Skip to main content
SpringerLink
Log in
Book cover

NMR: Principles and Applications to Biomedical Research pp 99–123Cite as

Artificial Intelligence Techniques and NMR Spectroscopy: Application to the Structure of Proteins in Solution

  • Chapter

  • 198 Accesses

Abstract

The determination of macromolecular structure (specifically of nucleic acids and proteins) is of crucial importance in many areas of molecular biology and provides important insights into biological function. This information is vital in many areas of biochemistry, biology and medicine. To date, X-ray crystallography has provided the most detailed and precise information about protein structure (Blundell and Johnson 1976). Crystal structures have been determined to atomic resolution less than 1.0 Å. Although X-ray crystallographic techniques often provide precise structural information, the application of these techniques is not always possible or appropriate. One limitation on the applicability of X-ray methodology is that many proteins do not form crystals of sufficient size or quality for crystallographic analysis. Another limitation is that X-ray structures provide information about proteins in their crystalline state which may differ from their native state in solution.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Altman RA and Jardetzky O (1986) New strategies for the determination of macromolecular structure in solution, J Biochem 100:1403–1423.

    Google Scholar 

  2. Billeter M, Braun WR and Wuthrich K (1982a) Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations, J Mol Biol 155:321–346.

    Article  Google Scholar 

  3. Billeter M, Braun WR and Wuthrich K (1982b) Secondary polypeptide structure from characteristic cross peak patterns in two-dimensional nuclear overhauser enhancement (NOESY) spectra: stereochemical and statistical studies of proton-proton distances in common secondary structures, J Mol Biol 155:1504.

    Article  Google Scholar 

  4. Blundell TL and Johnson LN (1976) Protein crystallography. New York: Academic Press.

    Google Scholar 

  5. Braun W and Go N (1985) Calculation of protein conformations by proton-proton distance constraints: A new efficient algorithm, J Mol Biol 186:611–626.

    Article  Google Scholar 

  6. Brinkley J, Cornelius C, Altman R, Hayes-Roth B, Lichtarge O, Duncan B, Buchanan B and Jardetzky O (1986) Technical report KSL-86-28, Application of constraint satisfaction techniques to the determination of protein tertiary structure, California: Stanford University.

    Google Scholar 

  7. Brinkley JF, Altman RB, Duncan BS, Buchanan BG and Jardetzky O (1987a) Submitted to J. Chemical Info, and Computer Science, The Heuristic Refinement Method for the Derivation of Protein Solution Structures:Validation on Cytochrame-b562.

    Google Scholar 

  8. Brinkley JF, Buchanan BG, Altman RB, Duncan BS and Cornelius CW (1987b) Technical Reports STAN-CS-87-1142 and KSL-87-05, A heuristic refinement method for spatial constraint satisfaction problems, California, Stanford University.

    Google Scholar 

  9. Brugge JA (1987) MS Thesis, Department of Computer Science. California: Stanford University, ABC:A knowledge-based system for determining structural components of proteins.

    Google Scholar 

  10. Brugge JA, Buchanan BG and Jardetzky O (1987) Submitted to J. Comput. Chem. in press, scheduled for publication July 1988, Toward automating the process of determining polypeptide secondary structure from 1H NMR data.

    Google Scholar 

  11. Buchanan B, Hayes-Roth B, Lichtarge O, Altman R, Brinkley J, Hewett M, Cornelius C, Duncan B and Jardetzky O (1985) Technical Report KSL-85-41. Stanford University, Stanford CA, The heuristic refinement method for deriving solution structures of proteins.

    Google Scholar 

  12. Clore G, Brunger A, Karplus M and Gronenborn A (1986) Application of molecular dynamics with interproton distance constraints to a three-dimensional protein structure determination: A model study of crambin, J Mol Biol 191:523–551.

    Article  Google Scholar 

  13. Duncan B, Buchanan BG, Hayes-Roth B, Lichtarge O, Altman R, Brinkley J, Hewett M, Cornelius C and Jardetzky O (1986) Protean: A new method of deriving solution structures of proteins. Bull Mag Res 8:111–119.

    Google Scholar 

  14. Frayman F (1985) PhD Thesis, Computer Science Department, Evanston, Illinois: Northwestern University, Proto; An approach for determining protein structures from nuclear magnetic resonance data: An exercise in large scale interdependent constraint satisfaction.

    Google Scholar 

  15. Gariepy J, Lane A, Frayman F, Wilbur D, Robien W, Schoolnik GK and Jardetzky O (1986) Structure of the toxic domain of the escherichia coli heat-stable enterotoxin ST 1, Biochemistry 25:7854–7866.

    Article  Google Scholar 

  16. Garvey A, Cornelius C and Hayes-Roth B (1987) Computational costs versus benefits of control reasoning, In: AAAI 87, p. 110–115.

    Google Scholar 

  17. Havel T and Wuthrich K (1984) A distance geometry program for determining the structures of small proteins and other macro-molecules from nuclear magnetic resonance measurements of intramolecular H-H proximities in solution. Bull Math Biol 46 4:673–698.

    MATH  Google Scholar 

  18. Hayes-Roth B (1985) A blackboard architecture for control, artificial intelligence 26:251–321.

    Article  Google Scholar 

  19. Hayes-Roth B, Buchanan B, Lichtarge O, Hewett M, Altman R, Brinkley J, Cornelius C, Duncan B and Jardetzky O (1986) Protean: Deriving protein structure from constraints: In: Proc of AAAI-86, Fifth National Congress on Artificial Intelligence 2., Morgan Kaufman, Publ., Los Altos, California, p. 904–909.

    Google Scholar 

  20. Jardetzky O (1984) A method for the definition of the solution structure of proteins from NMR and other physical measurements: The lac-repressor headpiece, In: Ovchinnikov Y (ed) Progress in Bioorganic Chemistry and Molecular Biology. Amsterdam: Elsevier Science Publishers B.V., p. 55–63.

    Google Scholar 

  21. Jardetzky O, Lane A, Lefevre J-F, Lichtarge O, Hayes-Roth B, Altman R and Buchanan B (1986) A new method for the determination of protein structures in solution from NMR, In: Maraviglia B, De Luca F, Campanella R (eds) Proc XXIII Congress Ampere on Magnetic Resonance. Italy, p. 64–69.

    Google Scholar 

  22. Jardetzky O and Lane AN (1988) Determination of the solution structure of proteins from NMR, In: Proc Int’l School of Physics Enrico Fermi, Italy: Il Nuovo Cimento (in press).

    Google Scholar 

  23. Kalk A and Berendsen HJ (1976) Proton magnetic relaxation and spin diffusion in proteins, J Mag Res 24:343–366.

    Google Scholar 

  24. Karplus M and McCammon JA (1983) Dynamics of proteins: elements and function, Ann Rev Biochem 52:263–300.

    Article  Google Scholar 

  25. Lefevre J-F, Lane AN and Jardetzky O (1987) Solution structure of the TRP operator of escherichia coli determined by NMR. Biochemistry 26:5076–5090.

    Article  Google Scholar 

  26. Levitt M (1983) Molecular dynamics of active protein I. Computer simulation of trajectories, J Mol Biol 168:595–620.

    Article  Google Scholar 

  27. Lichtarge O (1986) PhD Thesis; Biophysics Program. California: Stanford University, Structure determination of proteins in solution by NMR.

    Google Scholar 

  28. Lichtarge O, Cornelius CW, Buchanan BG and Jardetzky O (1987) Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data PROTEINS structure, Function & Genetics 2:340–358.

    Article  Google Scholar 

  29. Mackworth AK (1977) Consistency in networks of relations, Artificial Intelligence 8:99–118.

    Article  MATH  Google Scholar 

  30. Pardi A, Billeter M and Wuthrich K (1984) Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα in a globular protein, J Mol Biol 180:741–751.

    Article  Google Scholar 

  31. Paul RP (1981) Robot manipulators: mathematics, programming and control. Massachusetts: MIT Press.

    Google Scholar 

  32. Wider G, Macura S, Kumar A, Ernst RR and Wuthrich K (1984) Homonuclear two-dimensional 1H NMR of proteins. Experimental procedures. J Mag Res 56:207–234.

    Google Scholar 

  33. Wuthrich K (1986) NMR of proteins and nucleic acids. New York: John Wiley and Sons.

    Google Scholar 

Download references

Authors
  1. B. S. Duncan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. F. Brinkley
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. B. Altman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. B. G. Buchanan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. O. Jardetzky
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. The Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA

    Jay W. Pettegrew

Rights and permissions

Reprints and permissions

Copyright information

© 1990 Springer-Verlag New York Inc.

About this chapter

Cite this chapter

Duncan, B.S., Brinkley, J.F., Altman, R.B., Buchanan, B.G., Jardetzky, O. (1990). Artificial Intelligence Techniques and NMR Spectroscopy: Application to the Structure of Proteins in Solution. In: Pettegrew, J.W. (eds) NMR: Principles and Applications to Biomedical Research. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-3300-8_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4612-3300-8_5

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4612-7957-0

  • Online ISBN: 978-1-4612-3300-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation