Article
Biochemistry & Molecular Biology
Abhishek Kumar, Parijat Sarkar, Amitabha Chattopadhyay
Summary: The depletion of sphingolipids has been shown to reduce the cell surface expression of the serotonin(1A) receptor, without altering the total cellular level of the receptor. This impairment in receptor trafficking was reversed upon replenishment with sphingolipids, indicating a role for sphingolipids in neurotransmitter receptor signaling and trafficking.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
G. Aditya Kumar, Parijat Sarkar, Tomasz Maciej Stepniewski, Md Jafurulla, Shishu Pal Singh, Jana Selent, Amitabha Chattopadhyay
Summary: Several G protein-coupled receptors (GPCRs) exhibit cholesterol sensitivity, attributed to specific sequences and structural features like the CRAC motif. This study explored the molecular basis of cholesterol sensitivity in the serotonin(1A) receptor and found a crucial lysine residue for sensing altered membrane cholesterol levels. Insights from molecular dynamics simulations revealed that cholesterol-sensitive functional states in the receptor are associated with reduced conformational dynamics of extracellular loops.
Article
Cell Biology
Abhishek Kumar, Parijat Sarkar, Amitabha Chattopadhyay
Summary: G protein-coupled receptors (GPCRs) are important cellular signaling machinery and account for approximately 40% of drug targets. This study explores the contribution of sphingolipids, essential functional lipids implicated in neurological functions, in GPCR endocytosis. The results show that sphingolipid depletion inhibits the agonist-induced endocytosis of serotonin(1A) receptors in a concentration-dependent manner, highlighting the specific requirement of sphingolipids for this process. These findings reveal the regulatory role of sphingolipids in GPCR endocytosis and emphasize the importance of neurotransmitter receptor trafficking in health and disease.
Article
Immunology
Sofia R. Gardeta, Eva M. Garcia-Cuesta, Gianluca D'Agostino, Blanca Soler Palacios, Adriana Quijada-Freire, Pilar Lucas, Jorge Bernardino de la Serna, Carolina Gonzalez-Riano, Coral Barbas, Jose Miguel Rodriguez-Frade, Mario Mellado
Summary: The local lipid environment plays an important role in regulating CXCR4 organization and function, and modulating chemokine-triggered directed cell migration. Treatment of T cells with bacterial sphingomyelinase alters the lipid composition of the cell membrane, affecting membrane fluidity and CXCR4 nanoclustering and dynamics.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Denis S. Grebenkov
Summary: This paper investigates the depletion of a stock by a population of species that consume resources through ordinary diffusion. The exact form of the probability density of the depletion time is derived, and the dependence of this distribution on various factors is analyzed. The findings provide insights for better control and replenishment of resources.
Article
Chemistry, Physical
Zhaoqian Su, Kalyani Dhusia, Yinghao Wu
Summary: The binding of cell surface receptors with their extracellular ligands initiates various intracellular signaling pathways, but our understanding of the cellular functions of these receptors is limited. Membrane undulations negatively affect ligand-receptor interactions, and the preassembly of membrane receptors can accelerate ligand binding kinetics and reduce noise during the process. These findings underscore the importance of membrane environments in regulating the function of membrane receptors and suggest potential applications of the simulation method in specific receptor systems involved in cell signaling.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Timo N. Haschler, Harry Horsley, Monika Balys, Glenn Anderson, Jan-Willem Taanman, Robert J. Unwin, Jill T. Norman
Summary: SIRT5 plays a critical role in ischemic renal injury, with its depletion affecting mitochondrial function in murine and human proximal tubular epithelial cells.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jonathan W. Kanen, Annemieke M. Apergis-Schoute, Robyn Yellowlees, Frederique E. Arntz, Febe E. van der Flier, Annabel Price, Rudolf N. Cardinal, David M. Christmas, Luke Clark, Barbara J. Sahakian, Molly J. Crockett, Trevor W. Robbins
Summary: Serotonin plays a crucial role in updating responses to changing environmental circumstances, optimising behavior, and modifying autonomic responses to threats. Depleting serotonin precursor tryptophan leads to impairments in updating actions and autonomic responses, exacerbating reversal deficits in individuals.
MOLECULAR PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Marjorie Damian, Maxime Louet, Antoniel Augusto Severo Gomes, Celine M'Kadmi, Severine Denoyelle, Sonia Cantel, Sophie Mary, Paulo M. Bisch, Jean-Alain Fehrentz, Laurent J. Catoire, Nicolas Floquet, Jean-Louis Baneres
Summary: The membrane plays a crucial role in modulating the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific lipid interactions and bulk effects. PIP2 and GM3 induce shifts in the conformational equilibrium of GHSR, favoring G protein activation in different ways.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Hamid Reza Kalhor, Elham Taghikhani
Summary: The study investigated the effect of commonly used drugs on the release of warfarin bound to HSA in silico. Both s-ibuprofen and ascorbic acid were found to exhibit allosteric effects on the release of warfarin from HSA, with ibuprofen showing a stabilizing effect and ascorbic acid aiding in the release through destabilization of HSA. Molecular dynamics simulations provided valuable insights into the interactions of drugs with the protein and the mechanism of anticoagulant release.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Multidisciplinary
Bin Li, Kejiao Gao, Yurong Li, Yuansheng Li, Longyi Zhu, Xuanyu Fu, Xiyong Zhuo, Ying Wu, Ying Wan, Shengyuan Deng
Summary: Recent studies have shown that enzymes undergo chemotaxis during catalysis. This study demonstrated the chemotaxis of zinc porphyrin as a cofactor mimic and its directed motions induced by ligand-protein binding. The dissociation constant for selected recognition was obtained by measuring the chemotactic shift, and a statistical thermodynamic model was derived to explain the directional migration of receptors.
Article
Multidisciplinary Sciences
Ying Chen, Jinyi Zhang, Yuan Weng, Yueming Xu, Weiqiang Lu, Wei Liu, Mingyao Liu, Tian Hua, Gaojie Song
Summary: This study presents the structures of the human adenosine A2B receptor (A2BR) bound to its agonists NECA and BAY60-6583, elucidating the orthosteric binding pockets and their subtle differences. Selectivity is mainly determined by regions extended from the orthosteric pocket, and the key determinants for BAY60-6583's selectivity against A2BR are identified. This study provides a better understanding of ligand selectivity in the adenosine receptor family and offers a structural template for the development of A2BR ligands for related diseases.
Article
Chemistry, Organic
Nicolas Nyssen, Daniela Ajami, Adrien Ardelean, Florent Desroches, Jing Li, Michel Luhmer, Olivia Reinaud, Ivan Jabin
Summary: The study on a molecular capsule based on a calix[6]arene core reveals unique coordination modes to prevent guest molecule exchange and evaluates the impact of different closing mechanisms on binding ability. The selective binding of different ligands through metal ion coordination highlights the importance of rigidification of receptor conformation. However, increased rigidity may weaken host-guest interactions, affecting the induced-fit behaviors observed in the parent compound.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Su Hui Yang, Daulat Bikram Khadka, Jinhe Han, Soon-Young Na, Minsang Shin, Don-Kyu Kim, Byung-Chul Oh, Eun Young Kim, Hueng-Sik Choi, Won-Jea Cho
Summary: ERR gamma is an orphan nuclear receptor similar to estrogen receptors, but its endogenous ligand is unknown. Only stilbene and flavonol molecules have been found to modulate its transcriptional activity, but without selectivity. Therefore, virtual screening identified a novel ERR gamma inverse agonist, pyrazolamide 7, and its optimized derivative, pyrazolamide 19, showed potent and selective inverse agonistic activity towards ERR gamma. Pyrazolamide 19 exhibited strong affinity towards ERR gamma and inhibited the expression of hepcidin, fibrinogen, and gluconeogenic genes, suggesting potential antimicrobial, anti-coagulant, and antidiabetic activities.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Mark T. Agasid, Lars Sorensen, Leonhard H. Urner, Jun Yan, Carol Robinson
Summary: The use of mass spectrometry to study G protein-coupled receptors has revealed insights into sodium binding and ligand-induced changes, providing valuable information for understanding GPCR function.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Sourav Ganguly, Pushpendra Singh, Raman Manoharlal, Rajendra Prasad, Amitabha Chattopadhyay
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2009)
Article
Biochemistry & Molecular Biology
Sourav Ganguly, Andrew H. A. Clayton, Amitabha Chattopadhyay
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2011)
Article
Biochemistry & Molecular Biology
Sourav Ganguly, Yamuna Devi Paila, Amitabha Chattopadhyay
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2011)
Article
Biochemistry & Molecular Biology
Sandeep Shrivastava, Thomas J. Pucadyil, Yamuna Devi Paila, Sourav Ganguly, Amitabha Chattopadhyay
Article
Biochemistry & Molecular Biology
Sourav Ganguly, Roopali Saxena, Amitabha Chattopadhyay
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2011)
Article
Biophysics
Sourav Ganguly, Thomas J. Pucadyil, Amitabha Chattopadhyay
BIOPHYSICAL JOURNAL
(2008)
Article
Biophysics
Sourav Ganguly, Amitabha Chattopadhyay
BIOPHYSICAL JOURNAL
(2010)
Article
Biophysics
Sourav Ganguly, Andrew H. A. Clayton, Amitabha Chattopadhyay
BIOPHYSICAL JOURNAL
(2011)
Article
Chemistry, Medicinal
Enza Lacivita, Marcello Leopoldo, Anna Carmela Masotti, Carmela Inglese, Francesco Berardi, Roberto Perrone, Sourav Ganguly, Md Jafurulla, Amitabha Chattopadhyay
JOURNAL OF MEDICINAL CHEMISTRY
(2009)
Article
Multidisciplinary Sciences
Roopali Saxena, Sourav Ganguly, Amitabha Chattopadhyay
Article
Biochemistry & Molecular Biology
H. Raghuraman, Sourav Ganguly, Amitabha Chattopadhyay
BIOPHYSICAL CHEMISTRY
(2006)