. Analysis of co-occurred mutants indicated their structural and/or functional interaction among different SARS-COV-2 proteins. Identification of frequently mutated variants among COVID-19 patients might be useful for better clinical management, contact tracing and containment of the disease.

genomics↗