Inferring functional units in ion channel pores via relative entropy.
Anisotropic network model
Mechanical coupling relative entropy
Potassium channel (pores)
Journal
European biophysics journal : EBJ
ISSN: 1432-1017
Titre abrégé: Eur Biophys J
Pays: Germany
ID NLM: 8409413
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
received:
21
10
2019
accepted:
09
11
2020
revised:
11
10
2020
pubmed:
2
2
2021
medline:
5
10
2021
entrez:
1
2
2021
Statut:
ppublish
Résumé
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
Identifiants
pubmed: 33523249
doi: 10.1007/s00249-020-01480-7
pii: 10.1007/s00249-020-01480-7
pmc: PMC7872957
doi:
Substances chimiques
Ion Channels
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
37-57Subventions
Organisme : H2020 European Research Council
ID : 695078
Organisme : Deutsche Forschungsgemeinschaft
ID : GRK 1657
Références
Nat Struct Mol Biol. 2009 Jan;16(1):30-4
pubmed: 19098917
Biochim Biophys Acta. 2012 Feb;1818(2):303-17
pubmed: 21843502
J Chem Phys. 2008 Oct 14;129(14):144108
pubmed: 19045135
Biophys J. 2009 Jan;96(2):485-98
pubmed: 19167299
Nature. 2006 Mar 23;440(7083):570-4
pubmed: 16467789
Science. 2016 Aug 12;353(6300):664-9
pubmed: 27516594
Gene. 2008 Oct 1;422(1-2):30-6
pubmed: 18590806
J Chem Phys. 2013 Sep 7;139(9):090901
pubmed: 24028092
J Gen Physiol. 2010 Jun;135(6):563-73
pubmed: 20513758
Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6216-21
pubmed: 20212150
Nat Commun. 2016 Mar 29;7:11130
pubmed: 27021073
Nat Struct Biol. 2001 Oct;8(10):883-7
pubmed: 11573095
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jun;81(6 Pt 1):060104
pubmed: 20866366
Nature. 2013 Dec 5;504(7478):113-8
pubmed: 24305161
Nature. 2002 May 30;417(6888):515-22
pubmed: 12037559
Compr Physiol. 2012 Jul;2(3):2087-149
pubmed: 23723034
J Biol Chem. 2012 Dec 14;287(51):43063-70
pubmed: 23095758
Biophys J. 2008 Oct;95(7):3239-51
pubmed: 18621821
J Gen Physiol. 2018 Oct 1;150(10):1408-1420
pubmed: 30072373
Biophys J. 2002 Oct;83(4):2026-38
pubmed: 12324421
Biophys J. 2001 Jan;80(1):505-15
pubmed: 11159421
Sci Rep. 2018 Jul 10;8(1):10406
pubmed: 29991721
Biochemistry. 2004 Oct 26;43(42):13242-7
pubmed: 15491131
Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1293-301
pubmed: 22106262
Annu Rev Biophys. 2013;42:73-93
pubmed: 23451897
Phys Rev E. 2017 Nov;96(5-1):052405
pubmed: 29347718
Biophys J. 2006 Jun 1;90(11):3929-40
pubmed: 16533848
Chem Rev. 2016 Jul 27;116(14):7898-936
pubmed: 27333362
Nat Struct Mol Biol. 2009 Jan;16(1):35-41
pubmed: 19098915
Phys Rev Lett. 2005 Nov 4;95(19):198103
pubmed: 16384030
J Gen Physiol. 2011 Dec;138(6):571-80
pubmed: 22124115
J Chem Phys. 2011 Mar 7;134(9):094112
pubmed: 21384955
Biochemistry. 2005 Nov 8;44(44):14586-94
pubmed: 16262258
J Gen Physiol. 2009 Mar;133(3):295-305
pubmed: 19204189
J Biol Chem. 2018 Aug 17;293(33):12908-12918
pubmed: 29936413
Annu Rev Biophys. 2010;39:23-42
pubmed: 20192781
Science. 1983 May 13;220(4598):671-80
pubmed: 17813860
Proc Natl Acad Sci U S A. 2008 May 13;105(19):6900-5
pubmed: 18443286
Elife. 2019 Nov 26;8:
pubmed: 31769408
J Comput Chem. 2007 Jun;28(8):1400-10
pubmed: 17330878
Biochemistry. 2014 Aug 19;53(32):5365-73
pubmed: 25093676
Cell. 2010 Jun 11;141(6):1018-29
pubmed: 20564790
J Comput Biol. 2007 Jul-Aug;14(6):765-76
pubmed: 17691893
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15441-6
pubmed: 16223877
Bioinformatics. 2006 Nov 1;22(21):2695-6
pubmed: 16940322
Nature. 2002 May 30;417(6888):523-6
pubmed: 12037560
Phys Rev Lett. 1996 Aug 26;77(9):1905-1908
pubmed: 10063201
Phys Rev Lett. 2005 Feb 25;94(7):078102
pubmed: 15783858
J Phys Chem B. 2006 Aug 10;110(31):15045-8
pubmed: 16884212
PLoS Biol. 2007 May;5(5):e121
pubmed: 17472437
J Membr Biol. 2018 Jun;251(3):419-430
pubmed: 29476260
Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1949-53
pubmed: 11842204
J Chem Theory Comput. 2006 May;2(3):873-8
pubmed: 26626694
Channels (Austin). 2008 Nov-Dec;2(6):413-8
pubmed: 18797191
Biochim Biophys Acta. 2011 Feb;1808(2):580-8
pubmed: 20417613
Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5272-7
pubmed: 21402935
Curr Opin Struct Biol. 2005 Apr;15(2):144-50
pubmed: 15837171
FEBS Lett. 2000 Apr 21;472(1):83-7
pubmed: 10781810
Curr Opin Struct Biol. 2005 Oct;15(5):586-92
pubmed: 16143512
Sci Rep. 2017 Jan 11;7:40168
pubmed: 28074902
J Biol Chem. 2011 Apr 1;286(13):11299-306
pubmed: 21310959
Cell. 2017 Apr 20;169(3):422-430.e10
pubmed: 28431243
J Chem Theory Comput. 2011 Apr 12;7(4):1157-66
pubmed: 26606363
Biophys J. 2006 Oct 15;91(8):2860-73
pubmed: 16877518
Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6644-9
pubmed: 19346472
Neuron. 2014 Dec 17;84(6):1198-212
pubmed: 25500157
Biophys J. 2001 Nov;81(5):2530-46
pubmed: 11606268
Sci Rep. 2016 Jun 09;6:27562
pubmed: 27278891
Protein Sci. 2000 Sep;9(9):1753-73
pubmed: 11045621
Biochim Biophys Acta. 2015 Dec;1848(12):3197-204
pubmed: 26403836
Cell. 1999 Mar 19;96(6):879-91
pubmed: 10102275
PLoS Comput Biol. 2013;9(8):e1003209
pubmed: 24009495
Biophys J. 2011 May 18;100(10):2387-93
pubmed: 21575572
PLoS Comput Biol. 2014 Apr 03;10(4):e1003521
pubmed: 24699246
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11896-9
pubmed: 21730186
Nat Struct Mol Biol. 2013 Feb;20(2):159-66
pubmed: 23262489
J Chem Phys. 2013 Jan 28;138(4):044313
pubmed: 23387590
Nature. 2001 Nov 1;414(6859):37-42
pubmed: 11689935
Science. 1998 Apr 3;280(5360):69-77
pubmed: 9525859
Cell. 2017 Jan 12;168(1-2):111-120.e11
pubmed: 28086084
Biochim Biophys Acta. 2009 May;1788(5):1024-32
pubmed: 19366596
Biophys Chem. 2009 Oct;144(3):95-100
pubmed: 19665280
Biophys J. 2004 Apr;86(4):2137-44
pubmed: 15041654
Proteins. 2005 Jun 1;59(4):697-707
pubmed: 15822100