@inbook { ISI:000375719300020,
	title = {What can simulations tell us about GPCRs: integrating the scales},
	booktitle = {G Protein-Coupled Receptors: Signaling, Trafficking and Regulation},
	series = {Methods in Cell Biology},
	volume = {132},
	year = {2016},
	pages = {429-452},
	publisher = {Elsevier Academic Press Inc.},
	organization = {Elsevier Academic Press Inc.},
	address = {525 B Street, Suite 1900, San Diego, CA 92101-4495 USA :},
	abstract = {<p>The functional dynamics of G protein-coupled receptors (GPCRs) encompasses multiple spatiotemporal scales, ranging from femtoseconds to seconds and Angstroms to micrometers. Computational approaches, often in close collaboration with experimental methods, have been invaluable in unraveling GPCR structure and dynamics at these various hierarchical levels. The binding of natural and synthetic ligands to the wild-type and naturally occurring variant receptors have been analyzed by several computational methods. The activation of receptors from the inactive to the active state has been investigated by atomistic simulations and ongoing work on several receptors will help uncover general and receptor-specific mechanisms. The interaction of GPCRs with complex membranes that contain phospholipids and cholesterol have been probed by coarse-grain methods and shown to directly influence receptor association. In this chapter, we discuss computational approaches that have been successful in analyzing each scale of GPCR dynamics. An overview of these approaches will allow a more judicious choice of the appropriate method. We hope that an appreciation of the power of current computational approaches will encourage more critical collaborations. A comprehensive integration of the different approaches over the entire spatiotemporal scales promises to unravel new facets of GPCR function.</p>},
	isbn = {978-0-12-803612-9; 978-0-12-803595-5},
	issn = {0091-679X},
	doi = {10.1016/bs.mcb.2015.11.007},
	author = {Sengupta, Durba and Joshi, Manali and Athale, Chaitanya A. and Chattopadhyay, Amitabha},
	editor = {Shukla, AK}
}
@article {47726,
	title = {Water mediated allosteric network in beta 2AR T164I variant modulates agonist binding affinity},
	journal = {European Biophysics Journal with Biophysics Letters},
	volume = {50},
	year = {2021},
	month = {JUL},
	pages = {162},
	type = {Meeting Abstract},
	issn = {0175-7571},
	author = {Nikte, Siddhanta V. and Sonar, Krushna and Tandale, Aditi and Sengupta, Durba and Joshi, Manali}
}
@article {48673,
	title = {Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily},
	journal = {iScience},
	volume = {26},
	year = {2023},
	month = {JUL},
	pages = {107031},
	type = {Article},
	abstract = {<p>
	The Ras superfamily of GTPases regulate critical cellular processes by shuttling between GTP-bound ON and GDP-bound OFF states. This switching mechanism is attributed to the conformational changes in two loops, SWI and SWII, upon GTP binding and hydrolysis. Since these conformational changes vary across the Ras superfamily, there is no generic parameter to define their functional states. A unique wavelet coherence (WC) analysis-based approach developed here shows that the structural changes in switch regions could be mapped onto the wavelet coherence phase couplings (WPCs). Thus, WPCs could serve as unique parameters to define their functional states. Disentanglement of WPCs in oncogenic GTPases shows how breakdown of structural allostery leads to their aberrant function. These observations stand out even for simulated ensemble of switch region conformers. Overall, for the first time, we show that WPCs could unravel the latent structural deviations in Ras proteins to decode their universal switching mechanism.</p>
},
	doi = {10.1016/j.isci.2023.107031},
	author = {Motiwala, Zenia and Sandholu, Anand S. and Sengupta, Durba and Kulkarni, Kiran}
}
