@article {46342, title = {Differential dynamics underlying the Gln27Glu population variant of the beta(2)-adrenergic receptor}, journal = {Journal of Membrane Biology}, volume = {252}, year = {2019}, month = {OCT}, pages = {499-507}, type = {Article}, abstract = {

The beta (2)-adrenergic receptor (beta (2)AR) is a membrane-bound G-protein-coupled receptor and an important drug target for asthma. Clinical studies report that the population variant Gln27Glu is associated with a differential response to common asthma drugs, such as albuterol, isoproterenol and terbutaline. Interestingly, the 27th amino acid is positioned on the N-terminal region that is the most flexible and consequently the least studied part of the receptor. In this study, we probe the molecular origin of the differential drug binding by performing structural modeling and simulations of the wild-type (Gln) and variant (Glu) receptors followed by ensemble docking with the ligands, albuterol, isoproterenol and terbutaline. In line with clinical studies, the ligands were observed to interact preferentially with the Glu variant. Our results indicate that the Glu residue at the 27th position perturbs the network of electrostatic interactions that connects the N-terminal region to the binding site in the wild-type receptor. As a result, the Glu variant is observed to bind better to the three ligands tested in this study. Our study provides a structural basis to explain the variable drug response associated with the 27th position polymorphism in the beta (2)AR and is a starting step to identify genotype-specific therapeutics.

}, keywords = {beta(2)-Adrenergic receptor, G-protein-coupled receptor, GPCR, molecular dynamics, Pharmacogenetics, SNP}, issn = {0022-2631}, doi = {10.1007/s00232-019-00093-2}, author = {Bhosale, Sumedha and Nikte, V. Siddhanta and Sengupta, Durba and Joshi, Manali} } @article {47034, title = {Loss of a water-mediated network results in reduced agonist affinity in a beta(2)-adrenergic receptor clinical variant}, journal = {Biochimica ET Biophysica Acta-Proteins and Proteomics}, volume = {1869}, year = {2021}, month = {APR}, pages = {140605}, type = {Article}, abstract = {

The beta(2)-adrenergic receptor (beta(2)AR) is a member of the G protein-coupled receptor (GPCR) family that is an important drug target for asthma and COPD. Clinical studies coupled with biochemical data have identified a critical receptor variant, Thr164Ile, to have a reduced response to agonist-based therapy, although the molecular mechanism underlying this seemingly {\textquoteleft}{\textquoteleft}non-deleterious{\textquoteright}{\textquoteright} substitution is not clear. Here, we couple molecular dynamics simulations with network analysis and free-energy calculations to identify the molecular determinants underlying the differential drug response. We are able to identify hydration sites in the transmembrane domain that are essential to maintain the integrity of the binding site but are absent in the variant. The loss of these hydration sites in the variant correlates with perturbations in the intra-protein interaction network and rearrangements in the orthosteric ligand binding site. In conjunction, we observe an altered binding and reduced free energy of a series of agonists, in line with experimental trends. Our work identifies a functional allosteric pathway connected by specific hydration sites in beta(2)AR that has not been reported before and provides insight into water-mediated networks in GPCRs in general. Overall, the work is one of the first step towards developing variant-specific potent and selective agonists.

}, keywords = {beta(2)-Adrenergic receptor, G protein coupled receptor, GPCR, molecular dynamics, Pharmacogenetics, SNP}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2021.140605}, author = {Nikte, V. Siddhanta and Sonar, Krushna and Tandale, Aditi and Joshi, Manali and Sengupta, Durba} } @article {48233, title = {Comparative analysis and structural modeling of elaeis oleifera FAD2, a fatty acid desaturase involved in unsaturated fatty acid composition of american oil palm}, journal = {Biology-Basel}, volume = {11}, year = {2022}, month = {APR}, pages = {529}, type = {Article}, abstract = {

Simple Summary Palm oil has become the world{\textquoteright}s most important vegetable oil in terms of production quantity, and its overall demand is exponentially growing with the global population. The fatty acid composition and particularly the oleic/linoleic acid ratio are major factors influencing palm oil quality. In this study, we focused on FAD2, a fatty acid desaturase enzyme involved in the desaturation and conversion of oleic acid to linoleic acid in Elaeis oleifera, identified through in silico annotation analysis. Our phylogenetic and comparative studies revealed two SNP markers, SNP278 and SNP851, significantly correlated with the oleic/linoleic acid contents. Our study provides fundamental insights into the mechanism of fatty acids synthesis in oil palm and could support the application of molecular biology techniques to enhance the enzymatic activity and substrate affinity of EoFAD2. American oil palm (Elaeis oleifera) is an important source of dietary oil that could fulfill the increasing worldwide demand for cooking oil. Therefore, improving its production is crucial and could be realized through breeding and genetic engineering approaches aiming to obtain high-yielding varieties with improved oil content and quality. The fatty acid composition and particularly the oleic/linoleic acid ratio are major factors influencing oil quality. Our work focused on a fatty acid desaturase (FAD) enzyme involved in the desaturation and conversion of oleic acid to linoleic acid. Following the in silico identification and annotation of Elaeis oleifera FAD2, its molecular and structural features characterization was performed to better understand the mechanistic bases of its enzymatic activity. EoFAD2 is 1173 nucleotides long and encodes a protein of 390 amino acids that shares similarities with other FADs. Interestingly, the phylogenetic study showed three distinguished groups where EoFAD2 clustered among monocotyledonous taxa. EoFAD2 is a membrane-bound protein with five transmembrane domains presumably located in the endoplasmic reticulum. The homodimer organization model of EoFAD2 enzyme and substrates and respective substrate-binding residues were predicted and described. Moreover, the comparison between 24 FAD2 sequences from different species generated two interesting single-nucleotide polymorphisms (SNPs) associated with the oleic/linoleic acid contents.

}, keywords = {FAD2, Fatty acids, in silico annotation, linoleic acid ratio, oil palm, oleic, SNP, structural modeling}, doi = {10.3390/biology11040529}, author = {Ben Ayed, Rayda and Chirmade, Tejas and Hanana, Mohsen and Khamassi, Khalil and Ercisli, Sezai and Choudhary, Ravish and Kadoo, Narendra and Karunakaran, Rohini} }