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Molecular Dynamics Simulation of Protein Cages

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Protein Cages

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2671))

Abstract

Molecular dynamics (MD) simulations enable the description of the physical movement of the system over time based on classical mechanics at various scales depending on the models. Protein cages are a particular group of different-size proteins with hollow, spherical structures and are widely found in nature, which have vast applications in numerous fields. The MD simulation of cage proteins is particularly important as a powerful tool to unveil their structures and dynamics for various properties, assembly behavior, and molecular transport mechanisms. Here, we describe how to conduct MD simulations for cage proteins, especially technical details, and analyze some of the properties of interest using GROMACS/NAMD packages.

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References

  1. Uchida M, Klem MT, Allen M et al (2007) Biological containers: protein cages as multifunctional nanoplatforms. Adv Mater 19:1025–1042

    Article  CAS  Google Scholar 

  2. Zhao M, Ho H, Wu Y et al (2014) Western flower thrips (Frankliniella occidentalis) transmits maize chlorotic mottle virus. J Phytopathol 162:532–536

    Article  CAS  Google Scholar 

  3. Shenton W, Mann S, Cölfen H et al (2001) Synthesis of nanophase iron oxide in lumazine synthase capsids. Angew Chem Int Ed 40:442–445

    Article  CAS  Google Scholar 

  4. Kilcoyne SH, Cywinski R (1995) Ferritin: a model superparamagnet. J Magn Magn Mater 140:1466–1467

    Article  Google Scholar 

  5. Grant RA, Filman DJ, Finkel SE et al (1998) The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5:294–303

    Article  CAS  PubMed  Google Scholar 

  6. Ma Y, Nolte RJM, Cornelissen JJLM (2012) Virus-based nanocarriers for drug delivery. Adv Drug Deliv Rev 64:811–825

    Article  CAS  PubMed  Google Scholar 

  7. Molino NM, Wang S-W (2014) Caged protein nanoparticles for drug delivery. Curr Opin Biotechnol 28:75–82

    Article  CAS  PubMed  Google Scholar 

  8. Harrison PM, Arosio P (1996) The ferritins: molecular properties, iron storage function and cellular regulation. Biochim Biophys Acta (BBA)-Bioenerg 1275:161–203

    Article  Google Scholar 

  9. Chasteen ND, Harrison PM (1999) Mineralization in ferritin: an efficient means of iron storage. J Struct Biol 126:182–194

    Article  CAS  PubMed  Google Scholar 

  10. Douglas T, Dickson DPE, Betteridge S et al (1995) Synthesis and structure of an iron (III) sulfide-ferritin bioinorganic nanocomposite. Science (80- ) 269:54–57

    Article  CAS  Google Scholar 

  11. Mann S, Meldrum FC (1991) Controlled synthesis of inorganic materials using supramolecular assemblies. Adv Mater 3:316–318

    Article  CAS  Google Scholar 

  12. Mann S, Archibald DD, Didymus JM et al (1993) Crystallization at inorganic-organic interfaces: biominerals and biomimetic synthesis. Science (80- ) 261:1286–1292

    Article  CAS  Google Scholar 

  13. Varpness Z, Peters JW, Young M, Douglas T (2005) Biomimetic synthesis of a H2 catalyst using a protein cage architecture. Nano Lett 5:2306–2309

    Article  CAS  PubMed  Google Scholar 

  14. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590

    Article  CAS  PubMed  Google Scholar 

  15. Mayor U, Guydosh NR, Johnson CM et al (2003) The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421:863–867

    Article  CAS  PubMed  Google Scholar 

  16. Dror RO, Mildorf TJ, Hilger D et al (2015) Structural basis for nucleotide exchange in heterotrimeric G proteins. Science (80- ) 348:1361–1365

    Article  CAS  Google Scholar 

  17. Tajkhorshid E, Nollert P, Jensen MØ et al (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science (80- ) 296:525–530

    Article  CAS  Google Scholar 

  18. Plattner N, Noé F (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat Commun 6:1–10

    Article  Google Scholar 

  19. Kubas A, Orain C, De Sancho D et al (2017) Mechanism of O2 diffusion and reduction in FeFe hydrogenases. Nat Chem 9:88–95

    Article  CAS  PubMed  Google Scholar 

  20. Sanbonmatsu KY, Tung C-S (2007) High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol 157:470–480

    Article  CAS  PubMed  Google Scholar 

  21. Lu D, Wang H, Chen M et al (2021) 86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy. Comput Phys Commun 259:107624

    Article  CAS  Google Scholar 

  22. Shaw DE, Deneroff MM, Dror RO et al (2008) Anton, a special-purpose machine for molecular dynamics simulation. Commun ACM 51:91–97

    Article  Google Scholar 

  23. Shaw DE, Grossman JP, Bank JA et al (2014) Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In: SC’14: proceedings of the international conference for high performance computing, networking, storage and analysis. IEEE, pp 41–53

    Chapter  Google Scholar 

  24. Jung J, Nishima W, Daniels M et al (2019) Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. J Comput Chem 40:1919–1930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Shaw DE (2013) Millisecond-long molecular dynamics simulations of proteins on a special-purpose machine. Biophys J 104:45a

    Article  Google Scholar 

  26. Peng T, Lee H, Lim S (2012) Isolating a trimer intermediate in the self-assembly of E2 protein cage. Biomacromolecules 13:699–705

    Article  CAS  PubMed  Google Scholar 

  27. Laghaei R, Evans DG, Coalson RD (2013) Metal binding sites of human H-chain ferritin and iron transport mechanism to the ferroxidase sites: a molecular dynamics simulation study. Proteins Struct Funct Bioinformatics 81:1042–1050

    Article  CAS  Google Scholar 

  28. Sala D, Ciambellotti S, Giachetti A et al (2017) Investigation of the iron (II) release mechanism of human H-ferritin as a function of pH. J Chem Inf Model 57:2112–2118

    Article  CAS  PubMed  Google Scholar 

  29. Ode H, Nakashima M, Kitamura S et al (2012) Molecular dynamics simulation in virus research. Front Microbiol 3:258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Peng X, Lu C, Liu Z, Lu D (2021) The synergistic mechanisms of apo-ferritin structural transitions and Au (iii) ion transportation: molecular dynamics simulations with the Markov state model. Phys Chem Chem Phys 23:17158

    Article  CAS  PubMed  Google Scholar 

  31. Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56

    Article  CAS  Google Scholar 

  32. Case DA, Cheatham TE III, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Phillips JC, Hardy DJ, Maia JDC et al (2020) Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys 153:44130

    Article  CAS  Google Scholar 

  34. Brooks BR, Brooks CL III, Mackerell AD Jr et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  36. Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:1–11

    Article  Google Scholar 

  37. Baek M, DiMaio F, Anishchenko I et al (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science (80- ) 373:871–876

    Article  CAS  Google Scholar 

  38. Krissinel E (2015) Stock-based detection of protein oligomeric states in jsPISA. Nucleic Acids Res 43:W314–W319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical p K a predictions. J Chem Theory Comput 7:525–537

    Article  CAS  PubMed  Google Scholar 

  40. Anandakrishnan R, Aguilar B, Onufriev AV (2012) H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40:W537–W541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Onufriev AV, Izadi S (2018) Water models for biomolecular simulations. Wiley Interdiscip Rev Comput Mol Sci 8:e1347

    Article  Google Scholar 

  42. Onufriev A (2008) Implicit solvent models in molecular dynamics simulations: a brief overview. Annu Rep Comput Chem 4:125–137

    Article  CAS  Google Scholar 

  43. Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O (2011) MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem 32:2319–2327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Gowers RJ, Linke M, Barnoud J et al (2019) MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. Los Alamos National Lab. (LANL), Los Alamos

    Google Scholar 

  45. McGibbon RT, Beauchamp KA, Harrigan MP et al (2015) MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys J 109:1528–1532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Chemical Engineering, Tsinghua University, Beijing, China

    Chenlin Lu, Xue Peng & Diannan Lu

Authors
  1. Chenlin Lu
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  2. Xue Peng
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  3. Diannan Lu
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Corresponding author

Correspondence to Diannan Lu .

Editor information

Editors and Affiliations

  1. Tokyo Institute Of Technology, Yokohama, Japan

    Takafumi Ueno

  2. Chemical & Biomedical Enginering, Nanyang Technological University, Singapore, Singapore

    Sierin Lim

  3. Nanyang Technological University, Singapore, Singapore

    Kelin Xia

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Lu, C., Peng, X., Lu, D. (2023). Molecular Dynamics Simulation of Protein Cages. In: Ueno, T., Lim, S., Xia, K. (eds) Protein Cages. Methods in Molecular Biology, vol 2671. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3222-2_16

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  • DOI: https://doi.org/10.1007/978-1-0716-3222-2_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3221-5

  • Online ISBN: 978-1-0716-3222-2

  • eBook Packages: Springer Protocols

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