@article {44647, title = {Dynamics of loops at the substrate entry channel determine the specificity of iridoid synthases}, journal = {Febs Letters}, volume = {592}, year = {2018}, month = {AUG}, pages = {2624-2635}, abstract = {

Iridoid synthases belong to the family of short-chain dehydrogenase reductase involved in the biosynthesis of iridoids. Despite having high sequence and structural homology with progesterone 5 beta- reductase, these enzymes exhibit differential substrate specificities. Previously, two loops. L1 and L2 at substrate-binding pocket, were suggested to be involved in generating substrate specificity. However, the structural basis of specificity determinants was elusive. Here, combining sequence and structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we have shown that iridoid synthase contains two channels for substrate entry whose geometries are altered by L1-L2 dynamics, primarily orchestrated by interactions of residues Glu161 and Gly162 of L1 and Asn358 of L2. A complex interplay of these interactions confer the substrate specificity to the enzyme.

}, keywords = {iridoid synthase, iridoids, Molecular dynamics simulations, progesterone 5 beta-reductase, Substrate specificity}, issn = {1873-3468}, doi = {10.1002/1873-3468.13174}, author = {Sandholu, Anand S. and Mohole, Madhura and Duax, William L. and Thulasiram, Hirekodathakallu V. and Sengupta, Durba and Kulkarni, Kiran} } @article {44474, title = {Exploring GPCR lipid interactions by molecular dynamics simulations: excitements, challenges, and the way forward}, journal = {Journal of Physical Chemistry B}, volume = {122}, year = {2018}, month = {JUN}, pages = {5727-5737}, abstract = {Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.}, doi = {10.1021/acs.jpcb.8b01657}, author = {Sengupta, Durba and Prasanna, Xavier and Mohole, Madhura and Chattopadhyay, Amitabha} } @inbook {47149, title = {Molecular determinants of GPCR oligomerization}, booktitle = {Molecular determinants of GPCR oligomerization}, number = {GPCRs}, year = {2020}, pages = {97-108}, doi = {10.1016/B978-0-12-816228-6.00006-4}, author = {Mohole, Madhura and Kumar, G. Aditya and Sengupta, Durba and Chattopadhyay, Amitabha} } @article {46943, title = {Role of cholesterol-mediated effects in GPCR heterodimers}, journal = {Chemistry and Physics of Lipids}, volume = {227}, year = {2020}, month = {MAR}, pages = {104852}, type = {Article}, abstract = {

G protein-coupled receptors (GPCRs) are transmembrane receptors that mediate a large number of cellular responses. The organization of GPCRs into dimers and higher-order oligomers is known to allow a larger repertoire of downstream signaling events. In this context, a crosstalk between the adenosine and dopamine receptors has been reported, indicating the presence of heterodimers that are functionally relevant. In this paper, we explored the effect of membrane cholesterol on the adenosine(2A) (A(2A)) and dopamine D-3 (D-3) receptors using coarse-grain molecular dynamics simulations. We analyzed cholesterol interaction sites on the A(2A) receptor and were able to reproduce the sites indicated by crystallography and previous atomistic simulations. We predict novel cholesterol interaction sites on the D-3 receptor that could be important in the reported cholesterol sensitivity in receptor function. Further, we analyzed the formation of heterodimers between the two receptors. Our results suggest that membrane cholesterol modulates the relative population of several co-existing heterodimer conformations. Both direct receptor-cholesterol interaction and indirect membrane effects contribute toward the modulation of heterodimer conformations. These results constitute one of the first examples of modulation of GPCR hetero-dimerization by membrane cholesterol, and could prove to be useful in designing better therapeutic strategies.

}, keywords = {Adenosine(2A) receptor, Cholesterol, Dopamine D-3 receptor, G protein-coupled receptors, Heterodimer, MARTINI coarse-grain simulation}, issn = {0009-3084}, doi = {10.1016/j.chemphyslip.2019.104852}, author = {Prasanna, Xavier and Mohole, Madhura and Chattopadhyay, Amitabha and Sengupta, Durba} } @article {48347, title = {Synergistic and competitive lipid interactions in the serotonin1A receptor microenvironment}, journal = {ACS Chemical Neuroscience}, volume = {13}, year = {2022}, month = {DEC }, pages = {3403-3415}, type = {Article}, abstract = {

The interaction of lipids with G-protein-coupled receptors (GPCRs) has been shown to modulate and dictate several aspects of GPCR organization and function. Diverse lipid interaction sites have been identified from structural biology, bioinformatics, and molecular dynamics studies. For example, multiple cholesterol interaction sites have been identified in the serotonin1A receptor, along with distinct and overlapping sphingolipid interaction sites. How these lipids interact with each other and what is the resultant effect on the receptor is still not clear. In this work, we have analyzed lipid-lipid crosstalk at the receptor of the serotonin1A receptor embedded in a membrane bilayer that mimics the neuronal membrane composition by long coarse-grain simulations. Using a set of similarity coefficients, we classified lipids that bind at the receptor together as synergistic cobinding, and those that bind individually as competitive. Our results show that certain lipids interact with the serotonin1A receptor in synergy with each other. Not surprisingly, the ganglioside GM1 and cholesterol show a synergistic cobinding, along with the relatively uncommon GM1-phosphatidylethanolamine (PE) and cholesterol-PE synergy. In contrast, certain lipid pairs such as cholesterol and sphingomyelin appear to be in competition at several sites, despite their coexistence in lipid nanodomains. In addition, we observed intralipid competition between two lipid tails, with the receptor exhibiting increased interactions with the unsaturated lipid tails. We believe our work represents an important step in understanding the diversity of GPCR-lipid interactions and exploring synergistic cobinding and competition in natural membranes.

}, keywords = {GPCR, lipid crosstalk, Martini coarse-grain simulations, Membrane cholesterol, neuronal membranes}, issn = {1948-7193}, doi = {10.1021/acschemneuro.2c00422}, author = {Mohole, Madhura and Sengupta, Durba and Chattopadhyay, Amitabha} }