00827nas a2200217 4500008004100000022001400041245009600055210006900151260008000220300000900300490000800309100001800317700002000335700002000355700001900375700002400394700002000418700002500438700001800463856012800481 2012 eng d a0006-349500aMulti-Hit action of membrane active peptides: towards understanding bacterial cell killing0 aMultiHit action of membrane active peptides towards understandin a600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USAbBiophys SoccJAN a616A0 v1021 aMoiset, Gemma1 aCirac, Anna, D.1 aMika, Jacek, T.1 aKocer, Armagan1 aStuart, Marc, C. A.1 aSengupta, Durba1 aMarrink, Siewert-Jan1 aPoolman, Bert uhttps://library.ncl.res.in/content/multi-hit-action-membrane-active-peptides-towards-understanding-bacterial-cell-killing-002175nas a2200181 4500008004100000022001400041245013500055210006900190260009100259300001300350490000700363520141300370100002001783700002101803700002001824700001801844856013101862 2014 eng d a1553-734X00aMolecular Insights into the dynamics of pharmacogenetically important N-terminal variants of the human beta(2)-adrenergic receptor0 aMolecular Insights into the dynamics of pharmacogenetically impo a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcDEC ae10040060 v103 a

The human beta(2)-adrenergic receptor (beta(2)AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, beta(2)AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of beta(2)AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the beta(2)AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients.

1 aShahane, Ganesh1 aParsania, Chirag1 aSengupta, Durba1 aJoshi, Manali uhttps://library.ncl.res.in/content/molecular-insights-dynamics-pharmacogenetically-important-n-terminal-variants-human-beta2-002684nas a2200229 4500008004100000022001400041245008900055210006900144260007300213300001400286490000900300520185000309653002802159653000902187653000902196653003102205653002502236653002602261100002002287700002802307856011902335 2015 eng d a0005-273600aMolecular dynamics simulations of GPCR-cholesterol interaction: an emerging paradigm0 aMolecular dynamics simulations of GPCRcholesterol interaction an aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcSEP a1775-17820 v18483 a

G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates. Membrane cholesterol plays an important role in GPCR structure and function. Molecular dynamics simulations have been successful in exploring the effect of cholesterol on the receptor and a general consensus molecular view is emerging. We review here recent molecular dynamics studies at multiple resolutions highlighting the main features of cholesterol-GPCR interaction. Several cholesterol interaction sites have been identified on the receptor that are reminiscent of nonannular sites. These cholesterol hot-spots are highly dynamic and have a microsecond time scale of exchange with the bulk lipids. A few consensus sites (such as the CRAC site) have been identified that correspond to higher cholesterol interaction. Interestingly, high plasticity is observed in the modes of cholesterol interaction and several sites have been suggested to have high cholesterol occupancy. We therefore believe that these cholesterol hot-spots are indicative of `high occupancy sites' rather than `binding sites'. The results suggest that the energy landscape of cholesterol association with GPCRs corresponds to a series of shallow minima interconnected by low barriers. These specific interactions, along with general membrane effects, have been observed to modulate GPCR organization. Membrane cholesterol effects on receptor structure and organization, that in turn influences receptor cross-talk and drug efficacy, represent a new frontier in GPCR research. This article is part of a Special Issue entitled: Lipid-protein interactions. Guest Editors: Amitabha Chattopadhyay and jean-Marie Ruysschaert. (C) 2015 Elsevier B.V. All rights reserved.

10aCoarse-grain simulation10aCRAC10aGPCR10aLipid-receptor interaction10aMembrane cholesterol10aReceptor dimerization1 aSengupta, Durba1 aChattopadhyay, Amitabha uhttps://library.ncl.res.in/content/molecular-dynamics-simulations-gpcr-cholesterol-interaction-emerging-paradigm-001992nas a2200205 4500008004100000022001400041245010600055210006900161260007900230300001400309490000800323520120900331100001801540700002001558700002101578700001801599700002001617700002401637856012501661 2015 eng d a0006-349500aMolecular mechanism underlying recruitment and insertion of lipid-anchored LC3 protein into membranes0 aMolecular mechanism underlying recruitment and insertion of lipi a600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USAbCELL PRESScNOV a2067-20780 v1093 a

Lipid modification of cytoplasmic proteins initiates membrane engagement that triggers diverse cellular processes. Despite the abundance of lipidated proteins in the human proteome, the key determinants underlying membrane recognition and insertion are poorly understood. Here, we define the course of spontaneous membrane insertion of LC3 protein modified with phosphatidylethanolamine using multiple coarse-grain simulations. The partitioning of the lipid anchor chains proceeds through a concerted process, with its two acyl chains inserting one after the other. Concurrently, a conformational rearrangement involving the alpha-helix III of LC3, especially in the three basic residues Lys(65), Arg(68), and Arg(69), ensures stable insertion of the phosphatidylethanolamine anchor into membranes. Mutational studies validate the crucial role of these residues, and further live-cell imaging analysis shows a substantial reduction in the formation of autophagic vesicles for the mutant proteins. Our study captures the process of water-favored LC3 protein recruitment to the membrane and thus opens, to our knowledge, new avenues to explore the cellular dynamics underlying vesicular trafficking.

1 aThukral, Lipi1 aSengupta, Durba1 aRamkumar, Amrita1 aMurthy, Divya1 aAgrawal, Nikhil1 aGokhale, Rajesh, S. uhttps://library.ncl.res.in/content/molecular-mechanism-underlying-recruitment-and-insertion-lipid-anchored-lc3-protein-002198nas a2200241 4500008004100000022001400041245013700055210006900192260000800261300001200269490000800281520136100289653002801650653001501678653001001693653002501703653001501728100002201743700001801765700002001783700002801803856012501831 2018 eng d a0009-308400aMembrane-induced organization and dynamics of the N-terminal domain of chemokine receptor CXCR1: insights from atomistic simulations0 aMembraneinduced organization and dynamics of the Nterminal domai cJAN a142-1480 v2103 a

The CXC chemokine receptor 1 (CXCR1) is an important member of the G protein-coupled receptor (GPCR) family in which the extracellular N-terminal domain has been implicated in ligand binding and selectivity. The structure of this domain has not yet been elucidated due to its inherent dynamics, but experimental evidence points toward membrane-dependent organization and dynamics. To gain molecular insight into the interaction of the N-terminal domain with the membrane bilayer, we performed a series of microsecond time scale atomistic simulations of the N-terminal domain of CXCR1 in the presence and absence of POPC bilayers. Our results show that the peptide displays a high propensity to adopt a beta-sheet conformation in the presence of the membrane bilayer. The interaction of the peptide with the membrane bilayer was found to be transient in our simulations. Interestingly, a scrambled peptide, containing the same residues in a randomly varying sequence, did not exhibit membrane-modulated structural dynamics. These results suggest that sequence-dependent electrostatics, modulated by the membrane, could play an important role in folding of the N-terminal domain. We believe that our results reinforce the emerging paradigm that cellular membranes could be important modulators of function of G protein-coupled receptors such as CXCR1.

10aAll atom MD simulations10abeta-sheet10aCXCR110aMembrane interaction10aN-terminal1 aKharche, Shalmali1 aJoshi, Manali1 aSengupta, Durba1 aChattopadhyay, Amitabha uhttps://library.ncl.res.in/content/membrane-induced-organization-and-dynamics-n-terminal-domain-chemokine-receptor-cxcr100457nas a2200133 4500008004100000245005100041210005100092300001100143100002000154700001800174700002000192700002800212856008300240 2020 eng d00aMolecular determinants of GPCR oligomerization0 aMolecular determinants of GPCR oligomerization a97-1081 aMohole, Madhura1 aKumar, Aditya1 aSengupta, Durba1 aChattopadhyay, Amitabha uhttps://library.ncl.res.in/content/molecular-determinants-gpcr-oligomerization00544nas a2200157 4500008004100000022001400041245007400055210006900129260000800198300001200206490000800218100002100226700002000247700002000267856009900287 2021 eng d a0022-263100aMolecular interplay at the membrane and impact on cellular physiology0 aMolecular interplay at the membrane and impact on cellular physi cJUN a239-2420 v2541 aPucadyil, Thomas1 aKulkarni, Kiran1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-interplay-membrane-and-impact-cellular-physiology02060nas a2200169 4500008004100000020001800041245011900059210006900178260000800247300001200255490000800267520142900275100001801704700002101722700002001743856012701763 2022 eng d a978032398895700aMolecular determinants of GPCR pharmacogenetics: deconstructing the population variants in β2-adrenergic receptor0 aMolecular determinants of GPCR pharmacogenetics deconstructing t cJAN a361-3960 v1283 a

G protein-coupled receptors (GPCRs) are membrane proteins that play a central role in cell signaling and constitute one of the largest classes of drug targets. The molecular mechanisms underlying GPCR function have been characterized by several experimental and computational methods and provide an understanding of their role in physiology and disease. Population variants arising from nsSNPs affect the native function of GPCRs and have been implicated in differential drug response. In this chapter, we provide an overview on GPCR structure and activation, with a special focus on the β2-adrenergic receptor (β2-AR). First, we discuss the current understanding of the structural and dynamic features of the wildtype receptor. Subsequently, the population variants identified in this receptor from clinical and large-scale genomic studies are described. We show how computational approaches such as bioinformatics tools and molecular dynamics simulations can be used to characterize the variant receptors in comparison to the wildtype receptor. In particular, we discuss three examples of clinically important variants and discuss how the structure and function of these variants differ from the wildtype receptor at a molecular level. Overall, the chapter provides an overview of structure and function of GPCR variants and is a step towards the study of inter-individual differences and personalized medicine.

1 aJoshi, Manali1 aNikte, Siddhanta1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-determinants-gpcr-pharmacogenetics-deconstructing-population-variants-%CE%B2202523nas a2200205 4500008004100000022001400041245007500055210006900130260000800199300001200207490000800219520183200227653002702059653002302086653003102109100002002140700002702160700002002187856011002207 2022 eng d a0022-263100aMolecular mechanisms underlying caveolin-1 mediated membrane curvature0 aMolecular mechanisms underlying caveolin1 mediated membrane curv cJUN a225-2360 v2553 a

Caveolin-1 is one of the main protein components of caveolae that acts as a mechanosensor at the cell membrane. The interactions of caveolin-1 with membranes have been shown to lead to complex effects such as curvature and the clustering of specific lipids. Here, we review the emerging concepts on the molecular interactions of caveolin-1, with a focus on insights from coarse-grain molecular dynamics simulations. Consensus structural models of caveolin-1 report a helix-turn-helix core motif with flanking domains of higher disorder that could be membrane composition dependent. Caveolin-1 appears to be mainly surface-bound and does not embed very deep in the membrane to which it is bound. The most interesting aspect of caveolin-1 membrane binding is the interplay of cholesterol clustering and membrane curvature. Although cholesterol has been reported to cluster in the vicinity of caveolin-1 by several approaches, simulations show that the clustering is maximal in membrane leaflet opposing the surface-bound caveolin-1. The intrinsic negative curvature of cholesterol appears to stabilize the negative curvature in the opposing leaflet. In fact, the simulations show that blocking cholesterol clustering (through artificial position restraints) blocks membrane curvature, and vice versa. Concomitant with cholesterol clustering is sphingomyelin clustering, again in the opposing leaflet, but in a concentration-dependent manner. The differential stress due to caveolin-1 binding and the inherent asymmetry of the membrane leaflets could be the determinant for membrane curvature and needs to be further probed. The review is an important step to reconcile the molecular level details emerging from simulations with the mesoscopic details provided by state of the art experimental approaches. [GRAPHICS] .

10aCholesterol clustering10aMembrane curvature10aProtein-lipid interactions1 aPrakash, Shikha1 aMalshikare, Hrushikesh1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-mechanisms-underlying-caveolin-1-mediated-membrane-curvature02399nas a2200169 4500008004100000022001400041245008200055210006900137260000800206300001600214490000700230520181800237100001902055700002102074700002002095856011402115 2023 eng d a1463-907600aMolecular mechanisms underlying nanowire formation in pristine phthalocyanine0 aMolecular mechanisms underlying nanowire formation in pristine p cNOV a30259-302680 v253 a

Understanding the molecular processes of nanowire self-assembly is crucial for designing and controlling nanoscale structures that could lead to breakthroughs in functional materials. In this work, we focus on pristine phthalocyanines as a representative example of mesogenic supramolecular assemblies and have analyzed the formation of nanowires using classical molecular dynamics simulations. In the simulations, the molecules spontaneously form multi-columnar structures resembling supramolecular polymers that subsequently grow into more ordered aggregates. These self-assemblies are concentration dependent, leading to the formation of multi-columnar, dynamic aggregates at higher concentrations and nanowires at lower concentrations. The multi-columnar assemblies on a whole are more disordered than the nanowires, but have locally ordered domains of parallel facing molecules that can fluctuate while maintaining their overall shape. The nanowire formation at lower concentrations involves the initial interaction and clustering of randomly oriented phthalocyanine molecules, followed by the merging of small clusters into elongated segments and the eventual formation of a stable nanowire. We observe three main conformers in these self-assemblies, the parallel, T-shaped and edge-to-edge stacking of the phthalocyanine dimers. We calculate the underlying free energy landscape and show that the parallel conformers form the most stable configuration which is followed by the T-shaped and edge-to-edge dimer configurations. The findings provide insights into the mechanisms and pathways of nanowire formation and a step towards the understanding of self-assembly processes in supramolecular mesogens. Understanding the molecular processes of nanowire self-assembly of phthalocyanine molecules.

1 aPinjari, Aadil1 aSaraf, Deepashri1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-mechanisms-underlying-nanowire-formation-pristine-phthalocyanine03087nas a2200157 4500008004100000022001400041245006400055210006300119260000800182300001400190490000800204520257800212100002702790700002002817856009202837 2025 eng d a0006-349500aMembrane remodeling by the caveolin-1 8s oligomeric complex0 aMembrane remodeling by the caveolin1 8s oligomeric complex cOCT a3206-32160 v1243 a

Caveolin-1 is a scaffolding protein crucial for the formation of caveolae, specialized membrane structures that are involved in diverse cellular processes such as endocytosis, mechanosensing, and lipid regulation. Recently, a unique structure of the 8S oligomeric complex of caveolin-1 was resolved by cryoelectron microscopy, providing a foundational basis for understanding its molecular mechanisms. In this study, we probe the membrane interactions of the oligomeric caveolin-1 complex in membrane lipid bilayers and vesicles. We performed coarse-grained molecular dynamics simulations to delineate the interactions of the palmitoylated and nonpalmitoylated caveolin-1 with multicomponent membranes. During the simulations, the caveolin-1 complex binds to the membranes, partially to one of the leaflets in a shallow monotopic arrangement. A remodeling of the lipids in its vicinity of the complex was observed in both vesicles and planar bilayers. However, the caveolin-1 complex binds to vesicles without inducing any significant change to the curvature, whereas it appears to induce increased curvature in the planar bilayers leading to the formation of highly curved nanodomains. Cholesterol and phosphoserine lipid enrichment, hallmarks of caveolin-1 binding, were observed in a membrane topology-dependent manner. The differential cholesterol clustering observed between vesicles and bilayers highlights the curvature-dependent nature of caveolin-1-mediated lipid organization. Our work highlights the dual significance of lipid organization and membrane topology in the functional dynamics of caveolin-1, shedding light on its role in inducing and sensing membrane curvature, which is pivotal for various cellular processes. SIGNIFICANCE The rather unanticipated experimental structure of the oligomeric complex of caveolin-1 has opened up multiple questions such as how caveolin-1 interacts with cell membranes and how curvature can be induced or stabilized by a relatively flat protein complex. Here, we identify the molecular mechanisms underlying membrane curvature by caveolin-1 using coarse-grained molecular dynamics simulations. We show that the caveolin-1 complex can bind in a shallow monotopic arrangement and initiate clustering cholesterol and phosphoserine lipids. In vesicles, caveolin-1 binding does not lead to differences in curvature, but binding to planar bilayer leads to the formation of highly curved nanodomains. Our work is an important step to identify novel mechanisms of caveolin-1 stabilized or induced membrane curvature.

1 aMalshikare, Hrushikesh1 aSengupta, Durba uhttps://library.ncl.res.in/content/membrane-remodeling-caveolin-1-8s-oligomeric-complex02232nas a2200229 4500008004100000022001400041245007800055210006900133260000800202300001200210490000700222520147600229653002901705653001701734653003501751653002401786653002401810653002501834100002201859700002001881856010101901 2025 eng d a0887-358500aMolecular interactions of the pioneer transcription factor GATA3 With DNA0 aMolecular interactions of the pioneer transcription factor GATA3 cFEB a555-5660 v933 a

The GATA3 transcription factor is a pioneer transcription factor that is critical in the development, proliferation, and maintenance of several immune cell types. Identifying the detailed conformational dynamics and interactions of this transcription factor, as well as its clinically important population variants will allow us to unravel its mode of action. In this study, we analyze the molecular interactions of the GATA3 transcription factor bound to dsDNA as well as three clinically important population variants by atomistic molecular dynamics simulations. We identify the effect of the variants on the DNA conformational dynamics and delineate the differences compared to the wildtype transcription factor that could be related to impaired function. We highlight the structural plasticity in the binding of the GATA3 transcription factor and identify important DNA-protein contacts. Although the DNA-protein contacts are persistent and appear to be stable, they exhibit nanosecond timescale fluctuations and several binding/unbinding events. Further, we identify differential DNA binding in the three variants and show that the N-terminal binding is reduced in two of the variants. Our results indicate that reduced minor groove width and DNA diameter are important hallmarks for the binding of GATA3. Our work is an important step towards understanding the functional dynamics of the GATA3 protein and its clinically significant population variants.

10aDNA-protein interactions10aGATA protein10aMolecular dynamics simulations10amolecular mechanism10apopulation variants10atranscription factor1 aGharui, Sowmomita1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-interactions-pioneer-transcription-factor-gata3-dna02274nas a2200217 4500008004100000022001400041245010200055210006900157260000800226300001100234490000700245520154100252653001801793653002401811653002101835653002101856100001701877700001601894700002001910856012601930 2025 eng d a1613-681000aA Molecular View of Lipid Nanoparticles: Insights into their Morphology and Structural Plasticity0 aMolecular View of Lipid Nanoparticles Insights into their Morpho cOCT ae054040 v213 a

Lipid nanoparticles (LNPs) have emerged as versatile delivery vehicles for nucleic acid-based therapeutics. Despite their increasing importance, the molecular structure and physico-chemical characteristics of LNPs still remain unclear. In this review, the structural features and phase behavior of LNPs are highlighted. First, the various compositional elements, such as cationic lipids, helper lipids and sterols are discussed, illustrating their functional roles in the self-assembly and stability of LNPs. Molecular models derived from experimental and computational approaches are discussed to provide insights into the structural organization of the LNP components. The influence of sterols and helper lipids in modulating LNP architectures, including membrane fluidity and phase separation, which are key factors for both fusion potential and endosomal escape, is discussed. Variations in sterol content and headgroup chemistry can induce transitions from lamellar to non-lamellar structures, thereby influencing gene transfection outcomes. Further, how cationic lipids induce structural phase transitions, such as lamellar-to-hexagonal and inverse cubic rearrangements under physiological and acidic pH, mimicking extracellular and endosomal conditions, are described. These transitions play a pivotal role in ribonucleic acid (RNA) release and membrane fusion events. This comprehensive review allows to reconcile molecular and structural dynamics that would be necessary for rational design of RNA delivery systems.

10adrug delivery10alipid nanoparticles10aphase separation10avaccine delivery1 aPorte, Sudha1 aVadhana, V.1 aSengupta, Durba uhttps://library.ncl.res.in/content/molecular-view-lipid-nanoparticles-insights-their-morphology-and-structural-plasticity01875nas a2200181 4500008004100000022001400041245010400055210006900159260000800228300001700236490000700253520121700260100002701477700002101504700002401525700002001549856012401569 2026 eng d a1359-734500aMechanistic principles of antimicrobial peptides uncovered by charge density-based machine learning0 aMechanistic principles of antimicrobial peptides uncovered by ch cFEB aPMID 96108380 v623 a

Antimicrobial peptides (AMPs) are emerging as potent alternatives to conventional antibiotics, yet their diverse nature due to divergent mechanisms of action hinders rational design. Here, we present an electrostatics-stratified computational framework that uncovers key physicochemical principles governing AMP activity. Experimentally validated peptides were grouped by average charge per residue (i.e., the charge/length of the peptide) and analyzed through integrated sequence-, structure-, and chemistry-based descriptors. Distinct molecular signatures emerged across electrostatic regimes: low-charge/length peptides rely on amphipathic organization via structural compactness, whereas the intermediate-charge/length peptides exhibit balanced hydrophobicity and electrostatics. The high-charge peptides couple strong cationic attraction with lipophilicity and tryptophan anchoring to mainly disrupt membranes. Interestingly, hydrophobic moment, which is a measure of the amphipathicity, is found to be important in all three classes of AMPs. This study identifies distinguishing features of AMP sub-groups and suggests design guidelines for developing selective and potent next-generation AMPs.

1 aMalshikare, Hrushikesh1 aPriyakumar, Deva1 aChatterjee, Prathit1 aSengupta, Durba uhttps://library.ncl.res.in/content/mechanistic-principles-antimicrobial-peptides-uncovered-charge-density-based-machine