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. 2005 Sep 9:6:223.
doi: 10.1186/1471-2105-6-223.

SUPERFICIAL--surface mapping of proteins via structure-based peptide library design

Andrean Goede  1 , Ines S Jaeger, Robert Preissner
Affiliations

SUPERFICIAL--surface mapping of proteins via structure-based peptide library design

Andrean Goede et al. BMC Bioinformatics. .

Abstract

Background: The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being prevailant. Conventional mapping techniques with arrays of synthetic peptides have limitations with regard to the location of discontinuous or non-linear binding sites of proteins.

Results: We present a structure-based approach to the design of peptide libraries that mimic the whole surface or a particular region of a protein. Neighbouring sequence segments are linked by short spacers to conserve local conformation. To this end, we have developed SUPERFICIAL, a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions.

Conclusion: Based on 3D structures, SUPERFICIAL may help to negotiate some of the existing limitations, since binding sites consisting of several linear pieces can now be detected.

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Figures

Figure 2
Figure 2
Screenshot of SUPERFICIAL displaying the options. Sections A and B are the same for all submenus/menu items ("load protein", "show", "options" and "peptide"). Section A gives a short description of the options and may act as a guide for the user. In section B the subsequent results of the settings are shown and the user may check the effects on the size of the surface and the peptides. The options in C determine the surface of a protein, whereas the first entry ("percentage of atoms at surface per amino acid") has the greatest influence on the surface extension. Section D gives the definitions for peptide generation. All changes are visualised in B on sequence level. The whole protein is displayed in the submenu "show" (Fig. 3).
Figure 3
Figure 3
Screenshot of SUPERFICIAL showing the 3D view of the protein. The functionality of this tool is exemplified by the crystal structure of a complex between influenza virus neuraminidase and an antibody (PDB-code: 1a14).
Figure 4
Figure 4
Screenshot to illustrate the selection of a region (white ellipse). The peptide library will be generated for this region only.
Figure 1
Figure 1
Flow chart to illustrate the process from loading a protein to the generation of the peptide library.
See this image and copyright information in PMC

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