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Structural Variation and Odorant Binding for Olfactory Receptors Selected from the Six Major Subclasses of the OR Phylogenetic Tree

Malinska, Maura and Kim, Soo-Kyung and Goddard, William, III and Ashok, Manasa (2021) Structural Variation and Odorant Binding for Olfactory Receptors Selected from the Six Major Subclasses of the OR Phylogenetic Tree. In: Computational Materials, Chemistry, and Biochemistry: From Bold Initiatives to the Last Mile. Springer Series in Materials Science. No.284. Springer International Publishing , Cham, pp. 855-925. ISBN 978-3-030-18777-4. https://resolver.caltech.edu/CaltechAUTHORS:20210127-083243229

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Abstract

To provide some insight on odorant recognition, we partitioned the 398 human olfactory receptors (OR) into six subclasses based on the phylogenetic tree and predicted the 3D structure and binding site for the family head of each subclass. We used the GPCR Ensemble of Structures in Membrane BiLayer Environment (GEnSeMBLE) method that samples 10 trillion combinations of helix tilts and rotations to select an ensemble of the 25 most stable 7-helix packings. We found that the ensembles for the OR in all 6 subclasses exhibit the TM1-2-7 coupling characteristic of Class A G protein-coupled receptors (GPCRs). In many cases of tetrapod subclasses, the conserved R3.50:E6.30 TM3-TM6 coupling in the inactive GPCRs is replaced with D(E)3.39:H6.40 and D3.49:R(K)6.30 interactions. We found a different pattern for the fish-like class I, where D3.49 couples with residues in TM4 (R4.44 for O52D1-I and Q4.41/K4.38 for O52B6-I) instead of TM6. A variety of residues lining the binding site are involved depending on the ligand: Q103^(3.28) and N282^(7.39( for O52D1-I, Y91^(2.53) for O11H6-II, Q97^(3.28) for OR4Q2-III, S272^(7.35) for OR7D4-IV, S206^(5.43) for OR2J3-V, and T249^(6.45) for OR5P3-VI. Here, we provide the structures for the top25 for all 11 ORs, including the structures with ligands.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1007/978-3-030-18778-1_37DOIArticle
ORCID:
AuthorORCID
Malinska, Maura0000-0002-7138-7041
Kim, Soo-Kyung0000-0002-4498-5441
Goddard, William, III0000-0003-0097-5716
Additional Information:© Springer Nature Switzerland AG 2021. First Online: 26 January 2021. MM was supported by the Polish National Science Center (contract number UMO-2013/08/T/ST4/00494). Funding was provided by grants from NSF (EFRI-1332411) and NIH (R01AI040567) and by gifts to the MSC.
Funders:
Funding AgencyGrant Number
National Science Center (Poland)UMO-2013/08/T/ST4/00494
NSFEFRI-1332411
NIHR01AI040567
Other Numbering System:
Other Numbering System NameOther Numbering System ID
WAG1435
Series Name:Springer Series in Materials Science
Issue or Number:284
Record Number:CaltechAUTHORS:20210127-083243229
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210127-083243229
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107766
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:27 Jan 2021 19:56
Last Modified:06 Jun 2021 06:04

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