Biology subjects

Thirumalai, D.

Publications and source records attributed to Thirumalai, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Interchain base-stacking and spermine bridges govern ssDNA condensation and reentrant transitions

Polyvalent-cation-induced condensation and reentrant transition in double-stranded DNA are classically described by backbone electrostatics. Whether the same principles govern single-stranded DNA, whose solvent-exposed bases can interact within and between chains to form complex phases, is unknown. Here, we employ simulations and experiments to show that the tetravalent cation spermine (Spm4+) drives two equilibrium transitions in poly(dT) and poly(dA). The onset of phase separation, resulting in thermodynamic equilibrium between the dispersed low-density phase and high density coacervate, occurs at a low sequence independent Spm4+ concentration and is primarily driven by charge balance between phosphate groups and Spm4+. Strikingly, the condensed phases are stabilized by at most 1.5 (poly dT) and 2.5 (poly dA) bridging Spm4+ per chain. The ssDNA chains condense to form fluid-like networks without chain collapse. The fluidity of chains in the dense phases is confirmed by fluorescence recovery after photobleaching experiments. Both simulations and experiments show that the range of spermine concentration over which phase coexistence persists is sequence dependent and nearly threefold wider in poly(dA). At higher sequence dependent spermine concentrations, a reentrant phase, characterized by dissolution of the coacervates, emerges. The transition to the reentrant phase occurs when the number of bridging Spm4+ molecules vanishes at high sequence dependent spermine concentration. The combination of experiments and simulations show that the two phase transitions in ssDNA are driven by an interplay of stacking and electrostatic interactions.

biophysics↗

bioRxiv2026

Small Intestinal Submucosa (SIS)-dECM Bioink with Extrusion-Induced Collagen Organization for Tympanic Membrane Tissue Engineering

Tympanic membrane perforations remain a common clinical problem, and although surgical intervention through tympanoplasty achieves high success rates, it is associated with donor-site morbidity, surgical complexity and limited restoration of the native radial and circumferential collagen architecture. In this study, 3D extrusion printing was utilized to create an active scaffold and attempt to promote collagen organization through shear-mediated structural alignment. An alginate-carboxymethyl cellulose (CMC) hydrogel with bovine SIS-dECM was prepared and investigated for its suitability as a bioink alternative to tympanoplasty grafts. The physiochemical, rheological and printability characteristics of the hydrogel were assessed. Successful decellularization was confirmed by histological analysis. The incorporation of the SIS-dECM into the hydrogel led to increased swelling, lower apparent viscosity, yield stress and flow stress while maintaining favourable printability and filament stability. Polarized optical microscopy was also used to study the influence of printing speed on the alignment of collagen to mimic the native tympanic membrane radial collagen architecture. Compared with the cast controls, the printed samples presented stronger birefringence signals. Biological evaluation demonstrated that the 15% dECM hydrogel exhibited the highest live cell area percentage and live/dead ratio after 48 h. In addition, the chick chorioallantoic membrane assay demonstrated that the dECM-containing hydrogels improved vascular density. The findings establish a printable, biologically active dECM bioink capable of generating bulk collagen organization through extrusion printing as a platform for tympanic membrane regeneration.

bioengineering↗

bioRxiv2026

Molecular origins of heterogeneous aging and spatial organization in RNA condensates

The molecular origins of aging of biomolecular condensates, which play a central role in cellular organization, is poorly understood. Here, we use coarse-grained molecular simulations to investigate how RNA sequence and chain connectivity govern condensate aging over extended timescales. Condensates formed by CAG-repeat RNA undergo pronounced aging characterized by progressive dynamical slowing, loss of ergodicity, and the emergence of two distinct relaxation timescales. Aging proceeds heterogeneously in space, giving rise to a dynamically arrested, solid-like core surrounded by a more fluid shell. We demonstrate that aging is driven by sequence-encoded base pairing that favors RNA expansion, alignment and the formation of a dense interchain interaction network. These structural changes lead to increased topological entanglement, stabilizing long-lived conformations and reinforcing dynamic arrest in the condensate interior. Strikingly, a scrambled sequence with identical composition remains largely liquid-like. Our results establish RNA sequence patterning as a key determinant not only of phase separation but also of condensate aging and spatial organization. These findings provide a molecular framework for understanding the persistence and solidification of repeat RNA assemblies observed in diseases and suggest general physical principles by which entangled polymer networks drive aging in biomolecular condensates.

biophysics↗

bioRxiv2026

Shear effects in active models of normal and cancer cells

Mechanical properties of biological tissues, driven by passive and active forces, play a vital role in several processes ranging from development to cancer metastasis. However, the dynamical responses of cells in tissues, subject to mechanical deformations such as shear and the associated rheological properties, are not well characterized. Here, we use three-dimensional agent-based models for normal and cancer tissues to investigate their responses to simple shear as a function of cell stiffness and stochastic active forces. In the normal epithelium, with uniform strength of active force, the yield stress as a function of shear rate follows the Herschel-Bulkley form over a range of cell volume fraction. Strikingly, the shear rate dependence and the elasticity-dependent changes in the yield stress fall on master curves upon suitable scaling. To model cancer-like behavior, a certain fraction (Np) of cells was chosen to have enhanced activity and decreased stiffness. As Np increases, the extent of collective cell movement decreases, transitioning from affine (collective) to non-affine (individualistic) movement, a finding that is in accord with imaging experiments. Simulations of a model of a stiff solid tumor, with radius Rs embedded in normal tissue, show that as Rs increases, the yield stress increases. Interestingly, the cells migrate collectively as Rs increases. A Gaussian Mixture Model (GMM) and a mean field theory quantitatively account for the simulation as well as experimental results on cancerous, non-cancerous, and a mixture of these two types. The combined theoretical and experimental study establishes that heterogeneity in stiffness and activity determines non-affine movements in normal and cancer tissues.

biophysics↗

bioRxiv2026

Persistence length of short homopolymeric single-stranded DNA sequences in polyvalent cations

We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length (lp) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that lp for dT30 (T is thymine) and dA30 (A is adenine) is quantitatively fit using [Formula] ([Formula] is the bare persistence length,{lambda} is a dimensionless constant, and{kappa} -1 is the inverse Debye length) in the divalent cations Mg2+ and Ca2+. The dependence of lp on{kappa} is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Huckel potential. The [Formula] values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, lp is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of Spm4+, rationalizes the simulation results. The predicted dependence of lp in spermine awaits experimental test.

biophysics↗

bioRxiv2026

Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds

Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that condensin, a member of the SMC family involved in mitosis, takes occasional backward steps, thus coughing up the gains in the length of the extruded loop. To reveal the mechanism of the forward and backward steps simultaneously, we developed a theory using the stochastic kinetic model and the scrunching mechanism for LE. The calculations quantitatively account for the measured force-dependent step size and dwell time distributions in both the directions. By postulating the existence of an intermediate state in the ATP-driven cycle that is poised to take a forward or a backward step, we predict that its lifetime increases as the external mechanical force increases till a critical value and subsequently decreases at higher forces. The surprising finding of lifetime increase in an active motor, at sub-piconewton forces, is the characteristic of catch bonds, known in force-induced rupture of several passive protein complexes. The identification of catch bond-like states in condensin not only expands our understanding of LE but also highlights the significance of mechanical forces in regulating genome organization.

biophysics↗

bioRxiv2026

Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer

Hi-C, and more recently Micro-C, experiments suggest that genome organization is altered as normal cells become cancerous, often resulting in aberrant gene expression. In prostate cancer, there is evidence that large topologically associating domains in normal cells split and are accompanied by shifts in the epigenetic marks from inactive to active states. However, it is unclear whether changes in genome organization alone can account for the gene expression increase in cancer cells. By combining polymer physics concepts and data-driven modeling, we first calculated an ensemble of three-dimensional (3D) chromatin structures using only the 2D contact map as input. The enhancer-promoter (E-P) distance distributions for the overexpressed Androgen Receptor (AR) and Forkhead Box Protein A1 (FOXA1) are broad, with mean values exceeding the threshold for direct E-P contact. Importantly, the average E-P distances decrease in the cancer cells, compared to normal cells in the AR locus, whereas in FOXA1 they are roughly constant or increase modestly. Similarly, the number of multiway contacts increases as cancer progresses across cancer cell lines in the AR locus. In contrast, the number of multiway contacts in FOXA1 is similar in normal and cancer cells. Because the 3D characteristics do not explain the enhanced gene expression in cancer cells, we developed Activity-by-Multiway-Contact (AMC) Model that integrates the multiway contacts with enhancer biochemical activity. The AMC model provides a plausible mechanism for the overexpression of both AR and FOXA1 in prostate cancer. Moreover, using Micro-C data for breast cancer, we show that the number of multiway enhancer-promoter contacts increases in four of five genes studied. When multiway contacts are combined with biochemical activity, changes in gene expression found in the experiment, positively correlate with the AMC score. The predictions of the AMC model not only account for overexpression of genes in prostate and breast cancer but also provide a basis for understanding gene expression variations in other genes as well.

genomics↗

bioRxiv2025

Epigenetic state encodes locus-specific chromatin mechanics

Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory to infer locus-specific viscoelasticity from three-dimensional genome organization. Using chromatin structures derived from contact maps, we calculate frequency-dependent storage and loss moduli for individual loci and establish that the mechanical properties are determined both by chromatin epigenetic marks and organization. On large length scales, chromatin exhibits Rouse-like viscoelastic scaling, but this coarse behavior masks extensive heterogeneity at the single-locus level. Loci segregate into two mechanical subpopulations with distinct longest relaxation times: one characterized by single-timescale and another by multitimescale relaxation. The multi-timescale loci are strongly enriched in active marks, and the longest relaxation time for individual loci correlates inversely with effective local stiffness. Pull-release simulations further predict a time-dependent susceptibility: H3K27ac-rich loci deform more under sustained forcing yet can resist brief, large impulses. At finer genomic scales, promoters, enhancers, and gene bodies emerge as "viscoelastic islands" aligned with their focal interactions. Together, these results suggest that chromatin viscoelasticity is an organized, epigenetically coupled property of the 3D genome, providing a mechanistic layer that may influence enhancer-promoter communication, condensate-mediated organization, and response to cellular mechanical stress. The prediction that locus-specific mechanics in chromatin are controlled by 3D structures as well as the epigenetic states is amenable to experimental test.

biophysics↗

bioRxiv2025

Lever arm Flexibility Controls the extent of (Un)coupling to the Motor Domain in Myosin Motors

Dimeric myosin motors, with both heads simultaneously bound to filamentous actin, are in a frustrated conformation. The lever arm of each head would prefer to orient forward, but the inter-head tension hinders the relaxation to the state favored by a myosin monomer. Here, we investigate theoretically the impact of lever arm stiffness and coupling to the head domain using a polymer model. The theory for MV and MVI qualitatively reproduce the salient experimental observations. Furthermore, we construct chimeras in which the lever arm and head domains are swapped, and predict that the fluctuations of the LH lever arm of MVI are strongly impacted by the stiffness of the lever arm. Finally, by continuously and independently varying the lever arm persistence length and the strength of its coupling to the head domain we predict their roles in altering the average geometry and conformational flexibility of the dimer. We explore conditions under which LH lever arm flexibility and angle with respect to F-actin lead to coupling to the motor domain. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/669198v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1c27772org.highwire.dtl.DTLVardef@3015a9org.highwire.dtl.DTLVardef@de48eaorg.highwire.dtl.DTLVardef@1853176_HPS_FORMAT_FIGEXP M_FIG For Table of Contents Use Only C_FIG

biophysics↗

bioRxiv2025

Protein Folding accompanied by disulfide bond formation drives glutenin polymerization into multidimensional gluten networks

Wheat flour dough, which is routinely used to make bread, pasta and noodles, can be stretched several thousand-fold without rupture. The molecular basis of this extraordinary property arises due to the ability to crosslink glutenin subunits, the major constituent of dough, into linear and branched elastic networks. The mechanism by which the glutenin subunits self-assemble and polymerize is unknown. Here, we show, using mass spectrometry, confocal imaging and molecular dynamics simulations that structuring of two hydrophobic residues, phenylalanine and tyrosine, in the core region of the monomeric glutenin 1Dx5 N-terminal domain (1Dx5-NTD) initiates inter molecular interactions and network formation. Upon folding of monomeric 1Dx5-NTD, two cysteine residues (Cys10 and Cys40) form an intramolecular disulfide bond and poises the third cysteine (Cys25) to engage in inter molecular crosslink with other glutenin subunits. Propagation of such a disulfide linkage pattern results in the formation of a cohesive linear gluten network. In alternate pathways, crosslinking of Cys10 with Cys25 with a third glutenin subunit results in the creation of a junction, which drives the formation of a three-dimensional network. The disulfide patterns in the networks accord well with the measured chemical reactivity of each cysteine residue and the solvent accessibility of the associated side chains during 1Dx5-NTD interactions. Our study shows that the diversity in the folding of a single glutenin subunit that exposes the third cysteine to the solvent is the key event that initiates polymerization and directs the formation of networks with differing architecture. Significance statementGlutenin proteins polymerize to form intricate molecular networks that support the expansion of dough by several thousand-fold. Although network formation occurs spontaneously, the polymerization mechanism is unknown. There are multiple cysteine residues in glutenin that can form intra and intermolecular disulfide bonds. Multiple experimental techniques and molecular dynamics simulations are used to show that folding of glutenin, initiated by two hydrophobic residues, exposes cysteines that are poised to form intermolecular disulfide bonds. The disulfide crosslinking pattern, determined by the initial folding process, dictates the creation of a linear or branched network. The study demonstrates that the propensity to form linear or branched networks is encoded by the diversity of the disulfide patterns created at the level of monomeric folding.

biophysics↗

bioRxiv2025

Development and Characterization of 3D Printable Caprine derived dECM/DAS Crosslinked Hydrogels for Tissue Engineering Applications

The current hydrogels and crosslinkers used in tissue engineering often suffer from limited bioactivity and insufficient mechanical strength, which hinders effective tissue regeneration. To overcome these limitations, this study aims to develop a tunable hydrogel combining caprine-derived decellularized Extracellular Matrix (dECM) and dialdehyde starch (DAS) for potential use in tissue engineering. The dECM bioink was biohybridized with varying concentration of DAS crosslinker to create dECM/DAS hydrogels and its physicochemical and biological properties were characterized. FTIR analysis confirmed DASs successful formation through a strong carbonyl peak at 1732 cm-1. The rheological characterization indicates the shear-thinning behavior for dECM/DAS. The storage modulus was higher than that of the loss modulus in all the concentrations of DAS crosslinked hydrogel compared to dECM hydrogel. The gelation kinetics show that dECM and DAS crosslinked hydrogel begin to gel at temperatures above 25{degrees}C, which is suitable for developing implantable hydrogel. The hemocompatiblity study shows that the dECM and dECM/DAS hydrogels are non-hemolytic at less than 2%. Overall, this naturally derived dECM/DAS hydrogel demonstrates the potential to be utilized for tissue engineering applications.

bioengineering↗

bioRxiv2025

RNA structural complexity dictates its ion atmosphere

Electrostatic interactions mediated by the surrounding ions govern virtually every facet of RNA behavior. Most studies have focused on rigid, well-folded motifs, leaving the structurally heteregeneous, and biologically ubiquitous, flexible RNAs underexplored. To address this gap, we performed molecular dynamics simulation of three RNAs spanning the structural continuum: an unstructured poly-uridylic tract (rU30), a semiflexible cytosine-adenine-guanine (CAG) repeat, and the tightly folded Beet Western Yellow Virus (BWYV) pseudoknot. Despite carrying nearly identical net charge, their ion atmospheres diverge strikingly. rU30 envelops itself in a diffuse Mg2+ environment retained through two or more hydration shells, whereas the CAG repeat and pseudoknot favor more localized outer-sphere Mg2+ binding. In contrast, Ca2+ tends to form inner-sphere contacts with all three RNAs, regardless of their folds. Remarkably, the diffuse ion clouds around unstructured RNAs extend farther into solution than that of the folded RNAs, significantly broadening their electrostatic sphere of influence. Nonetheless, the ion exchange kinetics remain virtually unchanged, demonstrating a surprising decoupling between spatial distribution and dynamical turnover. Our findings reveal RNA structural flexibility as a powerful lever for tuning ionic screening, with important implications for biomolecular recognition, RNA-driven phase separation, and physical properties of RNA-rich condensate. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/654961v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@12e78aborg.highwire.dtl.DTLVardef@1f4328borg.highwire.dtl.DTLVardef@122561dorg.highwire.dtl.DTLVardef@143c5ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Controlling the morphologies and dynamics in three-dimensional tissues

A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the tissue scale, we created a minimal three dimensional model in which short-range repulsive elastic forces account for cell-cell interactions. Self-propulsion is modeled as active uncorrelated random stochastic forces, with strength {micro}, that act on individual cells and is the only source of cell motility. Strikingly, variations in polydispersity in cell size ({Sigma}) and cell elasticity (E), results in the formation of a variety of distinct "phases", driven entirely by {micro} . At low E, the tissue behaves like a liquid, at all values of {Sigma}, whereas at high E and {Sigma}, it has the characteristics of a glass. The tissue crystallizes at low {Sigma} provided E exceeds a critical value. Over a narrow range of E and {Sigma}, that lies between the boundaries of the liquid and glass phase, the effective viscosity increases like in a glass as the cell density increases and saturates as the cells are compressed beyond a certain value, creating the viscosity saturation (VS) phase. The VS phase does not form in systems at finite temperature in which the dynamics satisfies the Fluctuation Dissipation Theorem. In the glass phase, the tissue exhibits aging (relaxation times depend on the waiting time) behavior at high E values. Our findings provide a framework for designing tissues with tunable material properties by controlling the physical characteristics of cells.

biophysics↗

bioRxiv2025

Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma

The low complexity domain of Fused in Sarcoma (FUS-LC consisting of 214 residues) undergoes phase separation, resulting in a dense liquid-like phase that forms early and slowly matures to reach ordered gel-like state on long time scales. Upon maturation, core-1, comprising of the 57 residues (39-95) in the N-terminus become structured, resulting in the formation of a non-polymorphic fibril. The truncated FUS-LC-C (residues 110-214) construct forms a fibril in which core-2 (residues 112-150) adopts a {beta}-sheet structure. Using coarse-grained monomer SOP-IDP model simulations of FUS-LC, we predict that residues 155-190 in the C-terminal (core-3) form rapidly, followed by core-2, and finally core-1. The time scale of formation of the cores and their stabilities are inversely correlated, as anticipated by the Ostwalds rule of stages. Unbiased multichain simulations show that the chemical potentials in the two phases are equal and the calculated densities of the dense and dilute phases are in agreement with experiments. The dense phase, which forms by a nucleation mechanism, coarsens over time by a process that is reminiscent of Ostwald ripening. AlphaFold predictions of the core-3 structure and the simulations show that {beta}-strand emerges in the core-3 region early during the droplet formation, and drives the initiation of FUS-LC assembly. The techniques introduced here are general and could be used to probe assembly of other IDPs such as TDP-43, which shares many features with FUS-LC.

biophysics↗

bioRxiv2025

Water-mediated interactions between glycans are weakly repulsive and unexpectedly long-ranged

Glycans on the cell surface play an essential role in mediating cell-cell interactions as well as immune response. Despite their importance, interactions between them have not been fully characterized. Here, we reveal, using all-atom molecular dynamics simulations and free energy calculations, that water-mediated interactions between a pair of N-glycans without net charge are weakly repulsive with a range that exceeds their sizes. Unexpectedly, the effective glycan-glycan interactions decay logarithmically as the separation between them increases. Strikingly, this finding coincides exactly with the predicted interaction, which is entropic in origin, between two star polymers, consisting of long flexible polymers grafted onto colloidal particles. The weak repulsive interaction, which extends beyond the size of a glycan, is sensitive to the relative orientation of the glycans. The effective long-range repulsive interaction vanishes if the charges on water are turned off, thus establishing that electrostatic interactions, arising in part due to the persistent hydrogen bonds between water and the glycans, are responsible for the inter-glycan repulsion.

biophysics↗

bioRxiv2025

Static Three-Dimensional Structures Determine Fast Dynamics Between Distal Loci Pairs in Interphase Chromosomes

Live cell imaging experiments have shown that, although eukaryotic chromosomes are compact, the distal dynamics between enhancers and promoters are unexpectedly rapid and cannot be explained by standard polymer models. The discordance between the compact static chromatin organization (structure) and the relaxation times (dynamics) is a conundrum that violates the expected structure-function relationship. To resolve the puzzle, we developed a theory to predict chromatin dynamics by first calculating the accurate three-dimensional (3D) structure using static Hi-C contact maps or fixed-cell imaging data. The calculated 3D coordinates are used to accurately forecast the two-point dynamics reported in recent experiments that simultaneously monitor chromatin dynamics and transcription. Strikingly, the theory not only predicts the observed fast enhancerpromoter dynamics but also reveals a novel scaling relationship between two-point relaxation time and genomic separation that is in near quantitative agreement with recent experiments. The theory also predicts that cohesin depletion enhances single-locus diffusion. The acceleration of chromatin loci diffusion upon cohesin depletion are explained in terms of structure-based centrality measure used in graph theory. Our framework shows that chromatin dynamics can be predicted based solely on static experimental data, reinforcing the concept that the three-dimensional structure determines their dynamic behavior. The generality of the theory opens new avenues for exploring chromatin dynamics, especially transcriptional dynamics, across different biological contexts.

biophysics↗

bioRxiv2024

RNA encodes physical information

Most amino acids are encoded by multiple codons, making the genetic code degenerate. Synonymous mutations affect protein translation and folding, but their impact on RNA itself is often neglected. We developed a genetic algorithm that introduces synonymous mutations to control the diversity of structures sampled by an mRNA. The behavior of the designed mRNAs reveals a physical code layered in the genetic code. We find that mRNA conformational heterogeneity directs physical properties and functional outputs of RNA-protein complexes and biomolecular condensates. The role of structure and disorder of proteins in biomolecular condensates is well appreciated, but we find that RNA conformational heterogeneity is equally important. This feature of RNA enables both evolution and engineers to build cellular structures with specific material and responsive properties.

biophysics↗

bioRxiv2024

Impact of Guanidine Hydrochloride on the shapes of Prothymosin-α and α-Synuclein is dramatically different

The effects of Guanidine Hydrochloride (GdmCl) on two Intrinsically Disordered Proteins (IDPs) are investigated using simulations of the Self-Organized Polymer-IDP (SOP-IDP) model. The impact of GdmCl is taken into account using the Molecular Transfer Model(MTM). We show that, due to dramatic reduction in the stiffness of the highly charged Prothymosin- (ProT) with increasing concentration of GdmCl ([GdmCl]), the radius of gyration (Rg) decreases sharply till about 1.0M. Above 1.0M, ProT expands, caused by the swelling effect of GdmCl. In contrast, Rg of -Synuclein (Syn) swells as continuously as [GdmCl] increases, with most of the expansion occurring at concentrations less than 0.2M. Strikingly, the amplitude of the Small Angle X-ray Scattering (SAXS) profiles for ProT increases till [GdmCl]{approx} 1.0M and decreases beyond 1.0M. The [GdmCl]-dependent SAXS profiles for Syn, which has a pronounced bump at small wave vector (q [~] 0.5nm-1) at low [GdmCl] ([≤] 0.2M), monotonically decrease at all values of [GdmCl]. The contrasting behavior predicted by the combination of MTM and SOP-IDP simulations may be qualitatively understood by modeling ProT as a strongly charged polyelectrolyte with nearly uniform density of charges along the chain contour and Syn as a nearly neutral polymer, except near the C-terminus where the uncompensated negatively charged residues are located. The precise predictions for the SAXS profiles as a function of [GdmCl] can be readily tested.

biophysics↗