WinPep - WinGene

WinPep (and Wingene) is a small, easy to use application specially designed to help you with the analysis of polypeptide sequences.

WinPep offers several possibilities of amino acid sequence analysis. First, a set of basic physicochemical properties can be derived. This set includes: - sequence length,  - frequencies of amino acid occurrences, - isoelectric point [pKa values of Creighton (3)], - molecular weight and molar absorption coefficients for both native and denatured proteins. For more detailed analysis, a sequence-specific cleavage of the protein can be simulated.

After selecting one of several preset proteases and chemical agents or providing a recognition sequence of the user’s choice, all possible Quebecor - place LHP BioComputing head 1170 BioTechniques Vol. 26, No. 6 (1999) WinGene/WinPep: User-Friendly Software for the Analysis of Amino Acid Sequences BioTechniques 26:1170-1172 (June 1999) resulting peptide fragments are displayed with sequence position, length and molecular weight. This allows easy identification of fragments after HPLC and mass spectrometry. The sequence can be searched for the occurrence of any sequence motif.

The visualization of amphipathic helices, often involved in protein-protein interactions (3), can be achieved by the display of a (sub)sequence as a helical wheel in WinPep. To aid the identification of potential helices with strong amphipathy, a value referred to as “amphypathic moment” is calculated. This value is the gradient of the hydropathy of individual residues across an ideal helix. Consequently, values close to zero result from an even distribution of hydrophilic and hydrophobic amino acids around a hypothetical helix, while larger values indicate an asymmetric distribution. A plot of the amphipathic moment along the entire sequence can be displayed. While the amphipathic moment does not predict any structural elements, it constitutes a helpful tool for the design of biochemical experiments. Hydropathic plots are commonly used to identify putative transmembrane regions of proteins (6). With WinPep, it is possible to display a hydropathic plot based on a running window average with variable window size. The scales of Kyte and Doolittle (6) or Sweet and Eisenberg (8) are predefined.

Alternatively, individual scales can be provided. Thus, other tasks (e.g., the prediction of immunogenic epitopes) can individually be set up. Based on the currently active scale, the main hydropathy is calculated. Similarly, for the other graphic displays, hydropathic plots can be transferred into other applications through the clipboard (Copy&Paste). Figure 1 displays a screen of a hydropathic plot of cyclic nucleotide-gated channel 1 (CNGC1). This protein of an as-yet-unknown function but with homology to animal cyclic nucleotide-gated channels is encoded by a recently identified gene in the model plant Arabidopsis thaliana (5). Based on the display in Figure 1, the topology of six transmembrane helices similar to the channels in animals could be predicted. In contrast to the animal proteins, however, the fifth and sixth putative transmembrane helices are much further apart in CNGC1; this indicates that the plant protein could belong to a new, distinct family of channel proteins.