02181nas a2200193 4500008004100000022001400041245010100055210006900156260007100225300001400296490000700310520144300317100002101760700002401781700001501805700002401820700001801844856012501862 2015 eng d a0020-166900aPyrazine-based organometallic complex: synthesis, characterization, and supramolecular chemistry0 aPyrazinebased organometallic complex synthesis characterization  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAR a2543-25500 v543 a

The design, synthesis, and characterization of a new pyrazine-based ditopic platinum(II) organometallic complex are reported. The molecular structure of the organoplatinum pyrazine dipod was determined by single-crystal X-ray crystallography. The potential utility of this organometallic ditopic acceptor as a building block in the construction of neutral metallasupramolecular macrocycles containing the pyrazine motif was explored. Pyrazine motifs containing supramolecules were characterized by multinuclear NMR (including H-1 DOSY), mass spectrometry, and elemental analysis. The geometry of each supramolecular framework was optimized by employing the PM6 semi-empirical molecular orbital method to predict its shape and size. The ability of the pyrazine-based organoplatinum complex to act as a host for nitroaromatic guest (2,4-dinitrotoluene and PA) molecules was explored by isothermal titration calorimetry (ITC). The binding stoichiometry and thermodynamic parameters of these host guest complexation reactions were evaluated using ITC. Theoretical calculations were performed to obtain insight into the binding pattern between the organometallic host and nitroaromatic guests. The preferable binding propensity of the binding sites of complex 1 for both nitroaromatics (PA and 2,4-dinitrotoluene) determined by molecular simulation studies corroborates well with the experimental results as obtained by ITC experiments.

1 aBhowmick, Sourav1 aChakraborty, Sourav1 aDas, Atanu1 aRajamohanan, P., R.1 aDas, Neeladri uhttps://library.ncl.res.in/content/pyrazine-based-organometallic-complex-synthesis-characterization-and-supramolecular-001574nas a2200145 4500008004100000022001400041245009000055210006900145260000900214300001600223490000800239520105900247100001501306856010701321 2021 eng d a1520-610600aSystematic search for a predictor for the clinical observables of alzheimer's disease0 aSystematic search for a predictor for the clinical observables o cNOV  a12177-121860 v1253 aOne of the prevailing life-threatening incurable neurodegenerative diseases that are presently endangering human society as a whole, and hence, baffling the entire spectrum of the scientific and pharmaceutical world, is Alzheimer's disease (AD). AD is a manifestation of self-assembly of both wild-type (sporadic) and mutated (familial) forms of the amyloid-beta peptide, a proteolytic product of the amyloid precursor protein, where the self-assembly results in the genesis of pathogenic fibrillar aggregates. Currently prevailing diagnostic and hence therapeutic challenges originate from the unavailability of a specific predictor for clinical observables. The continuous emergence of novel pathogenic mutants with unpredictable phenotypes adds immensely to the nonspecific nature of the problem. The current research reports a simple physical parameter, the binding affinity of a protofilament to its protofibril, which predicts the clinical observables of familial AD with astounding accuracy and more importantly, without any adjustable parameters.1 aDas, Atanu uhttps://library.ncl.res.in/content/systematic-search-predictor-clinical-observables-alzheimers-disease02343nas a2200253 4500008004100000022001400041245009300055210006900148260000800217300001400225490000700239520147400246653003501720653002401755653002501779653002801804653003001832653002301862100002501885700002301910700001801933700001501951856012301966 2022 eng d a1948-719300aScan-find-scan-model: discrete site-targeted suppressor design strategy for amyloid-beta0 aScanfindscanmodel discrete sitetargeted suppressor design strate cJUL a2191-22080 v133 a

Alzheimer's disease is undoubtedly the most well-studied ranks at the top in terms of getting attention from the scientific community for structural property-based characterization. Even after decades of extensive research, there is existing volatility in terms of understanding and hence the effective tackling procedures against the disease that arises due to the lack of knowledge of both specific targetand site-specific drugs. Here, we develop a multidimensional approach based on the characterization of the common static-dynamic-thermodynamic trait of the monomeric protein, which efficiently identifies a small target sequence that contains an inherent tendency to misfold and consequently aggregate. The robustness of the identification of the target sequence comes with an abundance of a priori knowledge about the length and sequence of the target and hence guides toward effective designing of the target-specific drug with a very low probability of bottleneck and failure. Based on the target sequence information, we further identified a specific mutant that showed the maximum potential to act as a destabilizer of the monomeric protein as well as enormous success as an aggregation suppressor. We eventually tested the drug efficacy by estimating the extent of modulation of binding affinity existing within the fibrillar form of the A beta protein due to a single-point mutation and hence provided a proof of concept of the entire protocol.

10aconfigurational misfoldability10adrug developability10ainherent frustration10apotential aggregability10asequence-based mutability10atarget specificity1 aBhagavatula, Hasathi1 aSarkar, Archishman1 aSantra, Binit1 aDas, Atanu uhttps://library.ncl.res.in/content/scan-find-scan-model-discrete-site-targeted-suppressor-design-strategy-amyloid-beta02523nas a2200169 4500008004100000022001400041245012800055210006900183260000800252300001400260490000700274520188300281100002202164700001502186700002402201856012802225 2023 eng d a0006-296000aElectrostatic modulation of intramolecular and intermolecular interactions during the formation of an amyloid-like assembly0 aElectrostatic modulation of intramolecular and intermolecular in cMAY a1890-19050 v623 a

The mechanism of protein aggregation can be broadly viewedas ashift from the native-state stabilizing intramolecular to the aggregated-phasesustaining intermolecular interactions. Understanding the role ofelectrostatic forces on the extent of modulation of this switch hasrecently evolved as a topic of monumental significance as proteinaggregation has lately been connected to charge modifications of anaging proteome. To decipher the distinctive role of electrostaticforces on the extremely complicated phase separation landscape, weopted for a combined in vitro-in silico approach to ascertainthe structure-dynamics-stability-aggregabilityrelationship of the functional tandem RRM domains of the ALS-relatedprotein TDP-43 (TDP-43(tRRM)), under a bivariate solutioncondition in terms of pH and salt concentration. Under acidic pH conditions,the native TDP-43(tRRM) protein creates an aggregation-proneentropically favorable partially unfolded conformational landscapedue to enthalpic destabilization caused by the protonation of theburied ionizable residues and consequent overwhelming fluctuationsof selective segments of the sequence leading to anti-correlated movementsof the two domains of the protein. The evolved fluffy ensemble witha comparatively exposed backbone then easily interacts with incomingprotein molecules in the presence of salt via typical amyloid-aggregate-likeintermolecular backbone hydrogen bonds with a considerable contributionoriginating from the dispersion forces. Subsequent exposure to excesssalt at low pH conditions expedites the aggregation process via anelectrostatic screening mechanism where salt shows preferential bindingto the positively charged side chain. The applied target observable-specificapproach complementarity unveils the hidden information landscapeof an otherwise complex process with unquestionable conviction.

1 aPillai, Meenakshi1 aDas, Atanu1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/electrostatic-modulation-intramolecular-and-intermolecular-interactions-during-formation02400nas a2200217 4500008004100000022001400041245011200055210006900167260000800236300001200244490000700256520161500263653001301878653003401891653003101925653002401956653003301980100002302013700001502036856013102051 2023 eng d a0887-358500aGoverning dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-10 aGoverning dynamics and preferential binding of the AXH domain in cMAR a380-3940 v913 a

The present state of understanding the mechanism of Spinocerebellar Ataxia-1, a fatal neurodegenerative disease linked to the protein Ataxin-1 (ATXN1), is baffled by a set of self-contradictory, and hence, inconclusive observations. This fallacy poses a bottleneck to the effective designing of curable drugs as the field is currently missing the specific druggable site. To understand the fundamentals of pathogenesis, we tried to decipher the intricacies of the extremely complicated landscape by targeting the relevant species that supposedly dictate the structure-function paradigm. The atomic-level description and characterization of the dynamism of the systems reveal the existence of structural polymorphism in all the leading stakeholders of the overall system. The very existence of conformational heterogeneity in every species creates numerous possible combinations of favorable interactions because of the variability in segmental cross-talks and hence claims its role in the choice of routes between functional activity and dysfunctional disease-causing aggregation. Despite this emergent configurational diversity, there is a common mode of operative intermolecular forces that dictates the extent of stability of all the multimeric complexes due to the localized population of a specific type of residue. The present research proposes a dynamic switch mechanism between aggregability and functional activity, based on the logical interpretation of the estimated variables, which is practically dictated by the effective concentration of the interacting species involved in the cell.

10aAtaxin-110amolecular dynamics simulation10aneurodegenerative diseases10aProtein aggregation10aprotein misfolding disorders1 aTammara, Vaishnavi1 aDas, Atanu uhttps://library.ncl.res.in/content/governing-dynamics-and-preferential-binding-axh-domain-influence-aggregation-pathway-ataxin02450nas a2200157 4500008004100000022001400041245005700055210005600112260000800168300001400176490000800190520197000198100002302168700001502191856008602206 2023 eng d a1520-610600aMolecular mechanism of PSMa3 aggregation: a new view0 aMolecular mechanism of PSMa3 aggregation a new view cSEP a8317-83300 v1273 a

The emergence of a novel cross-alpha fibrillar structure, unlike the commonly observed sequence-independent cross-beta one, of a 22-residue bacterial virulent amphipathic alpha-helical peptide of the phenol soluble modulin (PSM) family, PSM alpha 3, with many deleterious effects on human life, has infused uncertainty to the paradigm of the intrinsically polymorphic, multivariate, multiphasic, and cross-sequence-cross-disease entangled protein aggregation landscape and hence on the identity of the therapeutic target. We, here, deconvolute the factors contributing to the genesis and hence the transition of lower to higher order aggregates of PSM alpha 3 in its natural state and three noncanonical designed variants using conventional and enhanced sampling approach-based atomistic simulations. PSM alpha 3 shows structural polymorphism with nominal alpha-helicity, substantial beta-propensity, and dominant random-coil features, irrespective of the extent of aggregation. Moreover, the individual features of the overall amphipathicity operate alternatively depending on the extent and organization of aggregation; the dominance gradually moves from charged to hydrophobic residues with the progressive generation of higher order aggregates (dimer to oligomer to fibril) and with increasing orderedness of the self-assembled construct (oligomer vs dimer/fibril). Similarly, the contribution of interchain salt bridges decreases with increasing order of aggregation (dimer to oligomer to fibril). However, the intrachain salt bridges consistently display their role in all phases of aggregation. Such phase-independent features also include equivalent roles of electrostatic and van der Waals forces on intrachain interactions, sole contribution of van der Waals forces on interchain cross-talk, and negligible peptide-water relationship. Finally, we propose a conjugate peptide-based aggregation suppressor having a single-point proline mutation.

1 aTammara, Vaishnavi1 aDas, Atanu uhttps://library.ncl.res.in/content/molecular-mechanism-psma3-aggregation-new-view01934nas a2200193 4500008004100000022001400041245010400055210006900159260000900228300001100237490000800248520126300256100001601519700001801535700001501553700002501568700001901593856012801612 2023 eng d a0021-960600aNon-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories0 aNonMarkov models of singlemolecule dynamics from informationtheo cAUG  a0641040 v1593 a

Whether single-molecule trajectories, observed experimentally or in molecular simulations, can be described using simple models such as biased diffusion is a subject of considerable debate. Memory effects and anomalous diffusion have been reported in a number of studies, but directly inferring such effects from trajectories, especially given limited temporal and/or spatial resolution, has been a challenge. Recently, we proposed that this can be achieved with information-theoretical analysis of trajectories, which is based on the general observation that non-Markov effects make trajectories more predictable and, thus, more ``compressible'' by lossless compression algorithms. Toy models where discrete molecular states evolve in time were shown to be amenable to such analysis, but its application to continuous trajectories presents a challenge: the trajectories need to be digitized first, and digitization itself introduces non-Markov effects that depend on the specifics of how trajectories are sampled. Here we develop a milestoning-based method for information-theoretical analysis of continuous trajectories and show its utility in application to Markov and non-Markov models and to trajectories obtained from molecular simulations.

1 aSong, Kevin1 aPark, Raymond1 aDas, Atanu1 aMakarov, Dmitrii, E.1 aVouga, Etienne uhttps://library.ncl.res.in/content/non-markov-models-single-molecule-dynamics-information-theoretical-analysis-trajectories02784nas a2200241 4500008004100000022001400041245017300055210006900228260000900297300001100306490000900317520187000326653002602196653002502222653003202247653002302279653003002302653003002332100001802362700001902380700001502399856012802414 2023 eng d a1570-963900aUnderstanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors0 aUnderstanding the mechanism of amylin aggregation From identifyi cJAN  a1408660 v18713 a

One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.

10aAggregation mechanism10aBridging information10aConformational polymorphism10aGeneric suppressor10aHelix -driven association10aStructural reorganization1 aGhosh, Ritama1 aGhosh, Shreyan1 aDas, Atanu uhttps://library.ncl.res.in/content/understanding-mechanism-amylin-aggregation-identifying-crucial-segments-tracing-dominant01994nas a2200169 4500008004100000022001400041245014800055210006900203260000900272300001400281490000800295520133600303100002201639700002001661700001501681856012801696 2024 eng d a1520-610600aCharacterization of the conformational hotspots of the RNA-dependent RNA polymerase complex identifies a unique structural malleability of nsp80 aCharacterization of the conformational hotspots of the RNAdepend cOCT  a9959-99750 v1283 a

Several antiviral therapeutic approaches have been targeted toward the RNA-dependent RNA polymerase (RdRp) complex that is involved in viral genome replication. In SARS-CoV-2, although the RdRp is a multiprotein complex, the focus has been on the ligand binding catalytic core (nonstructural protein nsp12), and not the multiprotein functional dynamics. In this study, we focus on the conformational ensembles of the RdRp complex and their modulation by the presence of RNA, performing comprehensive microsecond-scale atomistic simulations of the apo- and RNA-bound complex. We delineate the differential impact of RNA on the constituent proteins, such as conformational polymorphisms, dominant segment-specific fluctuations, and the switch in dynamical crosstalk within the complex. We distinguish dynamical signatures of nsp7, nsp8, and nsp12 in the apo-state that are reduced in the presence of the RNA and appear to ``prime'' the complex for activity. Importantly, we identify a unique structural malleability of the nsp8 protein with high conformational heterogeneity in the apo state, especially at three sites (Y71 for nsp8A, and D52 and A66 for nsp8B). Our work highlights the functional implications of the polymorphism of nsp8 structures and reveals possibilities for the development of allosteric inhibitors.

1 aGharui, Sowmomita1 aSengupta, Durba1 aDas, Atanu uhttps://library.ncl.res.in/content/characterization-conformational-hotspots-rna-dependent-rna-polymerase-complex-identifies02962nas a2200277 4500008004100000022001400041245013400055210006900189260000800258300001400266490000700280520195400287653002502241653002702266653002802293653003202321653002502353653003002378653003602408653002302444100002302467700002402490700002402514700001502538856013102553 2024 eng d a1948-719300aDeciphering the monomeric and dimeric conformational landscapes of the full-length TDP-43 and the impact of the C-terminal domain0 aDeciphering the monomeric and dimeric conformational landscapes  cNOV a4305-43210 v153 a

The aberrant aggregation of TAR DNA-binding protein 43 kDa (TDP-43) in cells leads to the pathogenesis of multiple fatal neurodegenerative diseases. Decoding the proposed initial transition between its functional dimeric and aggregation-prone monomeric states can potentially design a viable therapeutic strategy, which is presently limited by the lack of structural detail of the full-length TDP-43. To achieve a complete understanding of such a delicate phase space, we employed a multiscale simulation approach that unearths numerous crucial features, broadly summarized in two categories: (1) state-independent features that involve inherent chain collapsibility, rugged polymorphic landscape dictated by the terminal domains, high beta-sheet propensity, structural integrity preserved by backbone-based intrachain hydrogen bonds and electrostatic forces, the prominence of the C-terminal domain in the intrachain cross-domain interfaces, and equal participation of hydrophobic and hydrophilic (charged and polar) residues in cross-domain interfaces; and (2) dimerization-modulated characteristics that encompass slower collapsing dynamics, restricted polymorphic landscape, the dominance of side chains in interchain hydrogen bonds, the appearance of the N-terminal domain in the dimer interface, and the prominence of hydrophilic (specifically polar) residues in interchain homo- and cross-domain interfaces. In our work, the ill-known C-terminal domain appears as the most crucial structure-dictating domain, which preferably populates a compact conformation with a high beta-sheet propensity in its isolated state stabilized by intrabackbone hydrogen bonds, and these signatures are comparatively faded in its integrated form. Validation of our simulated observables by a complementary spectroscopic approach on multiple counts ensures the robustness of the computationally predicted features of the TDP-43 aggregation landscape.

10achain collapsibility10adomain-wisefluctuation10aelectrostatic dominance10ahydrogen bond switchability10along-range crosstalk10apersistent beta-character10aprotagonistic C-terminal domain10arugged phase space1 aTammara, Vaishnavi1 aDoke, Abhilasha, A.1 aJha, Santosh, Kumar1 aDas, Atanu uhttps://library.ncl.res.in/content/deciphering-monomeric-and-dimeric-conformational-landscapes-full-length-tdp-43-and-impact-c02461nas a2200181 4500008004100000022001400041245009000055210006900145260000900214300001400223490000700237520184400244100002302088700002202111700001702133700001502150856011402165 2024 eng d a1463-907600aFlagellar motor protein-targeted search for the druggable site of Helicobacter pylori0 aFlagellar motor proteintargeted search for the druggable site of cJAN  a2111-21260 v263 a

The deleterious impact of Helicobacter pylori (H. pylori) on human health is contingent upon its ability to create and sustain colony structure, which in turn is dictated by the effective performance of flagella - a multi-protein rotary nanodevice. Hence, to design an effective therapeutic strategy against H. pylori, we here conducted a systematic search for an effective druggable site by focusing on the structure-dynamics-energetics-stability landscape of the junction points of three 1 : 1 protein complexes (FliF(C)-FliG(N), FliG(M)-FliM(M), and FliY(C)-FliN(C)) that contribute mainly to the rotary motion of the flagella via the transformation of information along the junctions over a wide range of pH values operative in the stomach (from neutral to acidic). We applied a gamut of physiologically relevant perturbations in the form of thermal scanning and mechanical force to sample the entire quasi - and non-equilibrium conformational spaces available for the protein complexes under neutral and acidic pH conditions. Our perturbation-induced magnification of conformational distortion approach identified pH-independent protein sequence-specific evolution of precise thermally labile segments, which dictate the specific thermal unfolding mechanism of each complex and this complex-specific pH-independent structural disruption notion remains consistent under mechanical stress as well. Complementing the above observations with the relative rank-ordering of estimated equilibrium binding free energies between two protein sequences of a specific complex quantifies the extent of structure-stability modulation due to pH alteration, rationalizes the exceptional stability of H. pylori under acidic pH conditions, and identifies the pH-independent complex-sequence-segment-residue diagram for targeted drug design.

1 aTammara, Vaishnavi1 aAngrover, Ruchika1 aSirur, Disha1 aDas, Atanu uhttps://library.ncl.res.in/content/flagellar-motor-protein-targeted-search-druggable-site-helicobacter-pylori02704nas a2200253 4500008004100000022001400041245012700055210006900182260000800251300001400259490000700273520183800280653002002118653002702138653002202165653001902187653002402206653001402230100002202244700002202266700001502288700002402303856012302327 2024 eng d a1948-719300aPathological mutations D169G and P112H electrostatically aggravate the amyloidogenicity of the functional domain of TDP-430 aPathological mutations D169G and P112H electrostatically aggrava cNOV a4267-42830 v153 a

Aggregation of TDP-43 is linked to the pathogenesis of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Notably, electrostatic point mutations such as D169G and P112H, located within the highly conserved functional tandem RNA recognition motif (RRM) domains of the TDP-43 protein (TDP-43tRRM), have been identified in diseased patients as well. In this study, we address how the electrostatic mutations alter both the native state stability and aggregation propensity of TDP-43tRRM. The mutants D169G and P112H show increased chemical stability compared to the TDP-43tRRM at physiological pH. However, at low pH, both the mutants undergo a conformational change to form amyloid-like fibrils, though with variable rates-the P112H mutant being substantially faster than the other two sequences (TDP-43tRRM and D169G mutant) showing comparable rates. Moreover, among the three sequences, only the P112H mutant undergoes a strong ionic strength-dependent aggregability trend. These observations signify the substantial contribution of the excess charge of the P112H mutant to its unique aggregation process. Complementary simulated observables with atomistic resolution assign the experimentally observed sequence-, pH-, and ionic strength-dependent aggregability pattern to the degree of thermal lability of the mutation site-containing RRM1 domain and its extent of dynamical anticorrelation with the RRM2 domain whose combination eventually dictate the extent of generation of aggregation-prone partially unfolded conformational ensembles. Our choice of a specific charge-modulated pathogenic mutation-based experiment-simulation-combination approach unravels the otherwise hidden residue-wise contribution to the individual steps of this extremely complicated multistep aggregation process.

10aamyloid fibrils10aconformational changes10adisease mutations10aelectrostatics10aProtein aggregation10astability1 aPillai, Meenakshi1 aPatil, Anjali, D.1 aDas, Atanu1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/pathological-mutations-d169g-and-p112h-electrostatically-aggravate-amyloidogenicity02320nas a2200157 4500008004100000022001400041245007300055210007000128260000800198300001600206490000800222520178500230100002302015700001502038856010902053 2024 eng d a1520-610600aSelf-consistent molecular mechanism of β2-microglobulin aggregation0 aSelfconsistent molecular mechanism of β2microglobulin aggregatio cDEC a12425-124420 v1283 a

Despite the consensus on the origin of dialysis-related amyloidosis (DRA) being beta(2)-microglobulin (beta(2)m) aggregation, the debate on the underlying mechanism persists because of the continuous emergence of beta(2)m variant- and pH-dependent contradictory results. By characterizing the native monomeric (initiation) and aggregated fibrillar (termination) states of beta(2)m via a combination of two enhanced sampling approaches, we here propose a mechanism that explains the heterogeneous behavior of wild-type (WT) and pathogenic (V27M and D76N) beta(2)m variants in physiological and disease-pertinent acidic pH environments. It appears that the higher retainment of monomeric native folds at neutral pH (native-like) distinguishes pathogenic beta(2)m mutants from the WT (moderate loss). However, at acidic pH, all three variants behave similarly in producing a substantial amount of partially unfolded states (conformational switch, propensity), though with different extents (WT < V27M < D76N). Whereas at the fibrillar end, all beta(2)m variants display a pH-dependent protofilament separation pathway and a higher protofilament binding affinity (stability) at acidic pH, where the relative order of binding affinity (WT < V27M < D76N) remains consistent with pH modulation. Combining these observations, we conclude that beta(2)m variants possibly shift from native-like aggregation to conformational switch-initiated fibrillation as the pH is altered from neutral to acidic. The combined propensity-stability approach based on the initiation and termination points of beta(2)m aggregation not only assists us in deciphering the mechanism but also emphasizes the protagonistic roles of both terminal points in the overall aggregation process.

1 aTammara, Vaishnavi1 aDas, Atanu uhttps://library.ncl.res.in/content/self-consistent-molecular-mechanism-%CE%B22-microglobulin-aggregation02205nas a2200241 4500008004100000022001400041245009500055210006900150260000800219300001200227490000700239520141000246653002001656653002301676653001201699653002201711100002301733700002301756700002301779700001501802700002501817856012101842 2025 eng d a1572-388700aCharacterization of S-homocysteinylation of Human Insulin and Its Implications in Diabetes0 aCharacterization of Shomocysteinylation of Human Insulin and Its cOCT a598-6100 v443 a

Homocysteine thiolactone is a reactive thiol known for its interaction with various proteins. Nevertheless, there exists a paucity of information concerning the interaction between homocysteine thiolactone and human insulin, particularly regarding the mechanism by which homocysteine facilitates the reduction of disulfide bonds within insulin. In the present study, we have elucidated the binding sites of homocysteine to the cysteine residues (A6-B7 and A20-B19) that are implicated in the formation of intermolecular disulfide bonds in insulin through an in vitro reaction analyzed via LC-ESI MS/MS. This results in a reduction of disulfide bonds linking the A and B chains, which was corroborated by MALDI-TOF-MS and ESI-MS analysis. The secondary structure of insulin is affected by this modification, as evidenced by circular dichroism spectroscopy. In-silico studies also show that homocysteine affects the insulin structure. A glucose uptake assay conducted in Chinese hamster ovary (CHO) cells that stably express the insulin receptor revealed that HC-modified insulin is less effective in inducing glucose uptake compared to native insulin, suggesting that HC-induced structural modifications in insulin influence functional activity. This study provides insight into the HC-induced structural and functional changes in insulin and discusses the consequent implications for diabetes.

10aDisulfide bonds10aHomocysteinylation10ainsulin10aMass spectrometry1 aSheikh, Amreen, B.1 aJathar, Swaraj, M.1 aTammara, Vaishnavi1 aDas, Atanu1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/characterization-s-homocysteinylation-human-insulin-and-its-implications-diabetes02896nas a2200229 4500008004100000022001400041245011200055210006900167260000900236300001400245490000700259520209400266653001102360653001702371653003402388653001302422653003002435653003502465100002302500700001502523856012802538 2025 eng d a1948-719300aDecoding the relationship between alzheimer's disease and type-2 diabetes via the protein aggregation prism0 aDecoding the relationship between alzheimers disease and type2 d cAUG  a3003-30190 v163 a

Alzheimer's disease (AD) and type-2 diabetes (T2D) are two fatal human diseases and have been linked to the aberrant aggregation of two distinct peptides, amyloid-beta (A beta) and human islet amyloid polypeptide (hIAPP), respectively. These two peptide aggregates, even with distal deposition sites (brain and pancreas), act as mutual beneficiaries. We here unveiled the crosstalk in a self-consistent fashion using atomistic simulations by comparing the kinetics and thermodynamics of self- and cross-aggregations of A beta(42) and hIAPP and their modulations by preformed fibrillar templates. Templates (specifically hIAPP) generally accelerate aggregation, alter the relative order of aggregation rates (cross-aggregation > A beta self-aggregation > hIAPP self-aggregation for nontemplated and hIAPP self-aggregation > cross-aggregation > A beta self-aggregation for templated), and flip the mutual impact (hIAPP aggravates A beta aggregation in nontemplated and the reverse in templated). Higher instances of breaking larger aggregates and longer residence times of smaller aggregates decelerate aggregation, whereas interpeptide electrostatics (universal) and hydrogen bonds (templated) assist it. However, the equilibrium aggregability pattern contradicts kinetic rank-ordering, as A beta displays a higher aggregability than hIAPP, templates increase aggregability for both peptides, and A beta's self-aggregability supersedes cross-aggregability, which further surpasses hIAPP's self-aggregability. The equilibrium ensembles encompass polymorphic, nonfibrillar oligomers having substantially reduced alpha-helicity and slight beta-propensity, with both parallel and antiparallel interpeptide orientations, primarily stabilized by electrostatics. A higher equilibrium aggregability means a greater helix-breaking capacity, a bias toward parallel orientation, and a lesser structural polymorphism. Water expulsion from peptide surroundings and distortion of water tetrahedrality prove that aggregation follows the liquid-liquid phase separation (LLPS) model.

10aamylin10aAmyloid-beta10aliquid-liquidphase separation10aOligomer10aself vs cross-aggregation10aunseeded vs seeded aggregation1 aTammara, Vaishnavi1 aDas, Atanu uhttps://library.ncl.res.in/content/decoding-relationship-between-alzheimers-disease-and-type-2-diabetes-protein-aggregation