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Computer simulation of polypeptides in a confinement

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Abstract

A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms—hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain’s local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.

A scheme of a polypeptide chain built on a [310] lattice and confined to a slit formed by a pair of parallel impenetrable surfaces

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References

  1. Pande VS, Grosberg AY, Tanaka T (2000) Rev Mod Phys 72:259–314

    Article  CAS  Google Scholar 

  2. Mirny L, Shakhnovich E (2001) Annu Rev Biophys Biomol Struct 30:361–396

    Article  CAS  Google Scholar 

  3. Minton AP (2001) J Biol Chem 276:10577–10580

    Article  CAS  Google Scholar 

  4. Rivas G, Ferrone F, Hertzfeld J (2003) EMBO Rep 5:23–27

    Article  CAS  Google Scholar 

  5. Eggers DK, Valentine JA (2001) Protein Sci 10:250–261

    Article  CAS  Google Scholar 

  6. Kumar CV, Chaudhari A (2000) J Am Chem Soc 122:830–837

    Article  CAS  Google Scholar 

  7. Bolis D, Politou AS, Kelly G, Pastore A, Temussi PA (2004) J Mol Biol 336:203–212

    Article  CAS  Google Scholar 

  8. Peterson RW, Anbalagan K, Tommos C, Wand AJ (2004) J Am Chem Soc 126:9498–9499

    Article  CAS  Google Scholar 

  9. Zhou H-X, Dill KA (2001) Biochemistry 40:11289–11293

    Article  CAS  Google Scholar 

  10. Minton AP (1992) Biophys J 63:11090–1100

    Article  Google Scholar 

  11. Kinjo AR, Takada S (2002) Phys Rev E 66, art no 031811

  12. Betancourt MR, Thirumalai D (1999) J Mol Biol 287:627–644

    Article  CAS  Google Scholar 

  13. Klimov DK, Newfield D, Thirumalai D (2002) Proc Natl Acad Sci USA 99:8010–8024

    Article  Google Scholar 

  14. Takagi F, Koga N, Takada S (2003) Proc Natl Acad Sci USA 100:11367–11372

    Article  CAS  Google Scholar 

  15. Kolinski A, Madziar P (1998) Biopolymers 42:537–548

    Article  Google Scholar 

  16. Romiszowski P, Sikorski A (2000) Biopolymers 54:262–272

    Article  CAS  Google Scholar 

  17. Sikorski A, Romiszowski P (2003) Biopolymers 69:391–398

    Article  CAS  Google Scholar 

  18. Sikorski A, Romiszowski P (2005) J Mol Model 11:379–384

    Article  CAS  Google Scholar 

  19. Shakhnovich EI, Gutin AM (1993) Proc Natl Acad Sci USA 32:7195–7199

    Article  Google Scholar 

  20. Hansmann UHE, Okamoto Y (1999) In: Staufer D (ed) Annual reviews of computational physics VI. World Scientific, Singapore, p 129

    Google Scholar 

  21. Sikorski A, Romiszowski P (2002) J Chem Phys 116:1731–1736

    Article  CAS  Google Scholar 

  22. Romiszowski P, Sikorski A (2005) J Chem Phys 123, art no 104905

Download references

Acknowledgment

The computational part of this work was done using the computer cluster at the Computing Center of the Department of Chemistry, University of Warsaw.

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Authors and Affiliations

  1. Department of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland

    Andrzej Sikorski & Piotr Romiszowski

Authors
  1. Andrzej Sikorski
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  2. Piotr Romiszowski
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Correspondence to Andrzej Sikorski.

Additional information

Proceedings of “Modeling Interactions in Biomolecules II,” Prague, September 5th–9th, 2005.

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Sikorski, A., Romiszowski, P. Computer simulation of polypeptides in a confinement. J Mol Model 13, 327–333 (2007). https://doi.org/10.1007/s00894-006-0147-6

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  • DOI: https://doi.org/10.1007/s00894-006-0147-6

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