02063nas a2200145   4500008004100000022001400041245010500055210006900160260007100229300001600300490000800316520145300324100002001777856012001797       2012                        eng d  a1520-610600aCholesterol modulates the structure, binding modes, and energetics of caveolin-membrane interactions0 aCholesterol modulates the structure binding modes and energetics  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcDEC  a14556-145640 v1163 a<p>Caveolin-1 (cav-1) is an important membrane protein that plays a vital role in cellular signaling and trafficking by organizing membrane domains. The peptide interacts with cholesterol-rich membranes and induces large morphological changes in them, forming microdomains such as caveolae. Here, we use coarse-grain molecular dynamics simulations to study the interaction of cav-1 peptides with several model bilayer systems mimicking biological scenarios, such as cholesterol-rich domains, cholesterol-depleted domains, and unsaturated lipid domains. We show that cholesterol modulates the depth as well as orientation of cav-1 binding to membranes. Furthermore, the presence of cholesterol stabilizes more open conformations of cav-1, and we speculate that the binding modes and open conformations could be responsible for inducing morphological changes in the bilayer. We also calculated the partitioning free energy to different bilayers and show that binding to cholesterol-rich bilayers is more favorable than cholesterol-depleted bilayers and the binding to unsaturated bilayers is the least favorable. Binding to cholesterol-rich bilayers also changes the pressure profile of the bilayer to which it is bound and thereby affects the local spontaneous curvature. Our results highlight molecular details of protein-lipid interplay and provide new insights into the effects of cav-1 in tuning the morphology of cholesterol-rich membranes.</p>1 aSengupta, Durba  uhttps://library.ncl.res.in/content/cholesterol-modulates-structure-binding-modes-and-energetics-caveolin-membrane-002148nas a2200169   4500008004100000022001400041245011300055210006900168260007900237300001400316490000800330520144400338100002101782700002801803700002001831856012701851       2014                        eng d  a0006-349500aCholesterol modulates the dimer interface of the beta(2)-adrenergic receptor via cholesterol occupancy sites0 aCholesterol modulates the dimer interface of the beta2adrenergic  a600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USAbCELL PRESScMAR  a1290-13000 v1063 a<p>The beta(2)-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol. The recent high-resolution crystal structure of the beta(2)-adrenergic receptor revealed the presence of possible cholesterol-binding sites in the receptor. However, the functional relevance of cholesterol binding to the receptor remains unexplored. We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the beta(2)-adrenergic receptor in lipid bilayers containing cholesterol. A novel (to our knowledge) aspect of our results is that receptor dimerization is modulated by membrane cholesterol. We show that cholesterol binds to transmembrane helix IV, and cholesterol occupancy at this site restricts its involvement at the dimer interface. With increasing cholesterol concentration, an increased presence of transmembrane helices I and II, but a reduced presence of transmembrane helix IV, is observed at the dimer interface. To our knowledge, this study is one of the first to explore the correlation between cholesterol occupancy and GPCR organization. Our results indicate that dimer plasticity is relevant not just as an organizational principle but also as a subtle regulatory principle for GPCR function. We believe these results constitute an important step toward designing better drugs for GPCR dimer targets.</p>1 aPrasanna, Xavier1 aChattopadhyay, Amitabha1 aSengupta, Durba  uhttps://library.ncl.res.in/content/cholesterol-modulates-dimer-interface-beta2-adrenergic-receptor-cholesterol-occupancy-001742nas a2200169   4500008004100000022001400041245006700055210006600122260009000188300001000278490000600288520111000294100002101404700002001425700002801445856009901473       2016                        eng d  a2045-232200aCholesterol-dependent conformational plasticity in GPCR dimers0 aCholesteroldependent conformational plasticity in GPCR dimers  aMACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLANDbNATURE PUBLISHING GROUPcAUG  a318580 v63 a<p>The organization and function of the serotonin1A receptor, an important member of the GPCR family, have been shown to be cholesterol-dependent, although the molecular mechanism is not clear. We performed a comprehensive structural and dynamic analysis of dimerization of the serotonin1A receptor by coarse-grain molecular dynamics simulations totaling 3.6 ms to explore the molecular details of its cholesterol-dependent association. A major finding is that the plasticity and flexibility of the receptor dimers increase with increased cholesterol concentration. In particular, a dimer interface formed by transmembrane helices I-I was found to be sensitive to cholesterol. The modulation of dimer interface appears to arise from a combination of direct cholesterol occupancy and indirect membrane effects. Interestingly, the presence of cholesterol at the dimer interface is correlated with increased dimer plasticity and flexibility. These results represent an important step in characterizing the molecular interactions in GPCR organization with potential relevance to therapeutic interventions.</p>1 aPrasanna, Xavier1 aSengupta, Durba1 aChattopadhyay, Amitabha  uhttps://library.ncl.res.in/content/cholesterol-dependent-conformational-plasticity-gpcr-dimers00639nas a2200157   4500008004100000022001400041245008000055210006900135260008000204300001400284490000800298100002000306700002100326700002800347856010600375       2016                        eng d  a0006-349500aConformational dynamics of GPCR dimers is dependent on membrane cholesterol0 aConformational dynamics of GPCR dimers is dependent on membrane   a600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USAbBiophys SoccFEB  a356A-356A0 v1101 aSengupta, Durba1 aPrasanna, Xavier1 aChattopadhyay, Amitabha  uhttps://library.ncl.res.in/content/conformational-dynamics-gpcr-dimers-dependent-membrane-cholesterol02043nas a2200157   4500008004100000245010700041210006900148260003100217300001200248520141900260100002001679700001801699700002101717700002201738856012501760       2017                        eng d00aChapter 5: Experimental and computational approaches to study membranes and lipid-protein interactions0 aChapter 5 Experimental and computational approaches to study mem  bRoyal Society of Chemistry  a137-1603 a<p>Biological membranes are complex two-dimensional, non-covalent assemblies of a diverse variety of lipids and proteins. A hallmark of membrane organization is varying degrees of spatiotemporal heterogeneity spanning a wide range. Membrane proteins are implicated in a wide variety of cellular functions, and comprise ∼30% of the human proteome and ∼50% of the current drug targets. Their interactions with membrane lipids are recognized as crucial elements in their function. In this article, we provide an overview of experimental and theoretical approaches to analyze membrane organization, dynamics, and lipid-protein interactions. In this context, we highlight the wide range of time scales that membrane events span, and approaches that are suitable for a given time scale. We discuss representative fluorescence-based approaches (FRET and FRAP) that help to address questions on lipid-protein and protein-cytoskeleton interactions in membranes. In a complimentary fashion, we discuss computational methods, atomistic and coarse-grain, that are required to address a given membrane problem at an appropriate scale. We believe that the synthesis of knowledge gained from experimental and computational approaches will enable us to probe membrane organization, dynamics, and interactions at increasing spatiotemporal resolution, thereby providing a robust model for the membrane in health and disease.</p>1 aSengupta, Durba1 aKumar, Aditya1 aPrasanna, Xavier1 aChattopadhyay, A.  uhttps://library.ncl.res.in/content/chapter-5-experimental-and-computational-approaches-study-membranes-and-lipid-protein01700nas a2200121   4500008004100000245009600041210006900137520118700206100002001393700001901413700001801432856012801450       2017                        eng d00aCharacterizing clinically relevant natural variants of GPCRs using computational approaches0 aCharacterizing clinically relevant natural variants of GPCRs usi3 a<p>G protein-coupled receptors (GPCRs) are an important class of drug targets owing to their physiological role. A large number of clinically relevant single nucleotide polymorphisms (SNPs) have been observed in GPCRs that are linked to disease susceptibility and adverse drug response. It is therefore important to characterize the variants in order to improve GPCR therapeutics. Here, we discuss computational methods coupling molecular dynamics simulations with docking and free energy calculations to characterize the functional differences in GPCR variants. The hallmark of this approach is the explicit incorporation of receptor and membrane dynamics that allows us to analyze short- and long-range effects in the variant receptors. We use the SNPs reported in β2-adrenergic receptor (β2AR) as a test case and highlight the recent successes in analyzing structural and dynamic differences in a series of population variants. The computational approach we discuss here has a twofold benefit: it helps to unravel the molecular mechanisms underlying hypo- or hyperfunctionality of variant receptors as well as prioritizing novel variants that must be experimentally tested.</p>1 aSengupta, Durba1 aSonar, Krushna1 aJoshi, Manali  uhttps://library.ncl.res.in/content/characterizing-clinically-relevant-natural-variants-gpcrs-using-computational-approaches02094nas a2200169   4500008004100000022001400041245009000055210006900145260000800214300001200222490000800234520150600242100002001748700002001768700002001788856011601808       2021                        eng d  a1359-664000aCaveolin induced membrane curvature and lipid clustering: two sides of the same coin?0 aCaveolin induced membrane curvature and lipid clustering two sid  cDEC  a218-2350 v2323 aCaveolin-1 (cav-1) is a multi-domain membrane protein that is a key player in cell signaling, endocytosis and mechanoprotection. It is the principle component of cholesterol-rich caveolar domains and has been reported to induce membrane curvature. The molecular mechanisms underlying the interactions of cav-1 with complex membranes, leading to modulation of membrane topology and the formation of cholesterol-rich domains, remain elusive. In this study, we aim to understand the effect of lipid composition by analyzing the interactions of cav-1 with complex membrane bilayers comprised of about sixty lipid types. We have performed a series of coarse-grain molecular dynamics simulations using the Martini force-field with a cav-1 protein construct (residue 82-136) that includes the membrane binding domains and a palmitoyl tail. We observe that cav-1 induces curvature in this complex membrane, though it is restricted to a nanometer length scale. Concurrently, we observe a clustering of cholesterol, sphingolipids and other lipid molecules leading to the formation of nanodomains. Direct microsecond timescale interactions are observed for specific lipids such as cholesterol, phosphatidylserine and phosphatidylethanolamine lipid types. The results indicate that there is an interplay between membrane topology and lipid species. Our work is a step toward understanding how lipid composition and organization regulate the formation of caveolae, in the context of endocytosis and cell signaling.1 aPrakash, Shikha1 aKrishna, Anjali1 aSengupta, Durba  uhttps://library.ncl.res.in/content/caveolin-induced-membrane-curvature-and-lipid-clustering-two-sides-same-coin00559nas a2200157   4500008004100000022001400041245008000055210006900135260000900204300001400213490000800227100002000235700002000255700002000275856010600295       2021                        eng d  a0006-349500aCaveolin mediated curvature and clustering: from simple to complex membrane0 aCaveolin mediated curvature and clustering from simple to comple  cFEB   a232A-233A0 v1201 aPrakash, Shikha1 aKrishna, Anjali1 aSengupta, Durba  uhttps://library.ncl.res.in/content/caveolin-mediated-curvature-and-clustering-simple-complex-membrane02387nas a2200157   4500008004100000245011200041210006900153260000800222490000700230520177700237100002202014700001802036700002802054700002002082856012702102       2021                        eng d00aConformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR10 aConformational plasticity and dynamic interactions of the Ntermi  cMAY0 v173 a<p><span style="color: rgb(33, 33, 33); font-family: BlinkMacSystemFont, -apple-system, &quot;Segoe UI&quot;, Roboto, Oxygen, Ubuntu, Cantarell, &quot;Fira Sans&quot;, &quot;Droid Sans&quot;, &quot;Helvetica Neue&quot;, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400;">The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.</span></p>1 aKharche, Shalmali1 aJoshi, Manali1 aChattopadhyay, Amitabha1 aSengupta, Durba  uhttps://library.ncl.res.in/content/conformational-plasticity-and-dynamic-interactions-n-terminal-domain-chemokine-receptor02667nas a2200265   4500008004100000245013600041210006900177260000800246300001100254490000800265520177000273100001702043700001902060700002002079700002102099700001202120700001602132700001702148700002002165700003002185700002002215700002002235700001702255856012902272       2022                        eng d00aCopper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-10 aCopperII import and reduction are dependent on HisMet clusters i  cMAR  a1016310 v2983 a<p>
	Copper(I) is an essential metal for all life forms. Though Cu(II) is the most abundant and stable state, its reduction to Cu(I) via an unclear mechanism is prerequisite for its bioutilization. In eukaryotes, the copper transporter-1(CTR1) is the primary high-affinity copper importer, although its mechanism and role in Cu(II) reduction remain uncharacterized. Here we show that extracellular amino-terminus of human CTR1 contains two methionine-histidine clusters and neighboring aspartates that distinctly bind Cu(I) and Cu(II) preceding its import. We determined that hCTR1 localizes at the basolateral membrane of polarized MDCK-II cells and that its endocytosis to Common-Recycling-Endosomes is regulated by reduction of Cu(II) to Cu(I) and subsequent Cu(I) coordination by the methionine cluster. We demonstrate the transient binding of both Cu(II) and Cu(I) during the reduction process is facilitated by aspartates that also act as another crucial determinant of hCTR1 endocytosis. Mutating the first Methionine cluster ((7)Met-Gly-Met(9)) and Asp(13)( )abrogated copper uptake and endocytosis upon copper treatment. This phenotype could be reverted by treating the cells with reduced and nonreoxidizable Cu(I). We show that histidine clusters, on other hand, bind Cu(II) and are crucial for hCTR1 functioning at limiting copper. Finally, we show that two N-terminal His-Met-Asp clusters exhibit functional complementarity, as the second cluster is sufficient to preserve copper-induced CTR1 endocytosis upon complete deletion of the first cluster. We propose a novel and detailed mechanism by which the two His-Met-Asp residues of hCTR1 amino-terminus not only bind copper, but also maintain its reduced state, crucial for intracellular uptake.</p>
1 aKar, Sumanta1 aSen, Samarpita1 aMaji, Saptarshi1 aSaraf, Deepashri1 aRuturaj1 aPaul, Rupam1 aDutt, Sohini1 aMondal, Basudeb1 aRodriguez-Boulan, Enrique1 aSchreiner, Ryan1 aSengupta, Durba1 aGupta, Arnab  uhttps://library.ncl.res.in/content/copperii-import-and-reduction-are-dependent-his-met-clusters-extracellular-amino-terminus01829nas a2200217   4500008004100000022001400041245009100055210006900146260000900215490000700224520105300231653002101284653002101305653003701326653003501363653003101398100002001429700002001449700002001469856012201489       2023                        eng d  a1439-423500aCofilin-membrane interactions: electrostatic effects in phosphoinositide lipid binding0 aCofilinmembrane interactions electrostatic effects in phosphoino  cFEB 0 v243 a<p>
	The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP2 and PIP3 lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.</p>
10acomplex membrane10alipid clustering10aMartini coarse-grain simulations10aMolecular dynamics simulations10aProtein-lipid interactions1 aPrakash, Shikha1 aKrishna, Anjali1 aSengupta, Durba  uhttps://library.ncl.res.in/content/cofilin-membrane-interactions-electrostatic-effects-phosphoinositide-lipid-binding00738nas a2200205   4500008004100000022001400041245010300055210006900158260000900227300001100236490000800247653001700255100002600272700002400298700002000322700002000342700002400362700002000386856012600406       2024                        eng d  a0006-291X00aCell based assay using virus-like particles to screen AM type mimics for SARS-CoV-2 neutralisation0 aCell based assay using viruslike particles to screen AM type mim  cJUL   a1500820 v71810aMINIPROTEINS1 aGaur, Neeraj, Kailash1 aUrankar, Shreegauri1 aSengupta, Durba1 aChepuri, Ramana1 aMakde, Ravindra, D.1 aKulkarni, Kiran  uhttps://library.ncl.res.in/content/cell-based-assay-using-virus-particles-screen-am-type-mimics-sars-cov-2-neutralisation01994nas 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<p>
	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.</p>
1 aGharui, Sowmomita1 aSengupta, Durba1 aDas, Atanu  uhttps://library.ncl.res.in/content/characterization-conformational-hotspots-rna-dependent-rna-polymerase-complex-identifies