Assessing the relative stability of dimer interfaces in g protein-coupled receptors
Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debat...
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description | Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices. |
doi_str_mv | 10.1371/journal.pcbi.1002649 |
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Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1002649</identifier><identifier>PMID: 22916005</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology ; Biomedical research ; Crystal structure ; Dimerization ; Experiments ; G proteins ; Humans ; Lipid Bilayers ; Molecular dynamics ; Molecular Dynamics Simulation ; Molecular Structure ; Physiological aspects ; Polymerase chain reaction ; Proteins ; Receptors, G-Protein-Coupled - chemistry ; Studies</subject><ispartof>PLoS computational biology, 2012-08, Vol.8 (8), p.e1002649-e1002649</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>Johnston et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Johnston JM, Wang H, Provasi D, Filizola M (2012) Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors. PLoS Comput Biol 8(8): e1002649. doi:10.1371/journal.pcbi.1002649</rights><rights>2012 Johnston et al 2012 Johnston et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c699t-95b85225313f9642cb768e0383d6bc67ed0e20e7093f2a33e40856d05eb4ad1e3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420924/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420924/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22916005$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Johnston, Jennifer M</creatorcontrib><creatorcontrib>Wang, Hao</creatorcontrib><creatorcontrib>Provasi, Davide</creatorcontrib><creatorcontrib>Filizola, Marta</creatorcontrib><title>Assessing the relative stability of dimer interfaces in g protein-coupled receptors</title><title>PLoS computational biology</title><addtitle>PLoS Comput Biol</addtitle><description>Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices.</description><subject>Biology</subject><subject>Biomedical research</subject><subject>Crystal structure</subject><subject>Dimerization</subject><subject>Experiments</subject><subject>G proteins</subject><subject>Humans</subject><subject>Lipid Bilayers</subject><subject>Molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Structure</subject><subject>Physiological aspects</subject><subject>Polymerase chain reaction</subject><subject>Proteins</subject><subject>Receptors, G-Protein-Coupled - chemistry</subject><subject>Studies</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqVUstu1DAUjRCItgN_gCASm7LI4EfsxJtKo4rHSBVIFNaW41ynHiVxsJ2K_j0eJq06iA3ywlfX55z78MmyVxitMa3w-52b_aj69aQbu8YIEV6KJ9kpZowWFWX100fxSXYWwg6hFAr-PDshRGCOEDvNrjchQAh27PJ4A7mHXkV7C3mIqrG9jXe5M3lrB_C5HSN4ozSEFOZdPnkXwY6FdvPUQ5u4GqbofHiRPTOqD_ByuVfZj48fvl9-Lq6-ftpebq4KzYWIhWBNzQhhFFMjeEl0U_EaEK1pyxvNK2gREAQVEtQQRSmUqGa8RQyaUrUY6Cp7c9Cdehfkso8gcRLENcaJt8q2B0Tr1E5O3g7K30mnrPyTcL6Tykere5AtVoqzhnBjUIkpEUxhTSpRqkabxpikdbFUm5sBWg1j9Ko_Ej1-Ge2N7NytpCVBgpRJ4HwR8O7nDCHKwQYNfa9GcHPqO30PRiUTNEHf_gX993TrA6pTaQA7Gpfq6nRaGKx2Ixib8huK0ncLRPaEd0eEhInwK3ZqDkFur7_9B_bLMbY8YLV3IXgwD1vBSO7Net--3JtVLmZNtNePN_pAuncn_Q0wB-Xs</recordid><startdate>20120801</startdate><enddate>20120801</enddate><creator>Johnston, Jennifer M</creator><creator>Wang, Hao</creator><creator>Provasi, Davide</creator><creator>Filizola, Marta</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20120801</creationdate><title>Assessing the relative stability of dimer interfaces in g protein-coupled receptors</title><author>Johnston, Jennifer M ; Wang, Hao ; Provasi, Davide ; Filizola, Marta</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c699t-95b85225313f9642cb768e0383d6bc67ed0e20e7093f2a33e40856d05eb4ad1e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Biology</topic><topic>Biomedical research</topic><topic>Crystal structure</topic><topic>Dimerization</topic><topic>Experiments</topic><topic>G proteins</topic><topic>Humans</topic><topic>Lipid Bilayers</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular Structure</topic><topic>Physiological aspects</topic><topic>Polymerase chain reaction</topic><topic>Proteins</topic><topic>Receptors, G-Protein-Coupled - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Johnston, Jennifer M</au><au>Wang, Hao</au><au>Provasi, Davide</au><au>Filizola, Marta</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessing the relative stability of dimer interfaces in g protein-coupled receptors</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2012-08-01</date><risdate>2012</risdate><volume>8</volume><issue>8</issue><spage>e1002649</spage><epage>e1002649</epage><pages>e1002649-e1002649</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22916005</pmid><doi>10.1371/journal.pcbi.1002649</doi><oa>free_for_read</oa></addata></record> |
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subjects | Biology Biomedical research Crystal structure Dimerization Experiments G proteins Humans Lipid Bilayers Molecular dynamics Molecular Dynamics Simulation Molecular Structure Physiological aspects Polymerase chain reaction Proteins Receptors, G-Protein-Coupled - chemistry Studies |
title | Assessing the relative stability of dimer interfaces in g protein-coupled receptors |
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