@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 {47106, title = {Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants}, journal = {Biochemical and Biophysical Research Communications}, volume = {536}, year = {2021}, month = {JAN }, pages = {107-114}, type = {Article}, abstract = {

Sesquiterpene synthases catalyse cyclisation of farnesyl pyrophosphate to produce diverse sesquiterpenes. Despite utilising the same substrate and exhibiting significant sequence and structural homology, these enzymes form different products. Previous efforts were based on identifying the effect of divergent residues present at the catalytic binding pocket on the product specificity of these enzymes. However, the rationales deduced for the product specificity from these studies were not generic enough to be applicable to other phylogenetically distant members of this family. To address this problem, we have developed a novel approach combining sequence, structural and dynamical information of plant sesquiterpene synthases (SSQs) to predict product modulating residues (PMRs). We tested this approach on the SSQs with known PMRs and also on sesquisabinene synthase 1 (SaSQS1), a SSQ from Indian sandalwood. Our results show that the dynamical sectors of SSQs obtained from molecular dynamics simulation and their hydrophobicity and vicinity indices together provide leads for the identification of PMRs. The efficacy of the technique was tested on SaSQS1 using mutagenesis. To the best of our knowledge, this is a first technique of this kind which provides cues on PMRs of SSQs, with divergent phylogenetic relationship. (C) 2020 Elsevier Inc. All rights reserved.

}, keywords = {molecular dynamics, Product specificity, Sesquiterpene synthases, Statistical coupling analysis, X-ray crystallography}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2020.12.041}, author = {Singh, Sneha and Thulasiram, V, Hirekodathakallu and Sengupta, Durba and Kulkarni, Kiran} } @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 {48463, title = {Surface-induced demixing of self-assembled isomeric mixtures of citral}, journal = {Journal of Molecular Liquids}, volume = {381}, year = {2023}, month = {JUL }, pages = {121803}, type = {Article}, abstract = {

The self-assembly of organic molecules and their interactions with metal surfaces have been of considerable interest, both for developing novel functional materials and for understanding fundamental design principles of nanostructures. In this study, we investigate the solution and surface-induced self-assembly of two stereoisomers of citral molecules (geranial and neral) using atomistic molecular dynamics simulations. We demonstrate that the morphology of the aggregates in water is concentration dependent (ranging from distorted spherical to slab-like aggregates) but independent of isomer effects. The isomeric mixtures of citral indicate homogeneous mixing based on differential density maps and high values of Shannon entropy. Interestingly, surface-confinement of citral aggregates on a Cu(111) surface leads to phase segregation and demixing of the two isomers that is more apparent in the surface-bound monolayer in comparison to the adjacent layers. Positional ordering and formation of domains are observed over a series of isomeric citral mixtures with varying compositions, as indicated by high differential density and low values of Shannon entropy. Our work provides new insights into molecular self-assembly of organic molecules in nanostructures and metal-organic overlayers.(c) 2023 Elsevier B.V. All rights reserved.

}, keywords = {Citral, Isomers, Metal-organic interactions, molecular dynamics, Self-assembly, Shannon entropy}, issn = {0167-7322}, doi = {10.1016/j.molliq.2023.121803}, author = {Saraf, Deepashri and Prakash, Shikha and Pinjari, Aadil and Pujari, Bhalchandra and Sengupta, Durba} }