Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure.
Journal
Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704
Informations de publication
Date de publication:
09 May 2023
09 May 2023
Historique:
medline:
10
5
2023
pubmed:
19
4
2023
entrez:
19
04
2023
Statut:
ppublish
Résumé
Interdependence across time and length scales is common in biology, where atomic interactions can impact larger-scale phenomenon. Such dependence is especially true for a well-known cancer signaling pathway, where the membrane-bound RAS protein binds an effector protein called RAF. To capture the driving forces that bring RAS and RAF (represented as two domains, RBD and CRD) together on the plasma membrane, simulations with the ability to calculate atomic detail while having long time and large length- scales are needed. The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is able to resolve RAS/RAF protein-membrane interactions that identify specific lipid-protein fingerprints that enhance protein orientations viable for effector binding. MuMMI is a fully automated, ensemble-based multiscale approach connecting three resolution scales: (1) the coarsest scale is a continuum model able to simulate milliseconds of time for a 1 μm
Identifiants
pubmed: 37075065
doi: 10.1021/acs.jctc.2c01018
pmc: PMC10173464
doi:
Substances chimiques
Membrane Proteins
0
Lipids
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2658-2675Subventions
Organisme : NCI NIH HHS
ID : 75N91019D00024
Pays : United States
Références
Curr Opin Struct Biol. 2016 Oct;40:8-16
pubmed: 27341016
J Chem Theory Comput. 2022 Aug 9;18(8):5025-5045
pubmed: 35866871
ACS Cent Sci. 2018 Jun 27;4(6):709-717
pubmed: 29974066
J Chem Theory Comput. 2021 Dec 14;17(12):7930-7937
pubmed: 34852200
Life (Basel). 2021 Oct 12;11(10):
pubmed: 34685447
Nat Commun. 2015 May 26;6:7219
pubmed: 26008710
J Phys Chem B. 2020 Jul 2;124(26):5434-5453
pubmed: 32438809
Eur Phys J B. 2021;94(9):189
pubmed: 34720711
Cancer Discov. 2020 Jan;10(1):54-71
pubmed: 31658955
J Med Chem. 2020 Jan 9;63(1):52-65
pubmed: 31820981
J Phys Chem B. 2006 Feb 16;110(6):2934-41
pubmed: 16471904
J Chem Theory Comput. 2008 May;4(5):819-34
pubmed: 26621095
Biophys J. 2022 Oct 4;121(19):3630-3650
pubmed: 35778842
Biochem J. 2016 Jun 15;473(12):1719-32
pubmed: 27057007
J Chem Theory Comput. 2019 Oct 8;15(10):5448-5460
pubmed: 31498621
J Comput Aided Mol Des. 2017 Jan;31(1):147-161
pubmed: 27787702
Annu Rev Biophys. 2017 May 22;46:43-57
pubmed: 28301772
Biophys J. 2017 May 23;112(10):2159-2172
pubmed: 28538153
Chem Rev. 2016 Jul 27;116(14):7898-936
pubmed: 27333362
J Am Chem Soc. 2014 Sep 17;136(37):13053-8
pubmed: 25181471
J Phys Chem B. 2016 Aug 25;120(33):8547-56
pubmed: 27072779
Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11916-21
pubmed: 16880392
Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):15823-15829
pubmed: 31332011
Cancer Cell. 2020 Apr 13;37(4):543-550
pubmed: 32289276
J Phys Chem B. 2006 Aug 10;110(31):15045-8
pubmed: 16884212
Methods Mol Biol. 2019;2003:1-30
pubmed: 31218611
Chem Rev. 2019 May 8;119(9):5775-5848
pubmed: 30758191
J Chem Inf Model. 2012 Oct 22;52(10):2638-49
pubmed: 22978601
Proc Natl Acad Sci U S A. 2019 Mar 5;116(10):4244-4249
pubmed: 30760596
Curr Opin Struct Biol. 2018 Oct;52:87-94
pubmed: 30265901
J Chem Phys. 2020 Jul 28;153(4):045103
pubmed: 32752727
Proc Natl Acad Sci U S A. 2022 Jan 4;119(1):
pubmed: 34983849
J Chem Theory Comput. 2014 Feb 11;10(2):676-90
pubmed: 26580045
Acc Chem Res. 2010 Feb 16;43(2):220-30
pubmed: 19785400
Annu Rev Biophys Biomol Struct. 2003;32:425-43
pubmed: 12574064
J Chem Theory Comput. 2013 Jan 8;9(1):750-765
pubmed: 25100925
J Phys Chem B. 2013 Apr 4;117(13):3516-30
pubmed: 23406326
Cancer Res. 2012 May 15;72(10):2457-67
pubmed: 22589270
Biophys J. 2008 Sep 15;95(6):2806-21
pubmed: 18515394
J Chem Theory Comput. 2015 May 12;11(5):2144-55
pubmed: 26574417
Biopolymers. 1983 Dec;22(12):2577-637
pubmed: 6667333
Cancer Cell. 2014 Mar 17;25(3):272-81
pubmed: 24651010
Mol Cell Biol. 2014 Mar;34(5):862-76
pubmed: 24366544
J Chem Theory Comput. 2011 Apr 12;7(4):1157-66
pubmed: 26606363
Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8
pubmed: 25352545
J Thorac Oncol. 2006 Jan;1(1):7-9
pubmed: 17409820
Chem Rev. 2019 May 8;119(9):6184-6226
pubmed: 30623647
Interface Focus. 2019 Jun 6;9(3):20180075
pubmed: 31065343
Sci Rep. 2017 Jan 09;7:40109
pubmed: 28067274
J Phys Chem B. 2010 Jun 17;114(23):7830-43
pubmed: 20496934
Semin Cell Dev Biol. 2010 Jun;21(4):357-62
pubmed: 19922811
Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):27980-27988
pubmed: 33093207
J Am Chem Soc. 2011 Feb 2;133(4):880-7
pubmed: 21141956
Chem Rev. 2019 May 8;119(9):5607-5774
pubmed: 30859819
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
pubmed: 23341755
Phys Chem Chem Phys. 2016 Apr 7;18(13):8954-62
pubmed: 26960984
Biophys J. 2013 Feb 19;104(4):841-52
pubmed: 23442963
Biophys J. 1996 Jan;70(1):97-110
pubmed: 8770190
J Chem Phys. 2008 Jun 28;128(24):244114
pubmed: 18601324
Structure. 2015 Jul 7;23(7):1325-35
pubmed: 26051715
J Am Chem Soc. 2017 Feb 22;139(7):2664-2671
pubmed: 28122455
Curr Opin Struct Biol. 2013 Dec;23(6):878-86
pubmed: 24172141
Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021):
pubmed: 24982249
Faraday Discuss. 2010;144:347-57; discussion 445-81
pubmed: 20158037
Wiley Interdiscip Rev Comput Mol Sci. 2014 May;4(3):225-248
pubmed: 25309628
Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021):
pubmed: 24982256
Cancer Res. 2020 Jul 15;80(14):2969-2974
pubmed: 32209560
J Phys Chem B. 2007 Jul 12;111(27):7812-24
pubmed: 17569554
J Chem Theory Comput. 2013 Jan 8;9(1):687-97
pubmed: 26589065
Adv Mater. 2011 Nov 23;23(44):5130-47
pubmed: 21971955
Chem Soc Rev. 2013 Aug 21;42(16):6801-22
pubmed: 23708257
Curr Opin Struct Biol. 2005 Aug;15(4):423-31
pubmed: 16043343
Curr Opin Struct Biol. 2018 Oct;52:119-126
pubmed: 30508766
J Phys Chem B. 2020 Sep 10;124(36):7819-7829
pubmed: 32790367