Biology subjects

Mallick Gupta, A.

Publications and source records attributed to Mallick Gupta, A..

5 recordsLinked to original sources

bioRxiv2026

HepI and OpsX are functionally coupled but evolutionarily asymmetric heptosyltransferase variants: ecological transitions and operon modularization drive divergent constraints and flexibility

Lipopolysaccharide (LPS) inner-core biosynthesis is classically initiated by a heptosyltransferase enzyme most commonly Heptosyltranferase I (HepI), a conserved WaaC-like enzyme. An alternative heptosyltranferase variant, OpsX, occurs alone in a subset of Gram-negative bacteria and co-exist with WaaC-like enzyme within the same genome of other organisms, raising questions about the origin of these two vairants and their functional partitioning. Here, we present a comparative evolutionary analysis of HepI (K02841) and OpsX (K12982) across Gram-negative bacteria to resolve their functional coupling and divergence. Selection analyses reveal a consistent evolutionary asymmetry, with OpsX exhibiting elevated {omega} values relative to HepI across global datasets and within genomes encoding both systems. Residue-level analyses indicate conserved catalytic cores in both enzymes, but a broader distribution of relaxed constraints in OpsX, suggesting differential partitioning of functional pressure. HepI has undergone intensified purifying selection in host-associated lineages, whereas OpsX shows no corresponding shift, indicating distinct responses to ecological context. Gene-species tree reconciliation further reveals contrasting horizontal gene transfer (HGT) architectures: HepI displays an ecologically structured network enriched in pathogen- and opportunist-associated lineages, with recurrent hub-mediated exchanges and deeper lineage-integrated events, whereas OpsX exhibits a diffuse transfer regime dominated by non-pathogenic taxa and primarily recent terminal acquisitions. These differences persist in genomes co-encoding both systems, where HepI transfer signal remains strongly associated with lifestyle, while OpsX is largely uncoupled from ecological structure. Analysis of operon architecture reveals pathway partitioning between the two genes: HepI is embedded in a conserved downstream operon linked to glycosyltransferase-mediated core assembly, whereas OpsX occurs in a more variable context enriched for upstream ADP-heptose precursor biosynthesis genes. In dual-system genomes, HepI is reduced to a minimal downstream module while OpsX retains upstream functions, indicating coordinated operon modularization. Together, HepI and OpsX form a functionally coupled but evolutionarily asymmetric system shaped by ecological transitions and genomic reorganization. HighlightsO_LIHepI and OpsX represent functionally coupled but evolutionarily asymmetric LPS inner-core biosynthesis systems across Gram-negative bacteria. C_LIO_LIOpsX shows relaxed selective constraint and a diffuse horizontal gene transfer pattern, whereas HepI is under stronger purifying selection and ecologically structured transfer. C_LIO_LIOperon organization reveals pathway modularization, with HepI embedded in conserved downstream assembly modules and OpsX retaining upstream precursor-associated flexibility. C_LI

evolutionary biology↗

bioRxiv2025

Conserved inter-domain interactions drive trans-Golgi network localisation and trafficking of homologous copper-ATPases

Polytopic transmembrane Copper-ATPases are central regulators of the essential, redox-active micronutrient copper in all organisms. The vertebrate Cu-ATPase homologs ATP7A and ATP7B facilitate excess copper efflux, in addition to metalating cuproproteins. ATP7A and ATP7B exhibit copper-responsive basolateral and apical trafficking polarity respectively, in polarized epithelia. To elucidate the role of conserved functional domains in copper-responsive trafficking and copper transport, we substituted the copper-binding amino-terminal, Nucleotide-Binding (NBD) and C-terminal domain of ATP7B with that of ATP7A either singly or in combinations. The six chimeric Cu-ATPases generated, although functionally active, exhibited altered trafficking phenotypes. Notably, the N-terminal-substituted ATP7B exhibited constitutive trafficking to the basolateral membrane; however, the N-terminal and NBD double-substituted chimera gained steady-state TGN localization, indicating a putative interaction between the two domains critical for its TGN-localization. We analyzed orthologous Cu-ATPase domain sequences from diverse organisms and found that the N-terminal domain and NBD showed similar evolutionary relationships, unlike that of C-terminal domain, suggesting their co-evolution. This study for the first time correlates evolutionary stringency imparted onto Cu-ATPase domains with their significance in proper trafficking regulation.

cell biology↗

bioRxiv2023

Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics

Human coronaviruses like MERS CoV are known to utilize dipeptidyl peptidase 4 (DPP4), apart from angiotensin-converting enzyme 2(ACE2) as potential co-receptor for viral cell entry. DPP4, ubiquitous membrane-bound aminopeptidase is closely associated with elevation of disease severity in comorbidities. In SARS-CoV-2, there is inadequate evidence for combination of spike protein variants with DPP4, and underlying adversity in COVID19. To elucidate this mechanistic basis, we have investigated interaction of spike protein variants with DPP4 through molecular docking and simulation studies. The possible binding interactions between receptor binding domain (RBD) of different spike variants of SARS-CoV-2 and DPP4 have been compared with interactions observed in experimentally determined structure of complex of MERS-CoV with DPP4. Comparative binding affinity confers that Delta-CoV-2:DPP4 shows close proximity with MERS-CoV:DPP4, as depicted from accessible surface area, radius of gyration, number of hydrogen bonding and energy of interactions. Mutation in delta variant, L452R and T478K, directly participate in DPP4 interaction enhancing DPP4 binding. E484K in alpha and gamma variant of spike protein is also found to interact with DPP4. Hence, DPP4 interaction with spike protein gets more suitable due to mutation especially due to L452R, T478K and E484K. Furthermore, perturbation in the nearby residues Y495, Q474 and Y489 is evident due to L452R, T478K and E484K respectively. Virulent strains of spike protein are more susceptible to DPP4 interaction and are prone to be victimized in patients due to comorbidities. Our results will aid the rational optimization of DPP4 as a potential therapeutic target to manage COVID-19 disease severity.

bioinformatics↗

bioRxiv2022

Effect on the conformations of spike protein of SARS-CoV-2 due to mutation

The spike protein of SARS CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations appeared in variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wildtype from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between N-terminal domain and receptor binding domain leading to an obtuse angle cosine{theta} distribution in the trimeric structure in spike protein. Thus, increase in open-state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming linker loop where many residues undergo stabilization in the open state compared to the closed one.

biophysics↗

bioRxiv2021

Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2

SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein which may influence the pathogenesis of the concern SARS-CoV-2 through the development of antibody escape variants. We consider the effect of mutations in some of the epitope regions including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. P323L mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, the fluctuations in the dihedral angles in the epitope:paratope (IgG) interface increase which destabilize the interface. Such mutations may help in escaping antibody mediated immunity of the host.

bioinformatics↗