Biology subjects

Dantu, S. C.

Publications and source records attributed to Dantu, S. C..

7 recordsLinked to original sources

bioRxiv2026

A Charge-Encoded Rheostat Permits Helix Nucleation but Limits Propagation in Skp1

Molecular recognition by intrinsically disordered regions (IDRs) is widely thought to involve coupled folding and binding, yet the sequence features that regulate this transition remain underexplored. Here we show that helix 8 (H8), a disordered C-terminal segment of the SCF ubiquitin ligase adaptor Skp1, is intrinsically prevented from forming a stable helix by its own sequence grammar. Using an integrative approach to dissect its conformational dynamics, we find that H8 frequently nucleates helical structure but rarely propagates into a fully formed stable helix, populating instead a shallow metastable basin of helical intermediates. Contrary to conventional models of helix-coil exchange, where nucleation is rate limiting, helix initiation in H8 is readily accessible, while propagation is selectively suppressed by a glutamate-rich acidic patch. This acidic segment acts as a charge-sensitive conformational rheostat that limits helix extension and maintains H8 in a predominantly disordered state. As a result, H8 transiently samples partially helical conformations on the microsecond timescale without committing to a stable fold. We propose that this propagation-limited mechanism preserves conformational flexibility while maintaining recognition competence across a structurally diverse family of F-box binding partners. More broadly, our findings suggest that charged- hydrophobic-charged sequence patterning can encode conditional, context-dependent structure as a general organisational principle in intrinsically disordered proteomes.

biophysics↗

bioRxiv2024

Functionally Important Residues from Graph Analysis of Coevolved Dynamic couplings

The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine tune protein dynamics through compensatory mutations, either to improve the proteins performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics (MD) simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue-residue interactions, identifies communities of key residue groups and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings--residue pairs with critical dynamical interactions that have been preserved during evolution--DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded {beta}-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.

evolutionary biology↗

bioRxiv2023

Cleaving DNA with DNA: cooperative tuning of structure and reactivity driven by copper ions

Abstract/SummaryA copper-dependent self-cleaving DNA (DNAzyme or dexoxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics simulations and advanced EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction at unprecedented resolution. The minimized 46-nucleotide deoxyribozyme forms duplex and triplex substructures that flank a highly conserved catalytic core. The self-cleaving construct forms a bimolecular complex that has a distinct substrate and enzyme domains. Cleavage of the substrate is directed at one of two adjacent nucleotides and proceeds via an oxidative cleavage mechanism that is unique to the position cleaved. The use of isotopologues of nucleotides allowed us to provide atomic resolution for the copper-substrate complex. The spectroscopic analysis overcomes the major drawbacks related to the metal-soup scenario, also known as super-stoichiometric ratios of cofactors versus substrate, conventionally required for the cleavage reaction within those nucleic acids-based enzymes. Our results pave the way for analysis on mixtures where metals/lanthanides are used as cofactors, having demonstrated that our approach may reach resolution of single nucleotide and beyond. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic option towards the applicability of spectroscopic studies, both in vitro and in vivo matrices.

biophysics↗

bioRxiv2021

Structural dynamics of the β-coronavirus Mpro protease ligand binding sites

{beta}-coronaviruses alone have been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a back-up against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensible role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all non-redundant ligand-binding sites available for SARS-CoV2, SARS-CoV and MERS-CoV Mpro. Extensive adaptive sampling has been used to explore conformational dynamics employing convolutional variational auto encoder-based deep learning, and investigates structural conservation of the ligand binding sites using Markov state models across {beta}-coronavirus homologs. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across {beta}-coronavirus homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

biophysics↗

bioRxiv2019

The 'hidden side' of spin labeled oligonucleotides: Molecular Dynamics study focusing on the EPR-silent components of base pairing

Nitroxide labels are combined with nucleic acid structures and studied using electron paramagnetic resonance experiments (EPR). As X-ray/NMR structures are unavailable with the nitroxide labels, detailed residue level information, down to atomic resolution, about the effect of these nitroxide labels on local RNA structures is currently lacking. This information is critical to evaluate the choice of spin label. In this study, we compare and contrast the effect of TEMPO-based (NT) and rigid spin (C) labels (in both 2-O methylated and not-methylated forms) on RNA duplexes. We also investigate sequence-dependent effects of NT label on RNA duplex along with the more complex G-quadruplex RNA. Distances measured from molecular dynamics simulations between the two spin labels are in agreement with the EPR experimental data. To understand the effect of labeled oligonucleotides on the structure, we studied the local base pair geometries and global structure in comparison with the unlabeled structures. Based on the structural analysis, we can conclude that TEMPO-based and C labels do not significantly perturb the base pair arrangements of the native oligonucleotide. When experimental structures for the spin labelled DNA/RNA molecules are not available, general framework offered by the current study can be used to provide information critical to the choice of spin labels to facilitate future EPR studies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/537324v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1b37634org.highwire.dtl.DTLVardef@11556f3org.highwire.dtl.DTLVardef@1ff6c13org.highwire.dtl.DTLVardef@1063ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2018

Conformational dynamics of active site loops 5, 6 and 7 of enzyme Triosephosphate Isomerase: A molecular dynamics study

Triosephosphate Isomerase is a glycolytic enzyme catalyzing the interconversion of Dihydroxyacetone phosphate to Glyceraldehyde-3-phosphate. The active site is comprised of three distinct loops loop-6, loop-7 and loop-8. Based on loop-6 and loop-7 conformation we describe the enzyme as Open TIM and Closed TIM. Various NMR, X-ray crystallography and QM/MM simulation techniques have provided glimpses of individual events of what is essentially a dynamic process. We studied the conformational changes of two distinct loops (loop-6 and loop-7) enveloping the active site, in the presence of natural substrate, reaction intermediates and inhibitor molecules, by means of microsecond atomistic MD simulations in solution and crystal environment. Our studies have revealed that loop-6 samples open and closed conformations in both apo and holo TIM structures. As seen in solution state NMR experiments, we also observe that loop-6 N-terminus and C-terminus move independently. In our simulations we have also observed that backbone dihedrals of loop-7 residues G210 (G210-phi, G210-psi) and G211 (G211-phi) sample open and closed states in both apo and holo TIM structures. Whereas backbone dihedral angles of G211 (G211-psi) and S212 (S212-phi) adopt closed conformation only when the ligand is bound to the active site. As observed in chain-B of 1R2R crystal structures, we also observe that water molecules can also initiate flip of G211-psi and S212-phi dihedral angles into closed conformation. Except, loop-5, which has a dominant effect on the conformational behaviour of loop-6 N-terminus, we do not observe any influence of either loop-6 or loop-7 on the conformational dynamics of the other.

biophysics↗

bioRxiv2018

Structural plasticity of CENP-A regulated by H4 influences cellular levels and kinetochore assembly

The Histone variant CENP-ACse4 is a core component of the specialized nucleosome at the centromere in budding yeast. The level of Cse4 in cells is tightly regulated, primarily by ubiquitin-mediated proteolysis. However, the structural transitions in Cse4 that regulate centromere localization and interaction with regulatory components are poorly understood. Using time resolved fluorescence, NMR and molecular dynamics we show for the first time that soluble Cse4 can exist in a closed conformation, inaccessible to various regulatory components. We further determined that binding of its obligate partner H4, alters the inter-domain interaction within Cse4, ensuring an open state that will lend itself to proteolysis. This dynamic model allows kinetochore formation only in presence of H4, as the N-terminus, which is required for interaction with centromeric components will be unavailable in absence of H4. The specific requirement of H4 binding for the conformational regulation of Cse4 suggests a unique structure-based regulatory mechanism for Cse4 localization and prevention of premature kinetochore assembly.

biophysics↗