A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins

  1. Especial, João N. C.
  2. Rey, Antonio
  3. Faísca, Patrícia F. N.
Revue:
International Journal of Molecular Sciences

ISSN: 1422-0067

Année de publication: 2022

Volumen: 23

Número: 22

Pages: 13871

Type: Article

DOI: 10.3390/IJMS232213871 GOOGLE SCHOLAR lock_openAccès ouvert editor

D'autres publications dans: International Journal of Molecular Sciences

Objectifs de Développement Durable

Résumé

Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement.

€ Voir financement

Information sur le financement

Financeurs

  • FCT, Portugal
    • UID/MULT I/04046/2020
    • SFRH/BD/144345/2019
    • CA17139
    • PID2019-106557GB-C21
  • FCT
    • PTDC/FIS-OUT/28210/2017

Références bibliographiques

  • (1977), Nature, 268, pp. 495, 10.1038/268495a0
  • (2000), Nature, 406, pp. 916, 10.1038/35022623
  • (2013), Biochem. Soc. Trans., 41, pp. 533, 10.1042/BST20120339
  • (2000), Nucleic Acids Res., 28, pp. 235, 10.1093/nar/28.1.235
  • (2018), Nucleic Acids Res., 47, pp. D367
  • Bölinger, D., Sułkowska, J.I., Hsu, H.P., Mirny, L.A., Kardar, M., Onuchic, J.N., and Virnau, P. (2010). A Stevedore’s protein knot. PLoS Comput. Biol., 6.
  • (2022), Protein Sci., 31, pp. e4380
  • (2007), Curr. Opin. Chem. Biol., 11, pp. 595, 10.1016/j.cbpa.2007.10.002
  • (2020), AMS Contemp. Math., 746, pp. 129, 10.1090/conm/746/15006
  • (2015), Comput. Struct. Biotechnol. J., 13, pp. 459, 10.1016/j.csbj.2015.08.003
  • (2017), Curr. Opin. Struct. Biol., 42, pp. 6, 10.1016/j.sbi.2016.10.002
  • (2019), J. Phys. Condens. Matter, 31, pp. 443001, 10.1088/1361-648X/ab2f19
  • Soler, M.A., and Faísca, P.F.N. (2013). Effects of Knots on Protein Folding Properties. PLoS ONE, 8.
  • (1999), Chem. Phys. Lett., 314, pp. 141, 10.1016/S0009-2614(99)01123-9
  • (2005), Phys. Chem. Chem. Phys., 7, pp. 3910, 10.1039/b509983h
  • (2010), Phys. Biol., 7, pp. 16009, 10.1088/1478-3975/7/1/016009
  • (2014), J. Chem. Phys., 141, pp. 025101, 10.1063/1.4886401
  • (2021), J. Phys. Chem. B, 125, pp. 7359, 10.1021/acs.jpcb.1c03127
  • (2016), Phys. Chem. Chem. Phys., 18, pp. 26391, 10.1039/C6CP05086G
  • (2019), Phys. Chem. Chem. Phys., 21, pp. 11764, 10.1039/C9CP01701A
  • (2009), Proc. Natl. Acad. Sci. USA, 106, pp. 3119, 10.1073/pnas.0811147106
  • (2015), J. Chem. Phys., 143, pp. 243121, 10.1063/1.4934541
  • Skrbić, T., Micheletti, C., and Faccioli, P. (2012). The role of non-native interactions in the folding of knotted proteins. PLoS Comput. Biol., 8.
  • (2007), J. Mol. Biol., 368, pp. 884, 10.1016/j.jmb.2007.02.035
  • (2013), J. Phys. Chem. Lett., 4, pp. 3570, 10.1021/jz401842f
  • (2010), Proc. Natl. Acad. Sci. USA, 107, pp. 15403, 10.1073/pnas.1009522107
  • a Beccara, S., Skrbić, T., Covino, R., Micheletti, C., and Faccioli, P. (2013). Folding pathways of a knotted protein with a realistic atomistic force field. PLoS Comput. Biol., 9.
  • Binder, K. (1995). Monte Carlo and Molecular Dynamics Simulations in Polymer Science, Oxford University Press.
  • (2008), Proc. Natl. Acad. Sci. USA, 105, pp. 9621, 10.1073/pnas.0802494105
  • (2017), Biochem. Biophys. Res. Commun., 482, pp. 264, 10.1016/j.bbrc.2016.11.052
  • (1992), Science, 258, pp. 987, 10.1126/science.1279805
  • (1985), Proc. Natl. Acad. Sci. USA, 82, pp. 4225, 10.1073/pnas.82.12.4225
  • (2011), Phys. Chem. Chem. Phys., 13, pp. 17030, 10.1039/c1cp20402e
  • (2010), Nature, 465, pp. 637, 10.1038/nature09021
  • (2007), Nucleic Acids Res., 35, pp. W425, 10.1093/nar/gkm312
  • (1999), J. Mol. Biol., 290, pp. 253, 10.1006/jmbi.1999.2829
  • (1991), Science, 253, pp. 657, 10.1126/science.1871600
  • (1992), Biochemistry, 31, pp. 3597, 10.1021/bi00129a007
  • (2010), J. Chem. Phys., 132, pp. 224107, 10.1063/1.3432176
  • (2007), J. Chem. Phys., 127, pp. 175101, 10.1063/1.2780154
  • (2021), J. Phys. Chem. B, 125, pp. 6179, 10.1021/acs.jpcb.1c03313
  • (2010), Proteins Struct. Funct. Bioinform., 78, pp. 73, 10.1002/prot.22521
  • (1953), J. Chem. Phys., 21, pp. 1087, 10.1063/1.1699114
  • (2007), J. Chem. Theory Comput., 3, pp. 26, 10.1021/ct0502864