أعرض في EDS

Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling.

التفاصيل البيبلوغرافية
العنوان: Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling.
المؤلفون: Mukhaleva E; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010.; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Ma N; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010., van der Velden WJC; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Gogoshin G; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Branciamore S; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010.; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Bhattacharya S; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Rodin AS; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010.; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010., Vaidehi N; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010.; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010.
المصدر: BioRxiv : the preprint server for biology [bioRxiv] 2023 Oct 12. Date of Electronic Publication: 2023 Oct 12.
نوع المنشور: Preprint
اللغة: English
بيانات الدورية: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
مستخلص: Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior of interface interactions and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces it is challenging to determine which amino acid pair interactions are cooperative. In this work we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with G proteins. Our results reveal a strong co-dependency in the formation of interface GPCR:G protein contacts. This observation indicates that cooperativity of GPCR:G protein interactions is necessary for the coupling and selectivity of G proteins and is thus critical for receptor function. We have identified subnetworks containing polar and hydrophobic interactions that are common among multiple GPCRs coupling to different G protein subtypes (Gs, Gi and Gq). These common subnetworks along with G protein-specific subnetworks together confer selectivity to the G protein coupling. This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.
Competing Interests: Declaration Of Interests The authors declare no competing interests.
التعليقات: Update in: J Biol Chem. 2024 Jun;300(6):107362. doi: 10.1016/j.jbc.2024.107362. (PMID: 38735478)
References: Nat Chem Biol. 2022 Jan;18(1):109-115. (PMID: 34711980)
Elife. 2022 Mar 18;11:. (PMID: 35302493)
J Comput Chem. 2010 Mar;31(4):671-90. (PMID: 19575467)
Nature. 2011 Jul 19;477(7366):549-55. (PMID: 21772288)
EMBO J. 2023 Jun 1;42(11):e112940. (PMID: 37038975)
Cell. 2019 Jun 13;177(7):1933-1947.e25. (PMID: 31160049)
Nucleic Acids Res. 2012 Jan;40(Database issue):D370-6. (PMID: 21890895)
Math Biosci Eng. 2021 Oct 9;18(6):8603-8621. (PMID: 34814315)
J Chem Theory Comput. 2016 Nov 8;12(11):5575-5584. (PMID: 27709935)
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9867-72. (PMID: 16788072)
Biophys J. 2014 Jul 15;107(2):422-434. (PMID: 25028884)
Nat Commun. 2022 Dec 2;13(1):7428. (PMID: 36460632)
Nature. 2023 May;617(7960):417-425. (PMID: 37138078)
Int J Mol Sci. 2021 Feb 26;22(5):. (PMID: 33652558)
Structure. 2019 Apr 2;27(4):703-712.e3. (PMID: 30713025)
ACS Bio Med Chem Au. 2022 Nov 15;3(1):74-86. (PMID: 37101604)
Nat Commun. 2021 Apr 7;12(1):2086. (PMID: 33828102)
Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):12054-12059. (PMID: 31142646)
Commun Biol. 2021 May 27;4(1):635. (PMID: 34045638)
Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11956-11965. (PMID: 31138704)
Comput Struct Biotechnol J. 2022 Sep 01;20:4870-4884. (PMID: 36147664)
Nature. 2017 May 18;545(7654):317-322. (PMID: 28489817)
Nat Commun. 2020 Jun 22;11(1):3160. (PMID: 32572026)
Elife. 2018 May 04;7:. (PMID: 29726815)
Chem Sci. 2019 Jan 25;10(10):2869-2874. (PMID: 30996864)
Life Sci. 1997;60(13-14):1007-14. (PMID: 9121341)
J Biol Chem. 2016 Aug 19;291(34):17929-40. (PMID: 27330078)
Biochemistry. 2015 Feb 24;54(7):1534-41. (PMID: 25658131)
J Biol Chem. 2013 Jun 14;288(24):17167-78. (PMID: 23629648)
Nature. 2015 Aug 13;524(7564):173-179. (PMID: 26147082)
Elife. 2019 Dec 19;8:. (PMID: 31855179)
Nature. 2023 Mar;615(7953):734-741. (PMID: 36890236)
J Chem Phys. 2023 Apr 7;158(13):134108. (PMID: 37031148)
J Comput Chem. 2008 Aug;29(11):1859-65. (PMID: 18351591)
Life Sci Alliance. 2022 May 25;5(10):. (PMID: 35613896)
Endocrinology. 2005 Jan;146(1):477-85. (PMID: 15498884)
Mol Cell. 2022 Jul 21;82(14):2681-2695.e6. (PMID: 35714614)
Biophys J. 2009 Jul 8;97(1):50-8. (PMID: 19580743)
Nat Chem Biol. 2020 Aug;16(8):841-849. (PMID: 32367019)
Front Genet. 2020 Jun 18;11:648. (PMID: 32625238)
J Chem Inf Model. 2022 Dec 26;62(24):6727-6738. (PMID: 36073904)
Sci Rep. 2016 Dec 07;6:38564. (PMID: 27924846)
Biochemistry. 2020 Oct 27;59(42):4059-4071. (PMID: 33054162)
BMC Genomics. 2012;13 Suppl 1:S5. (PMID: 22369071)
PLoS One. 2012;7(1):e29420. (PMID: 22242170)
Nature. 2018 Jun;558(7711):559-563. (PMID: 29925945)
Biochemistry. 2018 Nov 13;57(45):6387-6390. (PMID: 30339352)
Nat Struct Mol Biol. 2021 Nov;28(11):936-944. (PMID: 34759376)
J Vis Exp. 2016 Sep 10;(115):. (PMID: 27684955)
Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4735-40. (PMID: 27071107)
Sci Signal. 2015 Dec 01;8(405):ra123. (PMID: 26628681)
J Biol Chem. 2017 Sep 29;292(39):16300-16309. (PMID: 28821615)
FASEB J. 2019 Apr;33(4):5005-5017. (PMID: 30601679)
Bioinformatics. 2016 Jan 15;32(2):309-11. (PMID: 26415722)
Nat Commun. 2022 Nov 5;13(1):6670. (PMID: 36335102)
Elife. 2019 Jun 28;8:. (PMID: 31251171)
Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9903-8. (PMID: 9707573)
PLoS One. 2013 Jun 24;8(6):e67244. (PMID: 23826246)
Cell Rep. 2022 Sep 13;40(11):111323. (PMID: 36103815)
Sci Rep. 2020 May 29;10(1):8779. (PMID: 32471984)
Nat Chem Biol. 2021 Dec;17(12):1238-1244. (PMID: 34556862)
Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658)
Nucleic Acids Res. 2020 Jan 8;48(D1):D1006-D1021. (PMID: 31691834)
ACS Pharmacol Transl Sci. 2018 Sep 07;1(2):73-83. (PMID: 32219204)
J Comput Chem. 2018 Jul 30;39(20):1568-1578. (PMID: 29464733)
J Phys Chem B. 2015 Apr 16;119(15):4917-28. (PMID: 25807267)
Mol Syst Biol. 2006;2:2006.0019. (PMID: 16738564)
J Comput Biol. 2017 Apr;24(4):340-356. (PMID: 27681505)
Mol Pharmacol. 2000 Nov;58(5):954-66. (PMID: 11040042)
PLoS Biol. 2021 Jun 4;19(6):e3001295. (PMID: 34086670)
Methods Mol Biol. 2010;662:121-47. (PMID: 20824469)
معلومات مُعتمدة: R01 GM117923 United States GM NIGMS NIH HHS; R01 LM013138 United States LM NLM NIH HHS; R01 LM013876 United States LM NLM NIH HHS
فهرسة مساهمة: Keywords: Bayesian network; G protein selectivity; GPCRs; Molecular Dynamics
تواريخ الأحداث: Date Created: 20231024 Latest Revision: 20240702
رمز التحديث: 20240702
مُعرف محوري في PubMed: PMC10592737
DOI: 10.1101/2023.10.09.561618
PMID: 37873104
قاعدة البيانات: MEDLINE
الوصف
تدمد:2692-8205
DOI:10.1101/2023.10.09.561618