دورية أكاديمية
Dynamic molecular portraits of ion-conducting pores characterize functional states of TRPV channels.
العنوان: | Dynamic molecular portraits of ion-conducting pores characterize functional states of TRPV channels. |
---|---|
المؤلفون: | Trofimov YA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia., Krylov NA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia., Minakov AS; M.V. Lomonosov Moscow State University, Moscow, Russia., Nadezhdin KD; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA., Neuberger A; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA., Sobolevsky AI; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA., Efremov RG; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. efremov@nmr.ru. |
المصدر: | Communications chemistry [Commun Chem] 2024 Jun 01; Vol. 7 (1), pp. 119. Date of Electronic Publication: 2024 Jun 01. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: Springer Nature Country of Publication: England NLM ID: 101725670 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3669 (Electronic) Linking ISSN: 23993669 NLM ISO Abbreviation: Commun Chem Subsets: PubMed not MEDLINE |
أسماء مطبوعة: | Original Publication: [London] : Springer Nature, [2018]- |
مستخلص: | Structural biology is solving an ever-increasing number of snapshots of ion channel conformational ensembles. Deciphering ion channel mechanisms, however, requires understanding the ensemble dynamics beyond the static structures. Here, we present a molecular modeling-based approach characterizing the ion channel structural intermediates, or their "dynamic molecular portraits", by assessing water and ion conductivity along with the detailed evaluation of pore hydrophobicity and residue packing. We illustrate the power of this approach by analyzing structures of few vanilloid-subfamily transient receptor potential (TRPV) channels. Based on the pore architecture, there are three major states that are common for TRPVs, which we call α-closed, π-closed, and π-open. We show that the pore hydrophobicity and residue packing for the open state is most favorable for the pore conductance. On the contrary, the α-closed state is the most hydrophobic and always non-conducting. Our approach can also be used for structural and functional classification of ion channels. (© 2024. The Author(s).) |
References: | Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13989-13995. (PMID: 31235590) Nat Commun. 2023 May 9;14(1):2659. (PMID: 37160865) Proc Natl Acad Sci U S A. 2005 May 10;102(19):6665-70. (PMID: 15870211) J Chem Inf Model. 2014 Apr 28;54(4):1189-99. (PMID: 24689707) Int J Biol Macromol. 2020 May 1;:. (PMID: 32371130) Bioinformatics. 2019 Aug 1;35(15):2585-2592. (PMID: 30535347) Science. 2018 May 4;360(6388):508-513. (PMID: 29724949) J Gen Physiol. 2018 Nov 5;150(11):1554-1566. (PMID: 30333107) Front Pharmacol. 2015 Nov 27;6:284. (PMID: 26640439) Proteins. 2010 Jun;78(8):1950-8. (PMID: 20408171) Nat Commun. 2022 Apr 28;13(1):2334. (PMID: 35484159) Nature. 2017 Sep 7;549(7670):60-65. (PMID: 28737760) Biophys J. 1993 Dec;65(6):2455-60. (PMID: 7508762) FASEB J. 2018 Feb;32(2):639-653. (PMID: 28970257) Nat Commun. 2021 Apr 12;12(1):2154. (PMID: 33846324) J Phys Chem Lett. 2018 Mar 15;9(6):1260-1264. (PMID: 29439562) Science. 1991 Jul 12;253(5016):164-70. (PMID: 1853201) Nat Commun. 2021 Nov 1;12(1):6284. (PMID: 34725357) Curr Opin Struct Biol. 2019 Oct;58:314-323. (PMID: 31378426) Nat Commun. 2023 Jun 23;14(1):3732. (PMID: 37353484) J Phys Chem B. 2008 Jul 31;112(30):9020-41. (PMID: 18593145) Nat Commun. 2018 Oct 10;9(1):4198. (PMID: 30305626) Cell Calcium. 2020 May;87:102168. (PMID: 32004816) Cell Rep. 2022 Apr 26;39(4):110737. (PMID: 35476976) Temperature (Austin). 2016 Nov 1;4(1):24-40. (PMID: 28349093) Nature. 2023 Sep;621(7977):206-214. (PMID: 37648856) Methods Enzymol. 1997;277:396-404. (PMID: 9379925) Elife. 2020 Aug 17;9:. (PMID: 32804077) Nat Struct Mol Biol. 2021 Jul;28(7):564-572. (PMID: 34239124) Nat Struct Mol Biol. 2020 Jul;27(7):635-644. (PMID: 32572252) Protein Sci. 2018 Jan;27(1):112-128. (PMID: 28836357) Int J Mol Sci. 2019 Sep 01;20(17):. (PMID: 31480555) J Chem Theory Comput. 2013 Jun 11;9(6):2733-2748. (PMID: 23914143) J Mol Biol. 2020 Aug 7;432(17):4783-4798. (PMID: 32615129) Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):8869-8878. (PMID: 30975749) Dokl Biochem Biophys. 2023 Feb;508(1):1-5. (PMID: 36653581) Nat Commun. 2023 Jun 23;14(1):3733. (PMID: 37353478) Nat Struct Mol Biol. 2018 Sep;25(9):805-813. (PMID: 30127359) Cell. 2021 Sep 30;184(20):5138-5150.e12. (PMID: 34496225) Faraday Discuss. 2018 Sep 28;209(0):231-247. (PMID: 29969132) Int J Mol Sci. 2021 Jun 10;22(12):. (PMID: 34200697) Nature. 2003 Dec 4;426(6966):517-24. (PMID: 14654832) Nat Struct Mol Biol. 2019 Jan;26(1):40-49. (PMID: 30598551) J Mol Biol. 2019 Aug 9;431(17):3353-3365. (PMID: 31220459) Sci Adv. 2024 May 3;10(18):eadn2453. (PMID: 38691614) Curr Med Chem. 2007;14(4):393-415. (PMID: 17305542) J Gen Physiol. 2020 Mar 2;152(3):. (PMID: 31972006) Sci Adv. 2020 Nov 27;6(48):. (PMID: 33246965) Sci Rep. 2016 Sep 09;6:33112. (PMID: 27612191) Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19492-7. (PMID: 22109551) J Phys Chem B. 2022 Sep 1;126(34):6428-6437. (PMID: 35998613) Elife. 2019 Sep 30;8:. (PMID: 31566564) ACS Nano. 2021 Dec 28;15(12):19098-19108. (PMID: 34784172) Nat Struct Mol Biol. 2019 Nov;26(11):994-998. (PMID: 31636415) Proteins. 2020 Oct;88(10):1319-1328. (PMID: 32447794) Nature. 2018 Jan 11;553(7687):233-237. (PMID: 29258289) Nat Chem Biol. 2023 Jan;19(1):72-80. (PMID: 36163384) Handb Exp Pharmacol. 2014;223:v - vi. (PMID: 25296415) J Physiol. 2018 Apr 1;596(7):1107-1119. (PMID: 29377132) |
معلومات مُعتمدة: | 464295817 Deutsche Forschungsgemeinschaft (German Research Foundation); R01 NS107253 United States NS NINDS NIH HHS; 23-14-00313 Russian Science Foundation (RSF); R01 NS083660 United States NS NINDS NIH HHS; R01 AR078814 United States AR NIAMS NIH HHS; R01 CA206573 United States CA NCI NIH HHS |
تواريخ الأحداث: | Date Created: 20240601 Latest Revision: 20240604 |
رمز التحديث: | 20240604 |
مُعرف محوري في PubMed: | PMC11144267 |
DOI: | 10.1038/s42004-024-01198-z |
PMID: | 38824263 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2399-3669 |
---|---|
DOI: | 10.1038/s42004-024-01198-z |