Skip to main content
SpringerLink
Log in

Development of a coarse-grained α-chitin model on the basis of MARTINI forcefield

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

At nanoscale, atomistic simulation is widely used for investigating crystalline chitin fibers, the structural component for many biological materials. However, the longitudinal dimension of naturally occurring chitin fibers exceeds hundreds of nanometer, beyond the investigation range of all-atom simulation due to the limitation of computational power. Under this context, coarse-grained simulation is a useful alternative that facilitates the investigation of a large system. We develop a coarse-grained model for describing the structural and mechanical properties of α-chitin. The developed coarse-grained model can reasonably predict these properties. Moreover, this model is consistent with existing coarse-grained force fields for proteins. The present model of α-chitin possesses good potential and applicability in the investigation of natural chitin-based materials at the length scale of several hundred nanometers.

Mapping atomistic α-chitin model into a coarse-grained modelᅟ

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Sikorski P, Hori R, Wada M (2009) Revisit of α-chitin crystal structure using high resolution X-ray diffraction data. Biomacromolecules 10(5):1100–1105

    Article  CAS  Google Scholar 

  2. Petrov M, Lymperakis L, Friák M, Neugebauer J (2013) Ab initio based conformational study of the crystalline α-chitin. Biopolymers 99(1):22–34

    Article  CAS  Google Scholar 

  3. Franca EF, Lins RD, Freitas LC, Straatsma T (2008) Characterization of chitin and chitosan molecular structure in aqueous solution. J Chem Theory Comput 4(12):2141–2149

    Article  CAS  Google Scholar 

  4. Nikolov S, Petrov M, Lymperakis L, Friák M, Sachs C, Fabritius H-O, Raabe D, Neugebauer J (2010) Revealing the design principles of high-performance biological composites using ab initio and multiscale simulations: the example of lobster cuticle. Adv Mater 22(4):519–526

    Article  CAS  Google Scholar 

  5. Vincent JF, Wegst UG (2004) Design and mechanical properties of insect cuticle. Arthropod Struct Dev 33(3):187–199

    Article  Google Scholar 

  6. Saranathan V, Osuji CO, Mochrie SG, Noh H, Narayanan S, Sandy A, Dufresne ER, Prum RO (2010) Structure, function, and self-assembly of single network gyroid (I4132) photonic crystals in butterfly wing scales. Proc Natl Acad Sci 107(26):11676–11681

    Article  CAS  Google Scholar 

  7. Miserez A, Li Y, Waite JH, Zok F (2007) Jumbo squid beaks: inspiration for design of robust organic composites. Acta Biomater 3(1):139–149

    Article  CAS  Google Scholar 

  8. Politi Y, Priewasser M, Pippel E, Zaslansky P, Hartmann J, Siegel S, Li C, Barth FG, Fratzl P (2012) A Spider’s fang: how to design an injection needle using chitin-based composite material. Adv Funct Mater 22(12):2519–2528

    Article  CAS  Google Scholar 

  9. Chen P-Y, Lin AY-M, McKittrick J, Meyers MA (2008) Structure and mechanical properties of crab exoskeletons. Acta Biomater 4(3):587–596. doi:10.1016/j.actbio.2007.12.010

    Article  Google Scholar 

  10. Guvench O, Mallajosyula SS, Raman EP, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, MacKerell AD Jr (2011) CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate–protein modeling. J Chem Theory Comput 7(10):3162–3180

    Article  CAS  Google Scholar 

  11. Huang J, MacKerell AD (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34(25):2135–2145

    Article  CAS  Google Scholar 

  12. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force‐field parameter sets 53A5 and 53A6. J Comput Chem 25(13):1656–1676

    Article  CAS  Google Scholar 

  13. Beckham GT, Crowley MF (2011) Examination of the α-chitin structure and decrystallization thermodynamics at the nanoscale. J Phys Chem B 115(15):4516–4522

    Article  CAS  Google Scholar 

  14. Jin K, Feng X, Xu Z (2013) Mechanical properties of chitin–protein interfaces: a molecular dynamics study. BioNanoScience 3(3):312–320. doi:10.1007/s12668-013-0097-2

    Article  Google Scholar 

  15. Yu Z, Xu Z, Lau D (2014) Effect of acidity on chitin–protein interface: a molecular dynamics study. BioNanoScience 4(3):207–215. doi:10.1007/s12668-014-0138-5

    Article  Google Scholar 

  16. Muzzarelli RA (2011) Chitin nanostructures in living organisms. In: Gupta NS (ed) Chitin, vol 34. Topics in geobiology. Springer, Dordrecht, pp 1–34. doi:10.1007/978-90-481-9684-5_1

    Google Scholar 

  17. Molinero V, Goddard WA (2004) M3B: a coarse grain force field for molecular simulations of malto-oligosaccharides and their water mixtures. J Phys Chem B 108(4):1414–1427

    Article  CAS  Google Scholar 

  18. Liu P, Izvekov S, Voth GA (2007) Multiscale coarse-graining of monosaccharides. J Phys Chem B 111(39):11566–11575

    Article  Google Scholar 

  19. Fukunaga H, Takimoto J-i, Doi M (2002) A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions. J Chem Phys 116(18):8183–8190

    Article  CAS  Google Scholar 

  20. Müller-Plathe F (2002) Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. Chem Phys Chem 3(9):754–769

    Google Scholar 

  21. Tschöp W, Kremer K, Batoulis J, Bürger T, Hahn O (1998) Simulation of polymer melts. I. Coarse‐graining procedure for polycarbonates. Acta Polym 49(2–3):61–74

    Article  Google Scholar 

  22. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27):7812–7824

    Article  CAS  Google Scholar 

  23. Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink S-J (2008) The MARTINI coarse-grained force field: extension to proteins. J Chem Theory Comput 4(5):819–834

    Article  CAS  Google Scholar 

  24. López CA, Rzepiela AJ, De Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ (2009) Martini coarse-grained force field: extension to carbohydrates. J Chem Theory Comput 5(12):3195–3210

    Article  Google Scholar 

  25. Reith D, Pütz M, Müller-Plathe F (2003) Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem 24(13):1624–1636

    Article  CAS  Google Scholar 

  26. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 117(1):1–19

    Article  CAS  Google Scholar 

  27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935. doi:10.1063/1.445869

    Article  CAS  Google Scholar 

  28. Rühle V, Junghans C, Lukyanov A, Kremer K, Andrienko D (2009) Versatile object-oriented toolkit for coarse-graining applications. J Chem Theory Comput 5(12):3211–3223

    Article  Google Scholar 

  29. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38

    Article  CAS  Google Scholar 

  30. Wohlert J, Berglund LA (2011) A coarse-grained model for molecular dynamics simulations of native cellulose. J Chem Theory Comput 7(3):753–760

    Article  CAS  Google Scholar 

  31. Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K (2003) Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J Chem Phys 119:3559

    Article  CAS  Google Scholar 

  32. Ehrlich H, Worch H (2007) Sponges as natural composites: from biomimetic potential to development of new biomaterials. Museu National, Rio de Janeiro, pp 303–312

    Google Scholar 

  33. Ehrlich H, Simon P, Carrillo-Cabrera W, Bazhenov VV, Botting JP, Ilan M, Ereskovsky AV, Muricy G, Worch H, Mensch A (2010) Insights into chemistry of biological materials: newly discovered silica-aragonite-chitin biocomposites in demosponges. Chem Mater 22(4):1462–1471

    Article  CAS  Google Scholar 

Download references

Acknowledgment

The authors are grateful to the support from Croucher Foundation through the Start-up Allowance for Croucher Scholars with the Grant No. 9500012, and the support from the Research Grants Council (RGC) in Hong Kong through the Early Career Scheme (ECS) with the Grant No. 139113.

Author information

Authors and Affiliations

  1. Department of Architecture and Civil Engineering, City University of Hong Kong, Hong Kong, China

    Zechuan Yu & Denvid Lau

  2. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    Denvid Lau

Authors
  1. Zechuan Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Denvid Lau
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Denvid Lau.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

A file containing the coarse-grained parameters of all the bonds, angles dihedrals as well as the non-bonded interactions is available online along with the electronic version. The settings of coarse-grained protein models are referred from online coarse-graining tutorial (http://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf). (DOCX 18 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yu, Z., Lau, D. Development of a coarse-grained α-chitin model on the basis of MARTINI forcefield. J Mol Model 21, 128 (2015). https://doi.org/10.1007/s00894-015-2670-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-015-2670-9

Keywords

Search

Navigation