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. 1994 Jan 4;91(1):113–117. doi: 10.1073/pnas.91.1.113

Structure from function: screening structural models with functional data.

L Jin 1, F E Cohen 1, J A Wells 1
PMCID: PMC42896  PMID: 7506411

Abstract

Structural constraints derived from different antibody epitopes on human growth hormone (hGH) were used to screen three-dimensional models of hGH that were generated by computer algorithms. Previously, alanine-scanning mutagenesis defined the residues that modulate binding to 21 different monoclonal antibodies to hGH. These functional epitopes were composed of 4-14 side chains whose alpha-carbons clustered within 4-23 A. Distance and topographic constraints for these functional epitopes were virtually the same as constraints derived from known x-ray structures of protein-antigen complexes. The constraints were used to evaluate about 1400 models of hGH that were computer-generated by a secondary-structure prediction and packing algorithm. On average each functional epitope reduced the number of models in the pool by a factor of 2, so that 8 monoclonal antibodies could reduce the number of possible models to < 10. The average root-mean-square deviation of alpha-carbon coordinates between the x-ray structure and either the pool of starting models or final models ranged from 13 to 16 A or 4 to 7 A, respectively, depending on the pool of starting models and the level of constraints imposed. All of the final models had the correct folding topography, and the best model was within 3.8 A root-mean-square deviation of the x-ray coordinates. This model was as close as it could have been because the models were built by using ideal helices and those in the x-ray structure are not. Our studies suggest that epitope mapping data can effectively screen structural models and, when coupled to predictive algorithms, can help to generate low-resolution models of a protein.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Amit A. G., Mariuzza R. A., Phillips S. E., Poljak R. J. Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution. Science. 1986 Aug 15;233(4765):747–753. doi: 10.1126/science.2426778. [DOI] [PubMed] [Google Scholar]
  2. Baldwin J. M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 1993 Apr;12(4):1693–1703. doi: 10.1002/j.1460-2075.1993.tb05814.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bass S. H., Mulkerrin M. G., Wells J. A. A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4498–4502. doi: 10.1073/pnas.88.10.4498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bazan J. F. Structural design and molecular evolution of a cytokine receptor superfamily. Proc Natl Acad Sci U S A. 1990 Sep;87(18):6934–6938. doi: 10.1073/pnas.87.18.6934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cohen F. E., Kuntz I. D. Prediction of the three-dimensional structure of human growth hormone. Proteins. 1987;2(2):162–166. doi: 10.1002/prot.340020209. [DOI] [PubMed] [Google Scholar]
  6. Cohen F. E., Richmond T. J., Richards F. M. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J Mol Biol. 1979 Aug 15;132(3):275–288. doi: 10.1016/0022-2836(79)90260-2. [DOI] [PubMed] [Google Scholar]
  7. Cunningham B. C., Wells J. A. Comparison of a structural and a functional epitope. J Mol Biol. 1993 Dec 5;234(3):554–563. doi: 10.1006/jmbi.1993.1611. [DOI] [PubMed] [Google Scholar]
  8. Garnier J. Protein structure prediction. Biochimie. 1990 Aug;72(8):513–524. doi: 10.1016/0300-9084(90)90115-w. [DOI] [PubMed] [Google Scholar]
  9. Jin L., Fendly B. M., Wells J. A. High resolution functional analysis of antibody-antigen interactions. J Mol Biol. 1992 Aug 5;226(3):851–865. doi: 10.1016/0022-2836(92)90636-x. [DOI] [PubMed] [Google Scholar]
  10. Kelley R. F., O'Connell M. P. Thermodynamic analysis of an antibody functional epitope. Biochemistry. 1993 Jul 13;32(27):6828–6835. doi: 10.1021/bi00078a005. [DOI] [PubMed] [Google Scholar]
  11. Marks J. D., Hoogenboom H. R., Bonnert T. P., McCafferty J., Griffiths A. D., Winter G. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J Mol Biol. 1991 Dec 5;222(3):581–597. doi: 10.1016/0022-2836(91)90498-u. [DOI] [PubMed] [Google Scholar]
  12. Novotny J., Bruccoleri R. E., Saul F. A. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry. 1989 May 30;28(11):4735–4749. doi: 10.1021/bi00437a034. [DOI] [PubMed] [Google Scholar]
  13. Näthke I. S., Heuser J., Lupas A., Stock J., Turck C. W., Brodsky F. M. Folding and trimerization of clathrin subunits at the triskelion hub. Cell. 1992 Mar 6;68(5):899–910. doi: 10.1016/0092-8674(92)90033-9. [DOI] [PubMed] [Google Scholar]
  14. O'Shea E. K., Rutkowski R., Kim P. S. Evidence that the leucine zipper is a coiled coil. Science. 1989 Jan 27;243(4890):538–542. doi: 10.1126/science.2911757. [DOI] [PubMed] [Google Scholar]
  15. Padlan E. A., Silverton E. W., Sheriff S., Cohen G. H., Smith-Gill S. J., Davies D. R. Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5938–5942. doi: 10.1073/pnas.86.15.5938. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Presnell S. R., Cohen B. I., Cohen F. E. A segment-based approach to protein secondary structure prediction. Biochemistry. 1992 Feb 4;31(4):983–993. doi: 10.1021/bi00119a006. [DOI] [PubMed] [Google Scholar]
  17. Sheriff S., Silverton E. W., Padlan E. A., Cohen G. H., Smith-Gill S. J., Finzel B. C., Davies D. R. Three-dimensional structure of an antibody-antigen complex. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8075–8079. doi: 10.1073/pnas.84.22.8075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Strickland E. H. Aromatic contributions to circular dichroism spectra of proteins. CRC Crit Rev Biochem. 1974 Jan;2(1):113–175. doi: 10.3109/10409237409105445. [DOI] [PubMed] [Google Scholar]
  19. Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu Rev Biochem. 1978;47:819–846. doi: 10.1146/annurev.bi.47.070178.004131. [DOI] [PubMed] [Google Scholar]
  20. Thornton J. M., Flores T. P., Jones D. T., Swindells M. B. Protein structure. Prediction of progress at last. Nature. 1991 Nov 14;354(6349):105–106. doi: 10.1038/354105a0. [DOI] [PubMed] [Google Scholar]
  21. Tramontano A., Chothia C., Lesk A. M. Structural determinants of the conformations of medium-sized loops in proteins. Proteins. 1989;6(4):382–394. doi: 10.1002/prot.340060405. [DOI] [PubMed] [Google Scholar]
  22. Wells J. A. Systematic mutational analyses of protein-protein interfaces. Methods Enzymol. 1991;202:390–411. doi: 10.1016/0076-6879(91)02020-a. [DOI] [PubMed] [Google Scholar]
  23. de Vos A. M., Ultsch M., Kossiakoff A. A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science. 1992 Jan 17;255(5042):306–312. doi: 10.1126/science.1549776. [DOI] [PubMed] [Google Scholar]

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