• Abstract
• Table of Contents
• Figures
• 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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GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Figures

• 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 ).

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• 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).

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• 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.

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• 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.

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• Figure 2.3.5 Sketch of the human profilin secondary structure as predicted in Figure and Figure by Chou‐Fasman method.

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• 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 ).

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• 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 .

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• Figure 2.3.8 Class and secondary structure predictions for human profilin I with the PSA method.

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• 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.

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• 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.

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