@article { ISI:000312519900005, title = {Cholesterol modulates the structure, binding modes, and energetics of caveolin-membrane interactions}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {50}, year = {2012}, month = {DEC}, pages = {14556-14564}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

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.

}, issn = {1520-6106}, doi = {10.1021/jp3077886}, author = {Sengupta, Durba} } @article { ISI:000333226900011, title = {Cholesterol modulates the dimer interface of the beta(2)-adrenergic receptor via cholesterol occupancy sites}, journal = {Biophysical Journal}, volume = {106}, number = {6}, year = {2014}, month = {MAR}, pages = {1290-1300}, publisher = {CELL PRESS}, type = {Article}, address = {600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA}, abstract = {

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.

}, issn = {0006-3495}, doi = {10.1016/j.bpj.2014.02.002}, author = {Prasanna, Xavier and Chattopadhyay, Amitabha and Sengupta, Durba} } @article { ISI:000381562500001, title = {Cholesterol-dependent conformational plasticity in GPCR dimers}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {AUG}, pages = {31858}, publisher = {NATURE PUBLISHING GROUP}, address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}, abstract = {

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.

}, issn = {2045-2322}, doi = {10.1038/srep31858}, author = {Prasanna, Xavier and Sengupta, Durba and Chattopadhyay, Amitabha} } @article { ISI:000375142200228, title = {Conformational dynamics of GPCR dimers is dependent on membrane cholesterol}, journal = {Biophysical Journal}, volume = {110}, number = {3, 1}, year = {2016}, note = {60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016}, month = {FEB}, pages = {356A-356A}, publisher = {Biophys Soc}, address = {600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA}, issn = {0006-3495}, author = {Sengupta, Durba and Prasanna, Xavier and Chattopadhyay, Amitabha} } @inbook {43964, title = {Chapter 5: Experimental and computational approaches to study membranes and lipid-protein interactions}, booktitle = {Computational biophysics of membrane proteins}, year = {2017}, pages = {137-160}, publisher = {Royal Society of Chemistry}, organization = {Royal Society of Chemistry}, chapter = {Experimental and computational approaches to study membranes and lipid-protein interactions}, abstract = {

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.

}, doi = {10.1039/9781782626695-00137}, author = {Sengupta, Durba and Kumar, G. Aditya and Prasanna, Xavier and Chattopadhyay, A.} } @inbook {43968, title = {Characterizing clinically relevant natural variants of GPCRs using computational approaches}, booktitle = {Methods in cell biology}, year = {2017}, abstract = {

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.

}, doi = {10.1016/bs.mcb.2017.07.013}, author = {Sengupta, Durba and Sonar, Krushna and Joshi, Manali} } @article {47574, title = {Caveolin induced membrane curvature and lipid clustering: two sides of the same coin?}, journal = {Faraday Discussions}, volume = {232}, year = {2021}, month = {DEC}, pages = {218-235}, type = {Article}, abstract = {Caveolin-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.}, issn = {1359-6640}, doi = {10.1039/d0fd00062k}, author = {Prakash, Shikha and Krishna, Anjali and Sengupta, Durba} } @article {47431, title = {Caveolin mediated curvature and clustering: from simple to complex membrane}, journal = {Biophysical Journal}, volume = {120}, year = {2021}, month = {FEB }, pages = {232A-233A}, type = {Meeting Abstract}, issn = {0006-3495}, doi = {10.1016/j.bpj.2020.11.1542}, author = {Prakash, Shikha and Krishna, Anjali and Sengupta, Durba} } @article {47462, title = {Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1}, journal = {Plos Computational Biology}, volume = {17}, year = {2021}, month = {MAY}, type = {Article}, abstract = {

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.

}, doi = {10.1371/journal.pcbi.1008593}, author = {Kharche, Shalmali and Joshi, Manali and Chattopadhyay, Amitabha and Sengupta, Durba} } @article {48207, title = {Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1}, journal = {Journal of Biological Chemistry}, volume = {298}, year = {2022}, month = {MAR}, pages = {101631}, type = {Article}, abstract = {

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.

}, doi = {10.1016/j.jbc.2022.101631}, author = {Kar, Sumanta and Sen, Samarpita and Maji, Saptarshi and Saraf, Deepashri and Ruturaj and Paul, Rupam and Dutt, Sohini and Mondal, Basudeb and Rodriguez-Boulan, Enrique and Schreiner, Ryan and Sengupta, Durba and Gupta, Arnab} } @article {48442, title = {Cofilin-membrane interactions: electrostatic effects in phosphoinositide lipid binding}, journal = {ChemPhysChem}, volume = {24}, year = {2023}, month = {FEB }, type = {Article}, abstract = {

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.

}, keywords = {complex membrane, lipid clustering, Martini coarse-grain simulations, Molecular dynamics simulations, Protein-lipid interactions}, issn = {1439-4235}, doi = {10.1002/cphc.202200509}, author = {Prakash, Shikha and Krishna, Anjali and Sengupta, Durba} } @article {49386, title = {Cell based assay using virus-like particles to screen AM type mimics for SARS-CoV-2 neutralisation}, journal = {BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, volume = {718}, year = {2024}, month = {JUL }, pages = {150082}, type = {Journal Article}, keywords = {MINIPROTEINS}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2024.150082}, author = {Gaur, Neeraj Kailash and Urankar, Shreegauri and Sengupta, Durba and Chepuri, V. Ramana and Makde, Ravindra D. and Kulkarni, Kiran} } @article {49216, title = {Characterization of the conformational hotspots of the RNA-dependent RNA polymerase complex identifies a unique structural malleability of nsp8}, journal = {Journal of Physical Chemistry B}, volume = {128}, year = {2024}, month = {OCT }, pages = {9959-9975}, type = {Article}, abstract = {

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 {\textquoteleft}{\textquoteleft}prime{\textquoteright}{\textquoteright} 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.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.4c03851}, author = {Gharui, Sowmomita and Sengupta, Durba and Das, Atanu} }