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Influence of Medium and Long Range Interactions in (α/β)8 Barrel Proteins

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Abstract

The residue-residue contacts and the role of medium and long rangeinteractions in 36 (α/β)8 barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the lowestmedium range contacts. The residue Cys has the highest long rangecontact followed by other hydrophobic residues namely Val, Ile andLeu. In the physico-chemically similar clusters identified in theseproteins, 25–40 percent residues are influenced by long rangecontacts, and the residues Cys, Ile, Val and Met are the mostpreferred ones.

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References

  1. MacArthur, M.W. and Thornton, J.M.: J. Mol. Biol. 218(1991), 397–412.

    Google Scholar 

  2. Karpeisky, M.Ya. and Ilyin, V.A.: J. Mol. Biol. 224(1992), 629–638.

    Google Scholar 

  3. Vtyurin, N.: Proteins 15(1993), 62–70.

    Google Scholar 

  4. Ponnuswamy, P.K. and Gromiha, M.M.: J. Theor. Biol. 166(1994), 63–74.

    Google Scholar 

  5. Gobel, U., Sander, C., Schneider, R. and Valencia, A.: Proteins 18(1994), 309–317.

    Google Scholar 

  6. Tanaka, S. and Scheraga, H.A.: Macromolecules 9(1976), 945–950.

    Google Scholar 

  7. Manavalan, P. and Ponnuswamy, P.K.: Arch. Biochem. Biophys. 184(1977), 476–487.

    Google Scholar 

  8. Warme, P.K. and Morgan, R.S.: J. Mol. Biol. 118(1978), 289–304.

    Google Scholar 

  9. Narayana, S.V.L. and Argos, P.: Int. J. Peptide Protein Res. 24(1984), 25–39.

    Google Scholar 

  10. Viswanathan, V.N.: Int. J. Biol. Macromol. 9(1987), 39–48.

    Google Scholar 

  11. Miyazawa, S. and Jernigan, R.L.: Macromolecules 18(1985), 534–552.

    Google Scholar 

  12. Burlety, S.K. and Petsko, G.A.: Science 229(1985), 23–29.

    Google Scholar 

  13. Heringa, J. and Argos, P.: J. Mol. Biol. 220(1991), 151–171.

    Google Scholar 

  14. Magalhaes, A., Margret, B., Hoflack, J., Gomes, J.N. and Scheraga, H.A.: J. Protein Chem. 13 (1994), 195–215.

    Google Scholar 

  15. Muthusamy, R. and Ponnuswamy, P.K.: J. Theor. Biol. 153(1991), 25–40.

    Google Scholar 

  16. Karlin, S., Zucker, M. and Brocchieri, L.: J. Mol. Biol. 239(1994), 227–248.

    Google Scholar 

  17. Karlin, S. and Zhu, Z.Y.: Proc. Natl. Acad. Sci. USA 93(1996), 8344–8349.

    Google Scholar 

  18. Zhu, Z.Y. and Karlin, S.: Proc. Natl. Acad. Sci. USA 93(1996), 8350–8355.

    Google Scholar 

  19. Gugolya, Z., Dostanyi, Zs. and Simon, I.: Proteins 27(1997), 360–366.

    Google Scholar 

  20. Gromiha, M.M. and Selvaraj, S.: J. Biol. Phys. 23(1997), 151–162.

    Google Scholar 

  21. Selvaraj, S. and Gromiha, M.M.: Protein Engng.(submitted) (1997).

  22. Farber, G.K. and Petsko, G.A.: Trends Biochem. Sci. 15(1990), 228–234.

    Google Scholar 

  23. Holm, L. and Sandor, C.: J. Mol. Biol. 233(1993), 123–138.

    Google Scholar 

  24. Sergeev, Y. and Lee, B.: J. Mol. Biol. 244(1994), 168–182.

    Google Scholar 

  25. Bernstein, F.C., Koetzle, T.F., Williams, J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M.: J. Mol. Biol. 112(1977), 535–542.

    Google Scholar 

  26. Abola, E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. and Weng, J.: Protein data Bank. In: F.H. Allen, G. Bergerhoff and R. Sievers (eds.), Crystallographic Databases–Information Content, Software Systems, Scientific Applications, 1987, pp. 107–132.

  27. Protein Data Bank, Brookhaven National Laboratory, Upton, NY, September, 1996.

  28. Manavalan, P. and Ponnuswamy, P.K.: Nature 275(1978), 673–674.

    Google Scholar 

  29. Ponnuswamy, P.K., Prabakaran, M. and Manavalan, P.: Biochim. Biophys. Acta. 623(1980), 301–306.

    Google Scholar 

  30. Ponnuswamy, P.K., Warme, P.K. and Scheraga, H.A.: Proc. Natl. Acad. Sci. 70(1973), 830–833.

    Google Scholar 

  31. Argos, P.: J. Mol. Biol. 193(1987), 385–396.

    Google Scholar 

  32. Fasman, G.D.: In: G.D. Fasman (ed.), Prediction of Protein Structure and Principles of Protein Conformation, 1989, New York: Plenum Press, pp. 193–316.

    Google Scholar 

  33. Gromiha, M.M. and Ponnuswamy, P.K.: Int. J. Peptide Protein Res. 45(1995), 225–240.

    Google Scholar 

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Authors and Affiliations

  1. Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Tsukuba, Japan

    M. Michael Gromiha

  2. Department of Physics, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India

    S. Selvaraj

Authors
  1. M. Michael Gromiha
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  2. S. Selvaraj
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Gromiha, M.M., Selvaraj, S. Influence of Medium and Long Range Interactions in (α/β)8 Barrel Proteins. Journal of Biological Physics 23, 209–217 (1997). https://doi.org/10.1023/A:1005071232497

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