00660nas a2200181 4500008004100000022001400041245009900055210006900154260000800223300000800231490000700239100002500246700001900271700001900290700002000309700001800329856013100347 2021 eng d a0175-757100aWater mediated allosteric network in beta 2AR T164I variant modulates agonist binding affinity0 aWater mediated allosteric network in beta 2AR T164I variant modu cJUL a1620 v501 aNikte, Siddhanta, V.1 aSonar, Krushna1 aTandale, Aditi1 aSengupta, Durba1 aJoshi, Manali uhttps://library.ncl.res.in/content/water-mediated-allosteric-network-beta-2ar-t164i-variant-modulates-agonist-binding-affinity02556nas a2200253 4500008004100000022001400041245010300055210007000158260000800228300001200236490000700248520172200255653002301977653003102000653002602031653000902057653001802066653002102084653002002105100002502125700001802150700002002168856011402188 2024 eng d a0887-358500aState-dependent dynamics of extramembrane domains in the β2-adrenergic receptor0 aStatedependent dynamics of extramembrane domains in the iβisub2s cMAR a317-3280 v923 a

G protein-coupled receptors (GPCRs) are membrane-bound signaling proteins that play an essential role in cellular signaling processes. Due to their intrinsic function of transmitting internal signals in response to external cues, these receptors are adapted to be highly dynamic in nature. The beta(2)-adrenergic receptor (beta 2AR) is a representative member of the family that has been extensively analyzed in terms of its structure and activation. Although the structure of the transmembrane domain has been characterized in the different functional states of the receptor, the conformational dynamics of the extramembrane domains, especially the intrinsically disordered regions are still emerging. In this study, we analyze the state-dependent dynamics of extramembrane domains of beta(2)AR using atomistic molecular dynamics simulations. We introduce a parameter, the residue excess dynamics that allows us to better quantify receptor dynamics. Using this measure, we show that the dynamics of the extramembrane domains are sensitive to the receptor state. Interestingly, the ligand-bound intermediate R' state shows the maximal dynamics compared to either the active R*G or inactive R states. Ligand binding appears to be correlated with high residue excess dynamics that are dampened upon G protein coupling. The intracellular loop-3 (ICL3) domain has a tendency to flip towards the membrane upon ligand binding, which could contribute to receptor ``priming.'' We highlight an important ICL1-helix-8 interplay that is broken in the ligand-bound state but is retained in the active state. Overall, our study highlights the importance of characterizing the functional dynamics of the GPCR loop domains.

10aallosteric pathway10abeta-2 adrenergic receptor10aextramembrane domains10aGPCR10aloop dynamics10aprotein dynamics10aprotein network1 aNikte, Siddhanta, V.1 aJoshi, Manali1 aSengupta, Durba uhttps://library.ncl.res.in/content/state-dependent-dynamics-extramembrane-domains-%CE%B22-adrenergic-receptor02774nas a2200241 4500008004100000022001400041245015600055210006900211260000800280300001400288490000700302520190400309653001902213653001602232653000902248653003602257653001502293653002702308100002502335700002002360700002802380856012402408 2026 eng d a1948-719300aSpecificity and promiscuity of phosphoinositide lipid interactions with the serotonin1A receptor: insights from submillisecond coarse-grain simulations0 aSpecificity and promiscuity of phosphoinositide lipid interactio cMAR a1104-11140 v173 a

G protein-coupled receptors (GPCRs) are lipid-dependent membrane receptors that serve as important cell signaling hubs. Phosphoinositide (PIP) lipids represent an important class of anionic lipids that play vital roles in neuronal function and signaling. PIP lipids have been reported to modulate GPCR function, although the specificity and molecular details of the interactions are still not clear. An important GPCR in this context is the serotonin(1A) receptor, a neurotransmitter GPCR, which has been reported to interact with phosphatidylinositol 4-phosphate (PIP1) lipids. In this work, we computationally analyzed the specificity of the serotonin(1A) receptor-PIP lipid interactions using coarse-grain molecular dynamics simulations. Our results predict that four anionic lipid sites are present at the receptor surface, although the relative populations are dependent on the lipid type. PIP1 lipids exhibit the highest interaction at a charged cleft formed by transmembrane helices VI and VII. We observed electrostatic interactions at a cluster of charged residues (Arg341, Lys342, Lys345) and hydrophobic and aromatic interactions at residue Ile349 and Tyr402. In contrast, phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3) lipids interact more with transmembrane helix IV. We observed that anionic phospholipids such as phosphatidylserine (PS) interact at these sites, although their occupancy at these sites is much reduced. By elucidating the molecular determinants of these interactions in silico, this study generates novel, testable hypotheses regarding the functional role of specific lipid-receptor contacts. Our work constitutes an important step in analyzing molecular signatures of phosphoinositide lipid-GPCR interactions in the overall context of diverse roles of phosphoinositides in neuronal function and signaling.

10aanionic lipids10aCholesterol10aGPCR10aMARTINIcoarse-grain simulations10aPIP lipids10aserotonin(1A) receptor1 aNikte, Siddhanta, V.1 aSengupta, Durba1 aChattopadhyay, Amitabha uhttps://library.ncl.res.in/content/specificity-and-promiscuity-phosphoinositide-lipid-interactions-serotonin1a-receptor