Biology subjects

Mondal, B.

Publications and source records attributed to Mondal, B..

16 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

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↗

bioRxiv2025

Deciphering the intra-tissue specific Collagen PTMs site-specific heterogeneity in Human Adrenal extracellular-matrix

The human adrenal is one of the pivotal glands of the endocrine system. Recently, the extracellular matrix (ECM) of the adrenal capsule and cortex was explored by dividing them into two fractions: outer (OF) and inner (IF). A significant variation in the levels of ECM proteins, including collagens, was documented. During the biosynthesis of collagen, it undergoes a plethora of PTMs exhibiting crucial roles such as cell-matrix interaction, adhesion, crosslinking, stability, etc. However, the site-specific identification and characterization of collagen PTMs remained challenging and is unknown for the human adrenal gland. We applied our in-house developed proteomics pipeline to identify several PTMS in 25 collagen chains from human adrenal-ECM. In the entire collagenome, we identified a total of 963 4-hydroxyproline (4-HyP), 201 3-hydroxyproline (3-HyP), 105 hydroxylysine (HyK), 17 galactosyl-hydroxylysine (G-HyK), and 35 glucosyl galactosyl-hydroxylysine (GG-HyK) sites. Although the site-specificity of collagen PTMs (3-HyP, HyK, G/GG-HyK) across fractions is conserved, the occupancies were different in a site-specific manner. Classically, a fully 3-hydroxylated site (P1164) of COL1A1 associated with osteogenesis imperfecta was found to be approximately fully hydroxylated ([~]99%) across fractions. Similarly, we also looked at the microheterogeneity of lysine modifications on one lysine residue (K862) of COL1A1. We observed that the hydroxylation level was higher in OF, while glycosylation levels were higher in IF. This may suggest a change in the crosslinking of collagen I across both fractions. Further, our analysis revealed much higher site-specific O-glycosylation in basement membrane collagen-IV, potentially facilitating the secretion of steroids from the adrenal gland. For the first time, we have annotated the collagen PTMs, developed a COL1A1 PTM map, and quantitated site-specific PTMs in the human adrenal gland. Taken together, this work revealed that intra-tissue-specific site-specific PTM collagen heterogeneity and lay the foundation for understanding their role in region-specific functions.

biochemistry↗

bioRxiv2025

Molecular insights into inhibitor action on a key bacterial metabolic enzyme Cystathionine β-Synthase

Tuberculosis (TB) remains a major global health threat, with Mycobacterium tuberculosis (Mtb) infecting nearly a quarter of the global population. Drug-resistant TB and HIV-TB co- infections emphasize the need for novel therapeutic approaches targeting essential metabolic pathways. Here, we investigated Mtb cystathionine {beta}-synthase (MtbCBS), a PLP-dependent enzyme critical for sulfur metabolism and redox regulation, owing its potential as a therapeutic target. We present the first high-resolution cryo-EM structure of MtbCBS bound to aminooxyacetic acid (AOAA), and employed molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, and comparative inhibition studies to reveal the molecular basis and determinants governing irreversible PLP-enzyme inhibition. Our Cryo-EM structural analysis revealed two highly conserved active-site residues, T75 and Q147, critically stabilizing the inhibitor complex. Through molecular mimic studies, we demonstrated the precise structural factors and electronic features critical for inhibition efficiency. These findings provide the first mechanistic rationale for PLP enzyme inhibition and offer a generalizable framework for designing covalent inhibitors targeting PLP-dependent enzymes implicated in infectious diseases, cancer, and neurological disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/662948v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@195c7c7org.highwire.dtl.DTLVardef@6ee0c8org.highwire.dtl.DTLVardef@1679dfborg.highwire.dtl.DTLVardef@1b4e000_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Proposed mechanism of MtbCBS inhibition by AOAA. Proposed mechanism of action of AOAA illustrated through a graphical representation. The cartoon shows the domains of MtbCBS. Tetrameric structure of MtbCBS with active site highlighted (in red dashes). Enlarged view indicating the PLP-AOAA blocked intermediate interacting with residue Q147. Reaction scheme depicting the previous missing understanding of active site residue role in -elimination. Schematic representation of AOAA inhibition mechanism in the catalytic cycle of MtbCBS. Reactions were drawn using ChemDraw. The proposed scheme highlights that AOAA (highlighted Red) binding is stabilized by nearby residues Q147 and T75, leading to the formation of PLP-AOAA covalent adduct, and substrates (highlighted green) were incapable of reverting the suicidal inhibition. The directionality and reversibility were mentioned for each step. C_FIG

biophysics↗

bioRxiv2025

Immunogenicity and Structural Features of a Stabilized Clade-C HIV-1 Env Derived from a Pediatric Elite-neutralizer

The envelope (Env) glycoprotein derived from circulating viruses in elite-neutralizers (who naturally develop broadly neutralizing antibodies (bNAbs)), serves as potential template for HIV-1 vaccine design. Herein, we report the structure and immunogenicity of soluble clade-C HIV-1 Env trimer (330) derived from a pediatric elite-neutralizer (AIIMS_330). Using SOSIP, NFL and ferritin-nanoparticle (NP) platforms, we engineered immunogens that preserved native-like Env conformation, exhibited high thermostability and nanomolar affinity for diverse bNAbs, with minimal reactivity to non-neutralizing antibodies. Cryo-EM structure solved at 5 [A] resolution of 330-SOSIP trimer-autologous bNAb 44m complex revealed interactions at GDIR motif, N332 supersite along with additional contacts at E293, K337, K446 and glycans N326, N442, N448, as compared to our previously reported BG505-44m structure. Rabbit immunizations with soluble and NP-displayed formats elicited autologous, and heterologous neutralization of tier-1 clade-C viruses. Herein we define a structurally resolved HIV-1 clade C Env that supports multivalent vaccine strategies and provides mechanistic insights toward rational HIV-1 immunogen design.

immunology↗

bioRxiv2024

Crosstalk between plasma membrane and Staphylococcus α-hemolysin during oligomerization

The infectious microbe Staphylococcus aureus releases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction interfaces between the host cell and toxin were merely explored. Herein, we monitored the active oligomeric states facilitated membrane disruption processes such as lysis, and protrusion in the plasma membrane and lipid membrane. Furthermore, necrosis was triggered in the neutrophil-like cells upon synergistic binding and oligomerization of the monomeric -HL. Additionally, we solved RBC membrane stabilized structure of different conformational states of this {beta}-PFT using a single-particle cryo-EM. We further confirmed that internal membrane fluidity was the deterministic factor associated with the formation of intermediate pre-pores, heptameric pore-like, and complete pore species. Together, this is the first study to unveil the structure-function analysis of pre-pore to pore transition of any small {beta}-PFT during its crosstalk with the cell. HighlightsO_LI-HL promotes necrosis in HL60 cells and lysis of shorter lipid bilayer region. C_LIO_LICryo-EM of small PFT in the cellular environment. C_LIO_LIStructural characterization of heptameric pore, pore-like, and pre-pore complex in the presence of RBCs. C_LIO_LIBilayer phase behavior (Ld/Lo) governs different conformational and geometrical variants of -HL. C_LI

biophysics↗

bioRxiv2023

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

Interactions between divalent cations (Mg2+ and Ca2+) and highly charged single stranded DNA (ssDNA) and double stranded DNA (dsDNA), as well as stacking interactions, are important in a variety of problems, including nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Towards this end, we created a computational model that explicitly takes into account monovalent and divalent ions, within the framework of the sequence-dependent coarse-grained Three Interaction Site (TIS) model for DNA. Molecular simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, in a buffer containing Na+ and Cl-, with varying amounts of the divalent cations, are used to show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the Small Angle X-ray Scattering (SAXS) profiles, which are also in excellent agreement with experiments. Strikingly, recapitulation of all the experimental findings was achieved without adjusting any of the parameters in the energy function to fit the data. At a molecular level, we find that Mg2+ and Ca2+ sense the differences between the major and minor grooves in dsDNA even though they are masked in ion-counting and SAXS experiments. The smaller Mg2+ binds predominantly to the minor grooves and phosphate groups whereas Ca2+ binds specifically only to the minor groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. In contrast, the near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations.

biophysics↗

bioRxiv2023

A cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase interacts with begomovirus capsid proteins and modulates virus retention within its vector

Begomoviruses are whitefly-transmitted ss-DNA viruses infecting dicotyledonous plants and contribute to major economic losses to global crop production. Invasion and establishment of an aggressive species of B. tabaci, known as the B cryptic species, has severely constrained vegetable production in the southeastern and southwestern United States. Disruption of genes/pathways critical for whitefly mediated transmission can be effective for the management of begomoviruses. In this study, yeast two hybrid (Y2H)-based screening of B. tabaci cDNA library identified a cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase (PDE4) of the whitefly as an interacting partner with capsid proteins (CPs) of old- and new-world begomoviruses. Interactions of PDE4 with begomovirus CPs were validated by GST-pull-down assays, co-immunoprecipitation, and co-immunolocalization in whitefly midgut. The PDE4 family of enzymes hydrolyze cAMP and regulate intracellular cAMP levels. This study revealed that elevation of cAMP within whitefly by chemically inhibiting or gene (PDE4) silencing resulted in increased retention and transmission of begomoviruses. Similarly, decreased cAMP levels resulted in reduced begomovirus retention. The results of this study demonstrate that whitefly mediated transmission of begomoviruses is regulated by intracellular cAMP by unknown mechanisms. ImportanceBegomoviruses, transmitted by the sweetpotato whitefly, (Bemisa tabaci Gennadius), are the causal agents of many economically important plant virus diseases. Lack of host plant resistance against begomoviruses, high whitefly abundance, and whiteflys ability to develop insecticide resistance rapidly often renders commonly used management practice ineffective. This study demonstrates how begomovirus retention within whitefly and its transmission can be modulated by altering cAMP expression of its insect vector. Naturally occurring bio-pesticides that target insect cAMPs are known. Our findings can lead to alternative strategies for the management of begomoviruses by targeting whitefly cAMP using chemicals, botanicals, or RNAi-based insecticides.

molecular biology↗

bioRxiv2023

Brewing COFFEE: a sequence-specific coarse-grained energy function for simulations of DNA-protein complexes

DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength ({lambda}DNAPRO) of the DNA-protein contact potential. For an optimal choice of{lambda} DNAPRO, the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/544064v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1190c18org.highwire.dtl.DTLVardef@169098eorg.highwire.dtl.DTLVardef@f24e75org.highwire.dtl.DTLVardef@1fd0bd1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

The MLL3/4 complexes and MiDAC act antagonistically as genome-wide regulators of H4K20ac to control a specific gene expression program

The mitotic deacetylase complex MiDAC has recently been shown to play a vital physiological role in embryonic development and neurite outgrowth. However, how MiDAC functionally intersects with other chromatin-modifying regulators is poorly understood. Here, we describe a physical interaction between the histone H3K27 demethylase UTX, a complex-specific subunit of the enhancer-associated MLL3/4 complexes, and MiDAC. We demonstrate that UTX bridges the association of the MLL3/4 complexes and MiDAC by interacting with ELMSAN1, a scaffolding subunit of MiDAC. Our data shows that MiDAC constitutes a negative genome-wide regulator of H4K20ac, an activity which is counteracted by the MLL3/4 complexes. MiDAC and the MLL3/4 complexes co-localize at many genomic regions, that are enriched for H4K20ac and the enhancer marks H3K4me1, H3K4me2 and H3K27ac. We find that MiDAC antagonizes the recruitment of the MLL3/4 complexes to negatively regulate H4K20ac, H3K4me2 and H3K27ac resulting in transcriptional attenuation of associated genes. In summary, our findings provide a paradigm how the opposing roles of chromatin-modifying components, such as MiDAC and the MLL3/4 complexes, balance the transcriptional output of specific gene expression programs.

molecular biology↗

bioRxiv2021

Redox state and cellular uptake of copper is regulated by the N-terminus of human Copper Transporter-1

Copper(I) is essential for all life forms. Though Cu(II) is most abundant state in environment, its reduction to Cu(I) is prerequisite for bio-utilization, by a mechanism that is uncharacterized. We show that in human Copper Transporter-1, two amino-terminal methionine-histidine clusters and neighbouring aspartates distinctly binds Cu(II) and Cu(I) preceding its import. The endocytosis of hCTR1 from basolateral membrane of polarized epithelia to Common-Recycling-Endosomes is dependent on copper reduction and Cu(I) coordination by methionines. The transient binding of both Cu(II) and Cu(I) during the reduction process facilitated by aspartates acts as another crucial determinant of hCTR1 endocytosis. Mutating 7Met-Gly-Met9 and Asp13 abrogates copper uptake and endocytosis that is correctable by reduced and non-reoxidizable Cu(I). Histidines clusters are crucial for hCTR1 functioning at limiting copper. Finally, we show that two N-terminal His-Met-Asp clusters exhibit functional complementarity in regulating Cu(I)-induced hCTR1 endocytosis. We propose a mechanistic model where His-Met-Asp residues of amino-terminal hCTR1 coordinates copper and maintains its reduced state crucial for uptake.

cell biology↗

bioRxiv2021

Energy Landscape of Ubiquitin is Weakly Multidimensional

Single molecule pulling experiments report time-dependent changes in the extension (X) of a biomolecule as a function of the applied force (f). By fitting the data to one-dimensional analytical models of the energy landscape, the hopping rates between the folded and unfolded states in two-state folders, the height and the location of the transition state (TS) can be extracted. Although this approach is remarkably insightful, there are cases for which the energy landscape is multidimensional (catch bonds being the most prominent). To assess if the unfolding energy landscape in small single domain proteins could be one dimensional, we simulated force-induced unfolding of Ubiquitin (Ub) using the coarse-grained Self-Organized Polymer-Side Chain (SOP-SC) model. Brownian dynamics simulations using the SOP-SC model reveal that the Ub energy landscape is weakly multidimensional (WMD) governed predominantly by a single barrier. The unfolding pathway is confined to a narrow reaction pathway that could be described as diffusion in a quasi 1D X-dependent free energy profile. However, a granular analysis using the Pfold analysis, which does not assume any form for the reaction coordinate, shows that X alone does not account for the height, and more importantly, the location of the TS. The f-dependent TS location moves towards the folded state as f increases, in accord with the Hammond postulate. Our study shows that, in addition to analyzing the f-dependent hopping rates, the transition state ensemble must also be determined without resorting to X as a reaction coordinate in order to describe the unfolding energy landscapes of single domain proteins, especially if they are only WMD. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/437368v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1fd1480org.highwire.dtl.DTLVardef@4d12c8org.highwire.dtl.DTLVardef@c4839org.highwire.dtl.DTLVardef@59aab9_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2020

Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation

Human{gamma} D (H{gamma}D) and{gamma} C (H{gamma}C) are double domained crystallin (Crys) proteins expressed in the nucleus of the eye lens. Structural perturbations in the protein often trigger aggregation, which eventually leads to cataract. To decipher the underlying molecular mechanism, it is important to characterize the partially unfolded conformations of Crys proteins. Using coarse grained protein models and molecular dynamics simulations, we studied the role of on-pathway folding intermediates in the early stages of aggregation. The multi-dimensional free energy surface revealed at least three different folding pathways with the population of partially structured intermediates. The two dominant pathways confirm sequential folding of the N-terminal [Ntd] and the C-terminal domains [Ctd], while the third, least favored pathway involves intermediates where both the domains are partially folded. A native like intermediate (I*), featuring the folded domains and disrupted inter domain contacts, gets populated in all the three pathways. I* forms domain swapped dimers by swapping the entire Ntds and Ctds with other monomers. Population of such oligomers can explain the increased resistance to unfolding resulting in hysteresis observed in the folding experiments of H{gamma}D Crys. An ensemble of double domain swapped dimers are also formed during refolding, where intermediates consisting of partially folded Ntds and Ctds swap secondary structures with other monomers. The double domain swapping model presented in our study provides structural insights into the early events of aggregation in Crys proteins and identifies the key secondary structural swapping elements, where introducing mutations will aid in regulating the overall aggregation propensity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/210443v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@fd37e6org.highwire.dtl.DTLVardef@60e7cdorg.highwire.dtl.DTLVardef@128386org.highwire.dtl.DTLVardef@178f240_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract figure C_FIG

biochemistry↗

bioRxiv2020

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program

MiDAC is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. On the one hand, MiDAC upregulates gene expression by mediating the removal of H4K20ac on the promoters and enhancers of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1). Conversely, MiDAC inhibits gene expression by reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis. Furthermore, loss of MiDAC results in neurite outgrowth defects that can be rescued by supplementation with SLIT3 and/or NTN1. These findings indicate a crucial role for MiDAC in regulating the ligands of the SLIT3 and NTN1 signaling axes to ensure the proper integrity of neurite development.

molecular biology↗

bioRxiv2019

A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping

Aggregation of misfolded prion proteins causes fatal neurodegenerative disorders in both humans and animals. There is an extensive effort to identify the elusive aggregation-prone conformations (N*) of prions, which are early stage precursors to aggregation. Ve studied temperature and force induced unfolding of the structured C-terminal domain of mouse (moPrP) and human prion proteins (hPrP) using molecular dynamics simulations and coarse-grained protein models. Ve find that these proteins sparsely populate intermediate states bearing the features of N* and readily undergo domain-swapped dimerization by swapping the short {beta}-strands present at the beginning of the C-terminal domain. Structure of the N* state is similar for both moPrP and hPrP, indicating a common pathogenic precursor across diferent species. Interestingly, disease-resistant hPrP (G127V) showed a drastic reduction in the population of N* state further hinting a pathogenic connection to these partially denatured conformations. This study proposes a plausible runaway domain swapping mechanism to describe the onset of prion aggregation.

biophysics↗

bioRxiv2018

Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein

Cosolvents modulate the stability of protein conformations and exhibit contrasting effects on the kinetics of aggregation by globular proteins and intrinsically disordered proteins (IDPs). The growth of ordered protein aggregates, after the initial nucleation step is believed to proceed through a dock-lock mechanism. We have studied the effect of two denaturants (guanidinium chloride (GdmCl) and urea) and four protective osmolytes (trimethylamine N-oxide (TMAO), sucrose, sarcosine, and sorbitol) on the free energy surface (FES) of the dock-lock growth step of protein aggregation using a coarse-grained protein model and metadynamics simulations. We have used the proteins cSrc-SH3 and A{beta}9-40 as model systems representing globular proteins and IDPs, respectively. The effect of cosolvents on protein conformations is taken into account using the molecular transfer model (MTM). The computed FES shows that protective osmolytes stabilize the compact aggregates, while denaturants destabilize them for both cSrc-SH3 and A{beta}9-40. However, protective osmolytes increase the effective energy barrier for the multi-step domain swapped dimerization of cSrc-SH3, which is critical to the growth of protein aggregates by globular proteins, thus slowing down overall aggregation rate. Contrastingly, denaturants decrease the effective barrier height for cSrc-SH3 dimerization, and hence enhances the aggregation rate in globular proteins. The simulations further show that cSrc-SH3 monomers unfold before dimerization and the barrier to monomer unfolding regulates the effective rate of agrgegation. In the case of IDP, A{beta}9-40, protective osmolytes decrease and denaturants increase the effective barriers in the dock-lock mechanism of fibril growth, leading to faster and slower growth kinetics, respectively.

biochemistry↗