Investigating Collagen as a Bio-Material by Molecular Dynamics Simulations
Keywords:collagen, polymer, hydrogen bonds, hydrophilic, hydrophobic
In this work, molecular dynamics simulation is used to describe and analyze the behavior of model collagen polymer (Pro-Pro-Gly)9. This project aims to highlight the important role of molecular dynamic simulation in determining the structural stability of collagen, and establishing collagen as a hydrophobic or hydrophilic protein under different temperatures. The system was simulated at four different temperatures (300, 310, 320, and 330 K). The results indicate that the average number of hydrogen bonds within the protein and the protein backbone was similar at each temperature. The solvent-accessible surface area of hydrophobic and hydrophilic atoms for the four temperatures indicates that the collagen model peptide is mostly hydrophobic. All the results show that the structure of the studied polymer was the least stable at 320 K and the most stable at lower temperatures (300 K). The average effect across the first 100 ns was investigated. The dominant states obtained within this time interval will be explored in following studies. Researchers can use the results of this work to develop collagen with the appropriate thermal stability for biological applications.
M. D. Shoulders and R. T. Raines: Collagen structure and stability. Annu. Rev. Biochem., Vol. 78, pp. 929–958, 2009. https://doi.org/10.1146/annurev.biochem.77.032207.120833
C. Hongo, K. Noguchi, K. Okuyama, Y. Tanaka, and N. Nishino: Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3. J. Biochem., Vol. 138, No. 2, pp. 135–144, Aug. 2005. https://doi.org/10.1093/jb/mvi108
J. Brinckmann: Collagens at a glance. Top. Curr. Chem., Vol. 247, pp. 1–6, 2005. https://doi.org/10.1007/b103817
G. Veit, B. Kobbe, D. R. Keene, M. Paulsson, M. Koch, and R. Wagener: Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain. J. Biol. Chem., Vol. 281, No. 6, pp. 3494–3504, 2006, https://doi.org/10.1074/jbc.M509333200
T. Hansson, C. Oostenbrink, and W. F. Van Gunsteren: Molecular dynamics simulations. Curr. Opin. Struct. Biol., Vol. 12, No. 2, pp. 190–196, 2002. https://doi.org/10.1016/S0959-440X(02)00308-1
M. C. Owen, A. Karner, R. Šachl, J. Preiner, M. Amaro, and R. Vácha: Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. J. Phys. Chem. B, Vol. 123, No. 35, pp. 7504–7517, Sep. 2019. https://doi.org/10.1021/acs.jpcb.9b05095
E. Leikina, M. V. Mertts, N. Kuznetsova, and S. Leikin: Type I collagen is thermally unstable at body temperature. Proc. Natl. Acad. Sci. U.S.A., Vol. 99, No. 3, pp. 1314–1318, 2002, https://doi.org/10.1073/pnas.032307099
W. Liu, Z. Tian, C. Li, and G. Li: Thermal denaturation of fish collagen in solution: A calorimetric and kinetic analysis. Thermochim. Acta, Vol. 581, pp. 32–40, 2014. https://doi.org/10.1016/j.tca.2014.02.012
I. Streeter and N. H. De Leeuw: A molecular dynamics study of the interprotein interactions in collagen fibrils. Soft Matter, Vol. 7, No. 7, pp. 3373–3382, 2011. https://doi.org/10.1039/c0sm01192d
S. Ebrahimi, A. Montazeri, and H. Rafii-Tabar: Molecular dynamics study of the interfacial mechanical properties of the graphene-collagen biological nanocomposite. Comput. Mater. Sci., Vol. 69, pp. 29–39, 2013. https://doi.org/10.1016/j.commatsci.2012.11.030
P. S. Chauhan et al.: Gromacs 5.0.7. Proteins Struct. Funct. Genet., Vol. 12, No. 3, pp. 169–200, 2011.
E. Monvall: Statsbudgeten: de stora reformerna gäller arbetslivet. Tidskr. Sver. Sjukskot., Vol. 43, No. 2, pp. 54–58, 1976.
P. Mark and L. Nilsson: Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J. Phys. Chem. A, Vol. 105, No. 43, pp. 9954–9960, 2001. https://doi.org/10.1021/jp003020w
J. Wong-ekkabut and M. Karttunen: The good, the bad and the user in soft matter simulations. Biochim. Biophys. Acta – Biomembr., Vol. 1858, No. 10, pp. 2529–2538, 2016, https://doi.org/10.1016/j.bbamem.2016.02.004
W. Humphrey, A. Dalke, and K. Schulten: VMD: Visual Molecular Dynamics. J. Mol. Graph., Vol. 14, No. 1, pp. 33-38, 1996. https://doi.org/10.1016/0263-7855(96)00018-5
J. Harris: Early Language Development: Implications for Clinical and Educational Practice. Early Lang. Dev. Implic. Clin. Educ. Pract., Vol. 16, No. 3, pp. 1–265, 2020. https://doi.org/10.4324/9781003028253
X. Daura, K. Gademann, B. Jaun, D. Seebach, W. F. Van Gunsteren, and A. E. Mark: Peptide folding: When simulation meets experiment. Angew. Chemie – Int. Ed., Vol. 38, No. 1–2, pp. 236–240, 1999. https://doi.org/10.1002/(sici)1521-3773(19990115)38:1/2<236::aid-anie236>3.0.co;2-m
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