Skip to main content
SpringerLink
Log in

Estimating polypeptideα-carbon distances from multiple sequence alignments

  • Published:
Journal of Mathematical Chemistry Aims and scope Submit manuscript

Abstract

The hydrophobic amino acids that make up the core of a protein can be expected to be closer together than the rest of the residues in the molecule and are likely to remain conserved during evolution due to their important role. In the present study, a general theoretical framework is provided for estimating interresidue distances from residue hydrophobicity and conservation deduced from multiple alignments. While the accurate prediction of individual distances by statistical procedures is theoretically impossible, the method is able to match the distribution of predicted distances to a prescribed distribution with good accuracy.

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.

Similar content being viewed by others

References

  1. G.M. Crippen and T.F. Havel,Distance Geometry and Molecular Conformation (Chemometrics Research Studies Press, Wiley, New York, USA, 1988).

    Google Scholar 

  2. W.R. Taylor, J. Mol. Evol.28 (1988)161.

    Google Scholar 

  3. M.O. Dayhoff, R.M. Schwartz and B.C. Orcutt, in:Atlas of Protein Sequence and Structure, Vol. 5, Suppl. 3, ed. M.O. Dayhoff (Nat. Biomed. Res. Foundation, Washington DC, USA, 1978) p. 345.

    Google Scholar 

  4. W.R. Taylor, Protein Eng.4 (1991)853.

    Google Scholar 

  5. M. Levitt, Biochemistry17 (1978)4277.

    Google Scholar 

  6. W.R. Taylor, Protein Eng.6 (1993)593.

    Google Scholar 

  7. B.W. Lindgren,Statistical Theory (Macmillan, New York, USA, 1976).

    Google Scholar 

  8. D.W. Marquardt, SIAM J. Appl. Math.11 (1963)431.

    Google Scholar 

  9. P. Valkó and S. Vajda,Müszaki-tudományos feladatok megoldása szeméyi számitógéppel (in Hungarian) (Müszaki Könyvkiadó, Budapest, Hungary, 1987).

    Google Scholar 

  10. L.M. Gregoret and F.E. Cohen, J. Mol. Biol219 (1991)109.

    Google Scholar 

  11. A. Aszôdi and W.R. Taylor, Biopolymers34 (1994)489.

    Google Scholar 

  12. I.N. Bronshtein and K.A. Semendyayev,Handbook of Mathematics (Verlag Harri Deutsch, Frankfurt am Main, Germany, 1985).

    Google Scholar 

  13. W.R. Taylor, J.M. Thornton and W.G. Turnell, J. Moi. Graphics1 (1983)30.

    Google Scholar 

  14. A. Aszódi and W.R. Taylor, Protein Eng.7 (1994)633.

    Google Scholar 

  15. W.H. Press, B.P. Flannery, S.A. Teukolsky and W.T. Vetterling, Numerical Recipes: The Art of Scientific Computing (Cambridge University Press, Cambridge, UK, 1992).

    Google Scholar 

  16. G. Mason, Nature217 (1968)733.

    Google Scholar 

  17. J. Edelman, Biopolymers32 (1992)3.

    Google Scholar 

  18. G.D. Scott, Nature194 (1992)956.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Mathematical Biology, National Institute for Medical Research, The Ridgeway, NW7 IAA, Mill Hill, London, UK

    András Aszódi & William R. Taylor

Authors
  1. András Aszódi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William R. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Aszódi, A., Taylor, W.R. Estimating polypeptideα-carbon distances from multiple sequence alignments. J Math Chem 17, 167–184 (1995). https://doi.org/10.1007/BF01164846

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF01164846

Keywords

Search

Navigation