Biology subjects

Baidya, L.

Publications and source records attributed to Baidya, L..

5 recordsLinked to original sources

bioRxiv2025

Why PAR is not RNA: ion atmospheres, bridging interactions, and ion-induced structural collapse

Poly(ADP-ribose) (PAR) is a highly charged, intrinsically flexible nucleic-acid-like homopolymer composed of ADP-ribose units. It serves as a critical post-translational modification that rapidly synthesized in response to DNA damage, and participates in diverse important cellular processes, including DNA repair, chromatin remodeling, and RNA biogenesis, often by promoting biomolecular phase separation. However, PARs conformational heterogeneity coupled with limited experimental characterization has hindered a mechanistic understanding of these processes. To address this challenge, we develop a five-bead coarse-grained model of PAR and perform molecular dynamics simulations to compare its conformational ensemble and ion atmosphere with those of RNA across diverse ion environments. Our simulations reveal that PAR undergoes a markedly stronger structural transition than RNA in response to divalent ions, driven by its preferential ion binding and effective ion-mediated bridging between phosphate groups. These interactions facilitate cooperative conformational changes and produce a compact, ion-rich atmosphere that is fundamentally distinct from RNA. Together, our work provides a physically grounded model for PAR, uncovers molecular features that differentiate PAR from RNA, and offers mechanistic insight into how PAR nucleates phase separation and organizes protein interactions at sites of DNA damage.

biophysics↗

bioRxiv2025

Transition Metal Binding Drives Folding of a Metalloregulatory Riboswitch by Modulating Conformational Flexibility at Helical Junctions

Transition metal ions are crucial for bacterias survival. Bacteria employ metalloregulatory riboswitches to respond to varying metal ion concentrations. The czcD (NiCo) transcription riboswitch specifically senses Co2+, Ni2+, and Fe2+ ions at micromolar concentrations amid millimolar Mg2+. We used computer simulations with multi-resolution RNA models to understand how global conformational changes in the NiCo riboswitch are coupled to the remarkable specific binding of Co2+. We show that the riboswitch folds through an intermediate state, where a partially folded four-way junction (4WJ) creates an anionic pocket large enough to accommodate the binding of solvated divalent ions. The binding of Co2+ is coupled to the stability of the weak non-canonical G{middle dot}A base pairs at the helical junction that drive the formation of native-like coaxial stacking of four helices. The Co2+ binding further twists the 4WJ, which locks the ions in the bound state. Electronic structure calculations show that enhanced orbital interactions between conserved guanines in the 4WJ and Co2+ are responsible for the high specificity of the riboswitch in binding to Co2+ over Mg2+. We provide a framework for understanding and engineering tunable RNA-based biosensors and developing antimicrobials, as metal intoxication is an evolutionary strategy to inhibit bacterial growth.

biophysics↗

bioRxiv2024

Metal Ion Sensing by Tetraloop-Like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion-RNA Inner Shell Contacts

Divalent metal ions influence the folding and function of RNA in the cells. The mechanism of how RNA structural elements in riboswitches sense specific metal ions is unclear. RNA interacts with ions through two distinct binding modes: direct interaction between the ion and RNA (inner-shell (IS) coordination) and indirect interaction between the ion and RNA mediated through water molecules (outer-shell (OS) coordination). To understand how RNA senses metal ions such as Mg2+ and Ca2+, we studied the folding of a small RNA segment from the Mg2+ sensing M-Box riboswitch using computer simulations. This RNA segment has the characteristics of a GNRA tetraloop motif and interestingly requires binding of a single Mg2+ ion. The folding free energy surface of this simple tetraloop system is multidimensional, with a population of multiple intermediates where the tetraloop and cation interact through IS and OS coordination. The partially folded compact tetraloop intermediates form multiple non-native IS contacts with the metal ion. Thermal fluctuations should break these strong non-native IS contacts so that the tetraloop can fold to the native state, resulting in higher folding free energy barriers. Ca2+ undergoes rapid OS to IS transitions and vice-versa due to its lower charge density than Mg2+. However, the ability of Ca2+ to stabilize the native tetraloop state is weaker as it could not hold the loop-closing nucleotides together due to its weaker interactions with the nucleotides. These insights are critical to understanding the specific ion sensing mechanisms in riboswitches, and the predictions are amenable for verification by NMR experiments.

biophysics↗

bioRxiv2022

pH Induced Switch in the Conformational Ensemble of an Intrinsically Disordered Protein Prothymosin-α and Its Implications to Amyloid Fibril Formation

Aggregation of intrinsically disordered proteins (IDPs) is the cause of various neu-rodegenerative diseases. Changes in solution pH can trigger IDP aggregation due to a shift in the IDP monomer population with a high aggregation propensity. Al-though there is experimental evidence that acidic pH promotes the compaction of IDP monomers, which subsequently leads to aggregation, the general mechanism is not clear. Using the IDP prothymosin- (proT), which is involved in multiple essential functions as a model system, we studied the pH effect on the conformational ensemble of proT and probed its role in aggregation using a coarse-grained IDP model and molecular dynamics simulations. We show that compaction in the proT dimension at low pH is due to the proteins collapse in the intermediate region (E41 - D80) rich in glutamic acid residues. Further, the {beta}-sheet content increases in this region upon pH change from neutral to acidic. We hypothesized that the conformations with high {beta}-sheet content could act as aggregation-prone (N*) states and nucleate the aggregation process. We validated our hypothesis by performing dimer simulations starting from N* and non-N* states. We show that simulations initiated using N* states as initial conformations form dimers within 1.5 s, whereas the non-N* states do not form dimers within this timescale. This study contributes to understanding the general principles of pH-induced IDP aggregation. The main result upon pH change from neutral to acidic, the intermediate region of proT is responsible for aggregation due to an increase in its {beta}-sheet forming propensity and forms the fibril core can be verified by experiments. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/497626v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@19971beorg.highwire.dtl.DTLVardef@fa98bforg.highwire.dtl.DTLVardef@422e5borg.highwire.dtl.DTLVardef@f18187_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Salt Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins

Salts modulate the behavior of intrinsically disordered proteins (IDPs). In low ionic strength solutions, IDP conformations are primarily perturbed by the screening of electrostatic interactions, independent of the identity of the salt. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, in high ionic strength solutions, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. Using a coarse-grained simulation model for the IDPs and experimentally measured water to salt solution transfer free-energies of various chemical groups, we studied the salt-specific transitions induced in the IDPs conformational ensemble. We probed the effect of three different salts, ranging from protective osmolyte to denaturant, on five IDPs belonging to various polymer classes classified based on charge content. The transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP polymer class. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through liquid-liquid phase separation.

biophysics↗