Springer Protocols: Abstract: Comparative Protein Structure Modeling: Introduction and Practical Examples with Modeller

Comparative Protein Structure Modeling: Introduction and Practical Examples with Modeller

By: Roberto Sánchez², Andrej Šali²

Abstract

Full Text

Download PDF (356K)

A useful three-dimensional (3D) model for a protein of unknown structure (the target) can frequently be built based on one or more related proteins of known structure (the templates). This is the aim of comparative or homology protein structure modeling. The necessary conditions are that the similarity between the target sequence and the template structures is detectable and that the correct alignment between them can be constructed. For reviews of comparative modeling, see refs. 1–5. This approach to structure prediction is possible because a small change in the protein sequence usually results in a small change in its 3D structure (6,7).

Affiliation(s): (2) Laboratories of Molecular Biophysics, The Rockefeller University, New York, NY

Book Title: Protein Structure Prediction: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 143 | Pub. Date: Aug-15-2000 | Page Range: 97-129 | DOI: 10.1385/1-59259-368-2:97

Subject: Protein Science

References

Download References

1.	Sánchez, R. and Šali, A. (1997) Advances in comparative protein-structure modeling. Curr. Opin. Struct. Biol. 7, 206–214.

2.	Marti-Renom, M. A., Stuart, A., Fiser, A., Sá-nchez, R., and Šali, A. (????) Comparative protein structure modeling of genes and genomes. Ann. Rev. Biophys. Biomolec. Struct., in press.

3.	Johnson, M. S., Srinivasan, N., Sowdhamini, R., and Blundell, T. L. (1994) Knowledge-based protein modelling. CRC Crit. Rev. Biochem. Mol. Biol. 29, 1–68.

4.	Bajorath, J., Stenkamp, R., and Aruffo, A. (1994) Knowledge-based model building of proteins: concepts and examples. Protein Sci. 2, 1798–1810.

5.	Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E., and Thornton, J. M. (1987) Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326, 347–352.

6.	Chothia, C. and Lesk, A. M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823–826.

7.	Hubbard, T. J. P. and Blundell, T. L. (1987) Comparison of solvent inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1, 159–171.

8.	Oliver, S. G. (1996) From DNA sequence to biological function. Nature 379, 597–600.

9.	Koonin, E. V. and Mushegian, A. R. (1996) Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr. Biol. 6, 757–762.

10.	Dujon, B. (1996) The yeast genome project: what did we learn? Trends Genet. 12, 263–270.

11.	Matsumoto, R., Šali, A., Ghildyal, N., Karplus, M., and Stevens, R. L. (1995) Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines in mouse mast cell protease-7 regulates its binding to heparin serglycin proteoglycan. J. Biol. Chem. 270, 19524–19531.

12.	Lesk, A. M. and Chothia, C. (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136, 225–270.

13.	Rost, B. and Sander, C. (1996) Bridging the protein sequence-structure gap by structure predictions. Annu. Rev. Biophys. Biomol. Struct. 25, 113–136.

14.	Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., and Ouellette, B. F. F. (1997) GenBank. Nucleic Acids Res. 26, 1–7.

15.	Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T., and Weng, J. (1987) Protein data bank, in Crystallographic Databases — Information, Content, Software Systems, Scientific Applications (Allen, F. H., Bergerhoff, G., and Sievers, R., eds.), Data Commission of the International Union of Crystallography, Cambridge, pp. 107–132.

16.	Chothia, C. (1992) One thousand families for the molecular biologist. Nature 360, 543–544.

17.	Holm, L. and Sander, C. (1996) Mapping the protein universe. Science 273, 595–602.

18.	Doolittle, R. F. (1990) Searching through sequence databases. Methods Enzymol. 183, 99–110.

19.	Altschul, S. F., Boguski, M. S., Gish, W., and Wootton, J. C. (1994) Issues in searching molecular sequence databases. Nat. Genet. 6, 119–129.

20.	Pearson, W. R. (1996) Effective protein sequence comparison. Methods Enzymol. 266, 227–258.

21.	Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84, 4355–4358.

22.	Gribskov, M. (1994) Profile analysis. Methods Mol. Biol. 25, 247–266.

23.	Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994) Hidden Markov Models in computational biology: applications to protein modeling. J. Mol. Biol. 235, 1501–1531.

24.	Eddy, S. R. (1996) Hidden Markov models. Curr. Opin. Struct. Biol. 6, 361–365.

25.	Bowie, J. U., Lüthy, R., and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164–170.

26.	Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992) A new approach to protein fold recognition. Nature 358, 86–89.

27.	Godzik, A., Kolinski, A., and Skolnick, J. (1992) Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227, 227–238.

28.	Sippl, M. J. and Flöckner, H. (1996) Threading thrills and threats. Structure 4, 15–19.

29.	Torda, A. E. (1997) Perspectives in protein-fold recognition. Curr. Opin. Struct. Biol. 7, 200–205.

30.	Dunbrack Jr., R. L., Gerloff, D. L., Bower, M., Chen, X., Lichtarge, O., and Cohen, F. E. (1997) Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, CA, December 13–16, 1996. Fold. Des. 2, R27–R42.

31.	Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.

32.	Browne, W. J., North, A. C. T., Phillips, D. C., Brew, K., Vanaman, T. C., and Hill, R. C. (1969) A possible three-dimensional structure of bovine α-lactalbumin based on that of hen’s egg-white lysozyme. J. Mol. Biol. 42, 65–86.

33.	Greer, J. (1981) Comparative model-building of the mammalian serine proteases. J. Mol. Biol. 153, 1027–1042.

34.	Jones, T. H. and Thirup, S. (1986) Using known substructures in protein model building and crystallography. EMBO J. 5, 819–822.

35.	Unger, R., Harel, D., Wherland, S., and Sussman, J. L. (1989) A 3-D building blocks approach to analyzing and predicting structure of proteins. Proteins 5, 355–373.

36.	Claessens, M., Cutsem, E. V., Lasters, I., and Wodak, S. (1989) Modelling the polypeptide backbone with “spare parts” from known protein structures. Protein Eng. 4, 335–345.

37.	Levitt, M. (1992) Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507–533.

38.	Havel, T. F. and Snow, M. E. (1991) A new method for building protein conformations from sequence alignments with homologues of known structure. J. Mol. Biol. 217, 1–7.

39.	Srinivasan, S., March, C. J., and Sudarsanam, S. (1993) An automated method for modeling proteins on known templates using distance geometry. Protein Sci. 2, 227–289.

40.	Šali, A. and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815.

41.	Brocklehurst, S. M. and Perham, R. N. (1993) Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipolyated H-protein from the pea leaf glycine cleavage system: a new automated methods for the prediction of protein tertiary structure. Protein Sci. 2, 626–639.

42.	Aszodi, A. and Taylor, W. R. (1996) Homology modelling by distance geometry. Fold. Des. 1, 325–334.

43.	Šali, A. and Overington, J. (1994) Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3, 1582–1596.

44.	Šali, A. (1995) Protein modeling by satisfaction of spatial restraints. Mol. Med. Today 1, 270–277.

45.	Sánchez, R. and Šali, A. (1997) Comparative protein modeling as an optimization problem. J. Mol. Struct. (Theochem.) 398, 489–496.

46.	Lüthy, R., Bowie, J. U., and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature 356, 83–85.

47.	Sippl, M. J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355–362.

48.	Laskowski, R. A., McArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291.

49.	Hooft, R., Vriend, G., Sander, C., and Abola, E. (1996) Errors in protein structures. Nature 381, 272.

50.	Sánchez, R. and Šali, A. (1997) Evaluation of comparative protein structure modeling by MODELLER-3. Proteins (Suppl.), 50–58.

51.	Guenther, B., Onrust, R., Šali, A., O’Donnell, M., and Kuriyan, J. (1997) Crystal structure of the δ #x2019; subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91, 335–345.

52.	Šali, A., Sánchez, R., and Badretdinov, A. (1997) MODELLER, A Protein Structure Modeling Program, URL http://guitar.rockefeller.edu./Modeller/Modeller.html

53.	Šali, A. and Blundell, T. L. (1994) Comparative protein modelling by satisfaction of spatial restraints, in Protein Structure by Distance Analysis (Bohr, H., and Brunak, S., eds.), IOS Press, Amsterdam, The Netherlands, pp. 64–86.

54.	Šali, A., Potterton, L., Yuan, F., van Vlijmen, H., and Karplus, M. (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318–326.

55.	Sánchez, R., Badretdinov, A. Y., Feyfant, E., and Šali, A. (1997) Homology protein structure modeling. Trans. Am. Cryst. Assoc. 32, 81–91.

56.	Xu, L. Z., Sánchez, R., Šali, A., and Heintz, N. (1996) Ligand specificity of brain lipid binding protein. J. Biol. Chem.271, 24711–24719.

57.	Needleman, S. B. and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol 48, 443–453.

58.	Sánchez, R. and Šali, A. Variable gap penalty function for protein sequence-structure alignments. In preparation.

59.	Sayle, R. and Milner-White, E. J. (1995) RasMol: biomolecular graphics for all. Trends Biochem. Sci. 20, 374.

60.	Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., and Kraut, J. (1982) Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1. 7 angstroms resolution. I. General features and binding of methotrexate. J. Biol. Chem. 257, 13,650.

61.	Johnson, M. S. and Overington, J. P. (1993) A structural basis for sequence comparisons: an evaluation of scoring methodologies. J. Mol. Biol. 233, 716–738.

62.	Barton, G. J. and Sternberg, M. J. E. (1987) A strategy for the rapid multiple alignment of protein sequences; confidence levels from tertiary structure comparisons. J. Mol. Biol. 198, 327–337.

63.	Sánchez, R. and Šali, A. (1998) Large-scale protein structure modeling of the saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. 95, 13,597–13,602

64.	Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

65.	Pearson, W. R. (1990) Rapid and sensitive comparison with FASTA and FASTP. Methods Enzymol. 183, 63–98.

66.	Alexandrov, N. N., Nussinov, R., and Zimmer, R. M. (1995) Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. World Scientific Publishing Co., Singapore, pp. 53–72

67.	Rost, B. (1995) TOPITS: threading one-dimensional predictions into three-dimensional structures. AAAI Press, Menlo Park, CA, pp. 314–321.

68.	Ficher, D. and Eisenberg, D. (1996) Fold recognition using sequence-derived predictions. Prot. Sci. 5, 947–955.

69.	Flockner, H., Braxenthaler, M., Lackner, P., Jaritz, M., Ortner, M., and Sippl, M. J. (1995) Progress in fold recognition. Proteins 23, 376–386.

70.	Sutcliffe, M. J., Haneef, I., Carney, D., and Blundell, T. L. (1987) Knowledge based modelling of homologous proteins, part I: three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377–384.

71.	Bruccoleri, R. E. (1993) Application of systematic conformational search to protein modeling. Mol. Sim. 10, 151–174.

72.	Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52–56.

73.	Peitsch, M. C. and Jongeneel, C. V. (1993) A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors. Int. Immunol. 5, 233–238.

74.	Colovos, C. and Yeates, T. O. (1993) Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci. 2, 1511–1519.

75.	Kraulis, P. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Cryst. 24, 946–950.

Comments (Loading...)

Post comment/View all comments