Bottom-Up Coarse-Grained Modeling of DNA.
DNA condensation
coarse-grained model
force matching
inverse Monte Carlo
molecular renormalization group
multi-scale coarse-graining
persistence length
relative entropy
Journal
Frontiers in molecular biosciences
ISSN: 2296-889X
Titre abrégé: Front Mol Biosci
Pays: Switzerland
ID NLM: 101653173
Informations de publication
Date de publication:
2021
2021
Historique:
received:
23
12
2020
accepted:
22
02
2021
entrez:
5
4
2021
pubmed:
6
4
2021
medline:
6
4
2021
Statut:
epublish
Résumé
Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.
Identifiants
pubmed: 33816559
doi: 10.3389/fmolb.2021.645527
pmc: PMC8010198
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
645527Informations de copyright
Copyright © 2021 Sun, Minhas, Korolev, Mirzoev, Lyubartsev and Nordenskiöld.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
J Chem Theory Comput. 2014 Aug 12;10(8):3541-9
pubmed: 26588318
Curr Opin Struct Biol. 2020 Oct;64:119-125
pubmed: 32738677
J Chem Phys. 2004 Jun 15;120(23):10896-913
pubmed: 15268120
Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jan;77(1 Pt 2):016707
pubmed: 18351960
Biophys J. 2009 Mar 4;96(5):1675-90
pubmed: 19254530
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr;65(4 Pt 1):041202
pubmed: 12005811
Biopolymers. 1981 Dec;20(12):2671-90
pubmed: 7034800
J Chem Theory Comput. 2013 Nov 12;9(11):4874-89
pubmed: 26583407
Phys Rev Lett. 2013 Mar 1;110(9):098101
pubmed: 23496746
ACS Cent Sci. 2016 Sep 28;2(9):660-666
pubmed: 27725965
J Chem Phys. 2006 Apr 28;124(16):164509
pubmed: 16674148
J Chem Phys. 2010 Jan 21;132(3):035105
pubmed: 20095755
J Chem Theory Comput. 2015 Aug 11;11(8):3932-45
pubmed: 26574472
J Chem Theory Comput. 2012 Jul 10;8(7):2540-2551
pubmed: 22798730
J Phys Chem Lett. 2014 Jun 5;5(11):1885-91
pubmed: 26273869
Nucleic Acids Res. 2019 Jun 20;47(11):5550-5562
pubmed: 31106383
J Chem Phys. 2007 Feb 28;126(8):084901
pubmed: 17343470
J Phys Chem B. 2005 Feb 24;109(7):2469-73
pubmed: 16851243
J Chem Phys. 2013 Sep 28;139(12):121906
pubmed: 24089718
J Phys Chem B. 2015 Jan 8;119(1):105-13
pubmed: 25469629
ACS Cent Sci. 2019 May 22;5(5):755-767
pubmed: 31139712
J Chem Theory Comput. 2016 Aug 9;12(8):4114-27
pubmed: 27300587
J Chem Phys. 2011 Mar 7;134(9):094112
pubmed: 21384955
Biophys Chem. 1991 May;40(2):169-79
pubmed: 1653052
Nucleic Acids Res. 2010 Jan;38(1):299-313
pubmed: 19850719
J Am Chem Soc. 2017 Aug 30;139(34):11674-11677
pubmed: 28777549
J Phys Chem B. 2009 Jun 4;113(22):7785-93
pubmed: 19425537
J Chem Theory Comput. 2015 Nov 10;11(11):5436-46
pubmed: 26574332
J Chem Phys. 2008 Oct 14;129(14):144108
pubmed: 19045135
Adv Colloid Interface Sci. 2010 Jul 12;158(1-2):32-47
pubmed: 19758583
J Chem Phys. 2014 Oct 28;141(16):165103
pubmed: 25362344
J Mol Model. 2014 Aug;20(8):2306
pubmed: 25024008
Biophys J. 2009 May 20;96(10):4044-52
pubmed: 19450476
J Phys Chem B. 2020 Jan 9;124(1):38-49
pubmed: 31805230
Biophys J. 2017 Apr 11;112(7):1302-1315
pubmed: 28402874
Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20340-5
pubmed: 21059937
Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6185-90
pubmed: 9177192
J Comput Chem. 2014 Apr 5;35(9):711-21
pubmed: 24738152
PLoS One. 2013;8(2):e54228
pubmed: 23418426
J Comput Chem. 2003 Oct;24(13):1624-36
pubmed: 12926006
J Chem Theory Comput. 2014 Aug 12;10(8):2891-2896
pubmed: 25136266
J Phys Chem B. 2007 Apr 26;111(16):4116-27
pubmed: 17394308
J Chem Phys. 2013 Oct 14;139(14):144903
pubmed: 24116642
J Chem Theory Comput. 2010 Mar 9;6(3):954-65
pubmed: 26613319
J Chem Theory Comput. 2020 Nov 10;16(11):6795-6813
pubmed: 33108737
Faraday Discuss. 2010;144:301-22; discussion 323-45, 467-81
pubmed: 20158036
J Chem Phys. 2012 Jun 14;136(22):226101
pubmed: 22713074
J Chem Theory Comput. 2020 Aug 11;16(8):4757-4775
pubmed: 32559068
Adv Colloid Interface Sci. 2016 Jun;232:36-48
pubmed: 26956528
J Chem Phys. 2015 Dec 28;143(24):243120
pubmed: 26723605
Biopolymers. 1981 Jul;20(7):1503-35
pubmed: 7023566
Faraday Discuss. 2010;144:43-56; discussion 93-110, 467-81
pubmed: 20158022
Biopolymers. 1982 May;21(5):923-34
pubmed: 7082770
J Chem Theory Comput. 2017 Apr 11;13(4):1539-1555
pubmed: 28029797
J Chem Theory Comput. 2016 Feb 9;12(2):676-93
pubmed: 26717419
J Chem Theory Comput. 2015 Apr 14;11(4):1792-808
pubmed: 26052263
J Mol Biol. 2016 Jan 16;428(1):221-237
pubmed: 26699921
J Chem Theory Comput. 2012 Jan 10;8(1):348-362
pubmed: 22368531
Biopolymers. 1981 Oct;20(10):2143-63
pubmed: 7284565
J Chem Phys. 2008 Jun 28;128(24):244114
pubmed: 18601324
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995 Oct;52(4):3730-3737
pubmed: 9963851
J Chem Phys. 2018 Jul 21;149(3):034101
pubmed: 30037247
J Chem Phys. 2011 Dec 7;135(21):214101
pubmed: 22149773
J Mol Model. 2017 Feb;23(2):66
pubmed: 28185115
J Phys Condens Matter. 2015 Feb 18;27(6):060301
pubmed: 25563698
Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8219-26
pubmed: 11459956
Biophys J. 2008 Dec;95(11):5073-83
pubmed: 18757560