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. 1996 May;5(5):895–903. doi: 10.1002/pro.5560050511

Protein design automation.

B I Dahiyat 1, S L Mayo 1
PMCID: PMC2143401  PMID: 8732761

Abstract

We have conceived and implemented a cyclical protein design strategy that couples theory, computation, and experimental testing. The combinatorially large number of possible sequences and the incomplete understanding of the factors that control protein structure are the primary obstacles in protein design. Our protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead-End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry from the vast number of possible solutions. Rotamer sequences were scored for steric complementarity using a van der Waals potential. A Monte Carlo search was then executed, starting at the optimal sequence, in order to find other high-scoring sequences. As a test of the design methodology, high-scoring sequences were found for the buried hydrophobic residues of a homodimeric coiled coil based on GCN4-p1. The corresponding peptides were synthesized and characterized by CD spectroscopy and size-exclusion chromatography. All peptides were dimeric and nearly 100% helical at 1 degree C, with melting temperatures ranging from 24 degrees C to 57 degrees C. A quantitative structure activity relation analysis was performed on the designed peptides, and a significant correlation was found with surface area burial. Incorporation of a buried surface area potential in the scoring of sequences greatly improved the correlation between predicted and measured stabilities and demonstrated experimental feedback in a complete design cycle.

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Selected References

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

  1. Beamer L. J., Pabo C. O. Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol. 1992 Sep 5;227(1):177–196. doi: 10.1016/0022-2836(92)90690-l. [DOI] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
  4. Chan M. K., Mukund S., Kletzin A., Adams M. W., Rees D. C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science. 1995 Mar 10;267(5203):1463–1469. doi: 10.1126/science.7878465. [DOI] [PubMed] [Google Scholar]
  5. Connolly M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 1983 Aug 19;221(4612):709–713. doi: 10.1126/science.6879170. [DOI] [PubMed] [Google Scholar]
  6. DeGrado W. F., Wasserman Z. R., Lear J. D. Protein design, a minimalist approach. Science. 1989 Feb 3;243(4891):622–628. doi: 10.1126/science.2464850. [DOI] [PubMed] [Google Scholar]
  7. Desjarlais J. R., Handel T. M. De novo design of the hydrophobic cores of proteins. Protein Sci. 1995 Oct;4(10):2006–2018. doi: 10.1002/pro.5560041006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dill K. A. Dominant forces in protein folding. Biochemistry. 1990 Aug 7;29(31):7133–7155. doi: 10.1021/bi00483a001. [DOI] [PubMed] [Google Scholar]
  9. Eisenberg D., McLachlan A. D. Solvation energy in protein folding and binding. Nature. 1986 Jan 16;319(6050):199–203. doi: 10.1038/319199a0. [DOI] [PubMed] [Google Scholar]
  10. Goldstein R. F. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J. 1994 May;66(5):1335–1340. doi: 10.1016/S0006-3495(94)80923-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Goodman E. M., Kim P. S. Periodicity of amide proton exchange rates in a coiled-coil leucine zipper peptide. Biochemistry. 1991 Dec 17;30(50):11615–11620. doi: 10.1021/bi00114a002. [DOI] [PubMed] [Google Scholar]
  12. Handel T. M., Williams S. A., DeGrado W. F. Metal ion-dependent modulation of the dynamics of a designed protein. Science. 1993 Aug 13;261(5123):879–885. doi: 10.1126/science.8346440. [DOI] [PubMed] [Google Scholar]
  13. Harbury P. B., Zhang T., Kim P. S., Alber T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science. 1993 Nov 26;262(5138):1401–1407. doi: 10.1126/science.8248779. [DOI] [PubMed] [Google Scholar]
  14. Hecht M. H., Richardson J. S., Richardson D. C., Ogden R. C. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science. 1990 Aug 24;249(4971):884–891. doi: 10.1126/science.2392678. [DOI] [PubMed] [Google Scholar]
  15. Hellinga H. W., Richards F. M. Optimal sequence selection in proteins of known structure by simulated evolution. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5803–5807. doi: 10.1073/pnas.91.13.5803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hopfinger A. J. Computer-assisted drug design. J Med Chem. 1985 Sep;28(9):1133–1139. doi: 10.1021/jm00147a001. [DOI] [PubMed] [Google Scholar]
  17. Hurley J. H., Baase W. A., Matthews B. W. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J Mol Biol. 1992 Apr 20;224(4):1143–1159. doi: 10.1016/0022-2836(92)90475-y. [DOI] [PubMed] [Google Scholar]
  18. Huyghues-Despointes B. M., Scholtz J. M., Baldwin R. L. Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide. Protein Sci. 1993 Oct;2(10):1604–1611. doi: 10.1002/pro.5560021006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jones D. T. De novo protein design using pairwise potentials and a genetic algorithm. Protein Sci. 1994 Apr;3(4):567–574. doi: 10.1002/pro.5560030405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kamtekar S., Schiffer J. M., Xiong H., Babik J. M., Hecht M. H. Protein design by binary patterning of polar and nonpolar amino acids. Science. 1993 Dec 10;262(5140):1680–1685. doi: 10.1126/science.8259512. [DOI] [PubMed] [Google Scholar]
  21. Kono H., Doi J. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry. Proteins. 1994 Jul;19(3):244–255. doi: 10.1002/prot.340190308. [DOI] [PubMed] [Google Scholar]
  22. Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
  23. Lee C., Levitt M. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature. 1991 Aug 1;352(6334):448–451. doi: 10.1038/352448a0. [DOI] [PubMed] [Google Scholar]
  24. Lim W. A., Sauer R. T. The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol. 1991 May 20;219(2):359–376. doi: 10.1016/0022-2836(91)90570-v. [DOI] [PubMed] [Google Scholar]
  25. Oas T. G., McIntosh L. P., O'Shea E. K., Dahlquist F. W., Kim P. S. Secondary structure of a leucine zipper determined by nuclear magnetic resonance spectroscopy. Biochemistry. 1990 Mar 27;29(12):2891–2894. doi: 10.1021/bi00464a001. [DOI] [PubMed] [Google Scholar]
  26. Pessi A., Bianchi E., Crameri A., Venturini S., Tramontano A., Sollazzo M. A designed metal-binding protein with a novel fold. Nature. 1993 Mar 25;362(6418):367–369. doi: 10.1038/362367a0. [DOI] [PubMed] [Google Scholar]
  27. Pomerantz J. L., Sharp P. A., Pabo C. O. Structure-based design of transcription factors. Science. 1995 Jan 6;267(5194):93–96. doi: 10.1126/science.7809612. [DOI] [PubMed] [Google Scholar]
  28. Ponder J. W., Richards F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 1987 Feb 20;193(4):775–791. doi: 10.1016/0022-2836(87)90358-5. [DOI] [PubMed] [Google Scholar]
  29. Quinn T. P., Tweedy N. B., Williams R. W., Richardson J. S., Richardson D. C. Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. Proc Natl Acad Sci U S A. 1994 Sep 13;91(19):8747–8751. doi: 10.1073/pnas.91.19.8747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Regan L., DeGrado W. F. Characterization of a helical protein designed from first principles. Science. 1988 Aug 19;241(4868):976–978. doi: 10.1126/science.3043666. [DOI] [PubMed] [Google Scholar]
  31. Wesson L., Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1992 Feb;1(2):227–235. doi: 10.1002/pro.5560010204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. van Gunsteren W. F., Mark A. E. Prediction of the activity and stability effects of site-directed mutagenesis on a protein core. J Mol Biol. 1992 Sep 20;227(2):389–395. doi: 10.1016/0022-2836(92)90895-q. [DOI] [PubMed] [Google Scholar]

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