@article { ISI:000351325200008, title = {Pyrazine-based organometallic complex: synthesis, characterization, and supramolecular chemistry}, journal = {Inorganic Chemistry}, volume = {54}, number = {6}, year = {2015}, month = {MAR}, pages = {2543-2550}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

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.

}, issn = {0020-1669}, doi = {10.1021/ic502581x}, author = {Bhowmick, Sourav and Chakraborty, Sourav and Das, Atanu and Rajamohanan, P. R. and Das, Neeladri} } @article {47662, title = {Systematic search for a predictor for the clinical observables of alzheimer{\textquoteright}s disease}, journal = {Journal of Physical Chemistry B}, volume = {125}, year = {2021}, month = {NOV }, pages = {12177-12186}, type = {Article}, abstract = {One 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{\textquoteright}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.}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.1c06725}, author = {Das, Atanu} } @article {48219, title = {Scan-find-scan-model: discrete site-targeted suppressor design strategy for amyloid-beta}, journal = {ACS Chemical Neuroscience}, volume = {13}, year = {2022}, month = {JUL}, pages = {2191-2208}, type = {Article}, abstract = {

Alzheimer{\textquoteright}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.

}, keywords = {configurational misfoldability, drug developability, inherent frustration, potential aggregability, sequence-based mutability, target specificity}, issn = {1948-7193}, doi = {10.1021/acschemneuro.2c00272}, author = {Bhagavatula, Hasathi and Sarkar, Archishman and Santra, Binit and Das, Atanu} } @article {48494, title = {Electrostatic modulation of intramolecular and intermolecular interactions during the formation of an amyloid-like assembly}, journal = {Biochemistry}, volume = {62}, year = {2023}, month = {MAY}, pages = {1890-1905}, type = {Article}, abstract = {

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.

}, issn = {0006-2960}, doi = {10.1021/acs.biochem.3c00014}, author = {Pillai, Meenakshi and Das, Atanu and Jha, Santosh Kumar} } @article {48447, title = {Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-1}, journal = {Proteins-Structure Function and Bioinformatics}, volume = {91}, year = {2023}, month = {MAR}, pages = {380-394}, type = {Article}, abstract = {

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.

}, keywords = {Ataxin-1, molecular dynamics simulation, neurodegenerative diseases, Protein aggregation, protein misfolding disorders}, issn = {0887-3585}, doi = {10.1002/prot.26436}, author = {Tammara, Vaishnavi and Das, Atanu} } @article {48711, title = {Molecular mechanism of PSMa3 aggregation: a new view}, journal = {Journal of Physical Chemistry B}, volume = {127}, year = {2023}, month = {SEP}, pages = {8317-8330}, type = {Article}, abstract = {

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.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.3c03806}, author = {Tammara, Vaishnavi and Das, Atanu} } @article {48828, title = {Non-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories}, journal = {Journal of Chemical Physics}, volume = {159}, year = {2023}, month = {AUG }, pages = {064104}, type = {Article}, abstract = {

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 {\textquoteleft}{\textquoteleft}compressible{\textquoteright}{\textquoteright} 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.

}, issn = {0021-9606}, doi = {10.1063/5.0158930}, author = {Song, Kevin and Park, Raymond and Das, Atanu and Makarov, Dmitrii E. and Vouga, Etienne} } @article {48325, title = {Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors}, journal = {Biochimica Et Biophysica Acta-Proteins and Proteomics}, volume = {1871}, year = {2023}, month = {JAN }, pages = {140866}, type = {Article}, abstract = {

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.

}, keywords = {Aggregation mechanism, Bridging information, Conformational polymorphism, Generic suppressor, Helix -driven association, Structural reorganization}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2022.140866}, author = {Ghosh, Ritama and Ghosh, Shreyan and Das, Atanu} }