Protein Secondary Structure Prediction
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- Abstract
- Table of Contents
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- Literature Cited
Abstract
This unit describes procedures developed for predicting protein structure from the amino acid sequence. The first of the four sections is an overview and brief history of structure prediction schemes. The second section describes four distinct prediction schemes, with emphasis on their differences. In the third part each prediction scheme is used to evaluate three proteins that have different folding patterns. The final section is a comparison of the prediction results and suggestions for secondary structure prediction.
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- Overview of Prediction Schemes
- Methods for Secondary Structure Prediction
- Application of Secondary Structure Prediction Methods
- Comparison of Prediction Schemes
- Recommendations and the Future
- Conclusions
- Accessibility of Software
- Figures
- Tables
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Figure 2.3.1 Helical wheel for a portion of the amphipathic helix of melittin. Residues in bold type form a hydrophobic side. Note that this is not a perfect amphipathic helix as the polar face includes Ala‐4, Ala‐15, and Val‐8. This helix also contains several glycine residues, which are not commonly found in helices (Table ). View Image -
Figure 2.3.2 Secondary structure prediction using the method of Chou and Fasman as implemented by Novotny and Auffray (). Predicted secondary structure for (A ) human hemoglobin β‐subunit, (B ) interleukin 1β, and (C ) human profilin I. Below the amino acid sequence are given the turn prediction (T), the α helix (thin line) and β strand prediction (thick line), the location of positive (upward spikes) or negative charges (downward spikes) as derived specifically from amino acid side chains, and a hydrophobicity profile (HB). View Image -
Figure 2.3.3 Secondary structure prediction for human profilin I using the method of Chou and Fasman as implemented by GCG:PepPlot algorithm. (A ) Predicted secondary structure and (B ) numerical output for residues 1 through 25. View Image -
Figure 2.3.4 Secondary structure prediction for human profilin I using the methods of Chou and Fasman and GOR as implemented by GCG: PeptideStructure algorithm and plotted using PlotStructure utility. (A ) Predicted secondary structure and (B ) numerical output for residues 1 through 35. View Image -
Figure 2.3.5 Sketch of the human profilin secondary structure as predicted in Figure and Figure by Chou‐Fasman method. View Image -
Figure 2.3.6 Sequence homologs and a portion of the sequence alignment statistics used in secondary structure prediction for human profilin I with PHD, the EMBL neural network method. Secondary structure prediction given in Figure . For description of column labels see Rost and Sander (,b) and EMBL Predictprotein Server (address given in Table ). View Image -
Figure 2.3.7 Secondary structure prediction for human profilin I with PHD, the EMBL neural network method. Sequence homologs and a portion of the sequence alignment used in the analysis are given in Figure . View Image -
Figure 2.3.8 Class and secondary structure predictions for human profilin I with the PSA method. View Image -
Figure 2.3.9 Summary of the secondary structure predicted for (A ) human hemoglobin β‐subunit, (B ) human interleukin 1β, and (C ) human profilin I. Each panel lists, from top to bottom, the amino acid sequence, the secondary structure determined experimentally, and the secondary structure predicted by each of the following: C‐F, the Chou and Fasman method; GOR, the GOR method; PHD, the EMBL neural network method; and PSA, the state‐space method. The location of helices (solid bars), turns (open bars), and sheet structure (hatched bars) are indicated. View Image -
Figure 2.3.10 Schematic representation of the three‐dimensional structure of human profilin I (Metzler et al., ) as displayed by Molscript (Kraulis, ). A seven‐stranded antiparallel β sheet bisects the molecule. The N‐ and C‐terminal α helices are on the left‐hand side, and the two interior α helices are on the right‐hand side in the view shown. View Image
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Literature Cited
| Literature Cited | |
| Bajorath, J., Stenkamp, R., and Aruffo, A. 1993. Knowledge‐based model building of proteins: Concepts and examples. Protein Sci. 2:1798‐1810. | |
| Baldwin, J.M. 1993. The probable arrangement of helixes in G protein–coupled receptors. EMBO J. 12:1693‐1703. | |
| Blundell, T.L. and Johnson, L.N. (eds.) 1976. Protein Crystallography. Academic Press, London. | |
| Branden, C. and Tooze, J. 1991. Introduction to Protein Structure. Garland Publishing, New York. | |
| Brookhaven. 1994. Protein Data Bank. Brookhaven National Laboratory, Upton, N.Y. | |
| Burgess, A.W., Ponnuswamy, P.K., and Scheraga, H.A. 1971. Analysis of conformations of amino acid residues and prediction of backbone topography in proteins. Isr. J. Chem. 12:239‐286. | |
| Chou, P.Y. 1989. Prediction of protein structural class from amino acid compositions. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) pp. 549‐586. Plenum, New York. | |
| Chou, P.Y. and Fasman, G.D. 1974a. Conformational parameters for amino acids in helical, beta sheet and random coil regions calculated from proteins. Biochemistry 13:211‐222. | |
| Chou, P.Y. and Fasman, G.D. 1974b. Prediction of protein conformation. Biochemistry 13:223‐245. | |
| Chou, P.Y. and Fasman, G.D. 1977. β‐turns in proteins. J. Mol. Biol. 115:135‐175. | |
| Chou, P.Y. and Fasman, G.D. 1978a. Empirical predictions of protein conformation. Annu. Rev. Biochem. 47:251‐276. | |
| Chou, P.Y. and Fasman, G.D. 1978b. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. 47:45‐148. | |
| DeGrado, W.F. 1988. Design of peptides and proteins. Adv. Protein Chem. 39:51‐124. | |
| Dill, K.A. 1990. Dominant forces in protein folding. Biochemistry 29:7133‐7155. | |
| Dunhill, P. 1968. The use of helical net diagrams to represent protein structures. Biophys. J. 8:865‐875. | |
| Fasman, G.D. 1985. A critique of the utility of the prediction of protein secondary structure. J. Biosci. 8:15‐23. | |
| Fasman, G.D. 1989a. The development of the prediction of protein structure. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) pp. 193‐316. Plenum, New York. | |
| Fasman, G.D. (ed.). 1989b. Prediction of Protein Structure and the Principles of Protein Conformation. Plenum, New York. | |
| Fermi, G. 1975. Three‐dimensional Fourier synthesis of human deoxyhaemoglobin at 2.5 angstroms resolution, refinement of the atomic model. J. Mol. Biol. 97:237‐256. | |
| Fersht, A.R. and Serrone, L. 1993. Principles of protein stability derived from protein engineering experiments. Curr. Opin. Struct. Biol. 3:75‐83. | |
| Finzel, B.C., Clancy, L.L., Holland, D.R., Muchmore, S.W., Watenpaugh, K.D., and Einspahr, H.M. 1989. Crystal structure of recombinant human interleukin‐1β at 2.0 angstroms resolution. J. Mol. Biol. 209:779. | |
| Fisher, M.F. 1964. A limiting law relating the size and shape of protein molecules to their composition. Proc. Natl. Acad. Sci. U.S.A. 51:1285‐1291. | |
| Garnier, J. and Robson, B. 1989. The GOR method for predicting secondary structure in proteins. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) pp. 417‐466. Plenum, New York. | |
| Garnier, J., Osguthorpe, D.J., and Robson, B. 1978. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:97‐120. | |
| Genetics Computer Group. 1994. (GCG) Wisconsin Sequence Analysis Package Program Manual. Genetics Computer Group, Inc., Madison, Wis. | |
| Goodman, E.M. and Kim, P.S. 1991. Periodicity of amide proton exchange rates in a coiled‐coil leucine zipper peptide. Biochemistry 30:11615‐11620. | |
| Greer, J. 1990. Comparative modeling: Application to the family of the mammalian serine proteases. Proteins Struct. Funct. Genet. 7:317‐334. | |
| Guzzo, A.V. 1965. The influence of amino acid sequence on protein structure. Biophys. J. 5:809‐822. | |
| Harbury, P.B., Zhang, T., Kim, P.S., and Alber, T. 1993. A switch between two‐, three‐, and four‐stranded coiled coils in GCN4 leucine zipper mutants. Science 262:1401‐1407. | |
| Harper, E.T. and Rose, G.D. 1993. Helix stop signals in proteins and peptides: The capping box. Biochemistry 32:7605‐7609. | |
| Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. A new approach to protein fold recognition. Nature 358:86‐89. | |
| Kabsch, W. and Sander, C. 1984. On the use of sequence homologies to predict different conformations. Proc. Natl. Acad. Sci. U.S.A. 81:1075‐1078. | |
| Kabsch, W. and Sander, C. 1985. Identical pentapeptides with different backbones. Nature 317:207. | |
| Kamtekar, S., Schiffer, J.M., Xiong, H., Babik, J.M., and Hecht, M.H. 1993. Protein design by binary patterning of polar and non‐polar amino acids. Science 262:1680‐1685. | |
| Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1‐63. | |
| Kneller, D.G., Cohen, F.E., and Largridge, R. 1990. Improvements in protein secondary structure prediction by an enhanced neural network. J. Mol. Biol. 214:171‐182. | |
| Kraulis, P.J. 1991. MOLSCRIPT: A program to produce detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946‐950. | |
| Krystek, Jr., S.R., Bruccoleri, R.E., and Novotny, J. 1991. Stabilities of leucine zipper dimers estimated by an empirical force energy method. Int. J. Pept. Protein Res. 38:229‐236. | |
| Kuntz, I.D. 1972. Protein folding. J. Am. Chem. Soc. 94:4009‐4012. | |
| Lesk, A.M. 1991. Protein architecture. IRL Press, Oxford. | |
| Levitt, M. and Chothia, C. 1976. Structural patterns in globular proteins. Nature 261:552‐558. | |
| Lewis, P.N., Momany, F.A., and Scheraga, H.A. 1971. Folding of polypeptide chains in proteins: A proposed method of folding. Proc. Natl. Acad. Sci. U.S.A. 68:2293‐2297. | |
| Lim, V.I. 1974. Algorithms for prediction of α helices and β‐structural regions in globular proteins. J. Mol. Biol. 88:873‐894. | |
| Lovejoy, B., Choe, S., Cascio, D., McRorie, D.K., DeGrado, W.F., and Eisenberg, D. 1993. Crystal structure of a synthetic triple‐stranded α‐helical bundle. Science 259:1288‐1293. | |
| Metzler, W.J., Constantine, K., Friedrichs, M.S., Bell, A., Ernst, E., Lavoie, T.B., and Mueller, L. 1993. Characterization of the three‐dimensional structure of human profilin: 1H, 13C and 15N assignments and global folding pattern. Biochemistry 32:13818‐13829. | |
| Metzler, W.J., Farmer, B.T., II, and Mueller, L. 1995. Refined solution structure of human profilin I. Protein Sci. 4:450‐459. | |
| Nagano, K. 1973. Logical analysis of the mechanism of protein folding. I. Prediction of helices, loops and β‐structures from primary structure. J. Mol. Biol. 75:401‐420. | |
| Novotny, J. and Auffray, C. 1984. A program for prediction of protein secondary structure from nucleotide sequence data: Application to histocompatability antigens. Nucl. Acids Res. 12:243‐255. | |
| Oppenheimer, N.J. and James, T.L. (eds.) 1989. Nuclear magnetic resonance (Part B). Methods Enzymol. Volume 177: | |
| O'Shea, E.K., Rutkowski, R., and Kim, P.S. 1992. Mechanism of specificity in the Fos‐Jun oncoprotein heterodimer. Cell 68:699‐708. | |
| Pauling, L. and Corey, R.B. 1951. The pleated sheet, a new layer of configuration of polypeptide chains. Proc. Natl. Acad. Sci. U.S.A. 37:251‐256. | |
| Pauling, L., Corey, R.B., and Branson, H.R. 1951. The structure of proteins: Two hydrogen‐bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U.S.A. 37:205‐211. | |
| Presta, L.G. and Rose, G.D. 1988. Helix signal in proteins. Science 240:1632‐1641. | |
| Prevelige, P., Jr. and Fasman, G.D. 1989. Chou‐Fasman prediction of the secondary structure of proteins. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) pp. 391‐416. Plenum, New York. | |
| Prothero, J.W. 1966. Correlation between the distribution of amino acids in alpha helices. Biophys. J. 6:367‐370. | |
| Ptitsyn, O.B. and Finkelstein, A.V. 1970. Biofizika 15:757‐768. | |
| Quinn, N. and Sejnowski, T.J. 1988. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202:865‐884. | |
| Richardson, J.S. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34:167‐339. | |
| Richardson, J.S. and Richardson, D.C. 1988. Amino acid preferences for specific locations at the ends of α‐helices. Science 240:1648‐1652. | |
| Robson, B. and Pain, R.H. 1971. Analyses of the code relating sequence to conformation in proteins: Possible implication for the mechanism of formation of helical regions. J. Mol. Biol. 58:237‐259. | |
| Rost, B. and Sander, C. 1993a. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl. Acad. Sci. U.S.A. 90:7558‐7562. | |
| Rost, B. and Sander, C. 1993b. Prediction of protein structure at better than 70% accuracy. J. Mol. Biol. 232:584‐599. | |
| Roy, S. and Rose, G.D. 1980. Hydrophobic basis of packing in globular proteins. Proc. Natl. Acad. Sci. U.S.A. 8:4643‐4647. | |
| Sander, C. and Schneider, R. 1991. Database of homology‐derived structures and the structural meaning of sequence alignment. Proteins Struct. Funct. Genet. 9:56‐68. | |
| Schiffer, M. and Edmundson, A.B. 1967. The use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys. J. 7:121. | |
| Schulz, G.E. 1988. A critical evaluation of methods for prediction of protein secondary structures. Annu. Rev. Biophys. Chem. 17:1‐21. | |
| Schulz, G.E., Barry, C.D., Friedman, J., Chou, P.Y., Fasman, G.D., Finkelstein, A.V., Lim, V.I., Ptitsyn, O.B., Kabat, E.A., Wu, T.T., Levitt, M., Robson, B., and Nagano, K. 1974. Comparison of predicted and experimentally determined secondary structure of adenyl kinase. Nature 250:140‐142. | |
| Schulz, G.E. and Schirmer, R.H. 1979. Principles of Protein Structure. Springer‐Verlag, New York and Heidelberg. | |
| Sippl, M.J. and Weitckus, S. 1992. Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations. Proteins Struct. Funct. Genet. 13:258‐271. | |
| Stultz, C.M., White, J.V., and Smith, T.F. 1993. Structural analysis based on state‐space modeling. Protein Sci. 2:305‐314. | |
| Wuthrich, K. 1986. MR of Proteins and Nucleic Acids. John Wiley & Sons, New York. | |
| Wyckoff, H.W., Hirs, C.H.W., and Timasheff, S.N. (eds.) 1985. Diffraction methods for biological molecules (Parts A and B). Methods Enzymol. Volumes 114 and 115 | |
| Key Reference | |
| Fasman, 1989b. See above. | |
| Provides extensive descriptions and a historical perspective describing methods for protein structure prediction. |
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