A Novel Database of Disulfide Patterns and its Application to the Discovery of Distantly Related Homologs

Tick-derived Kunitz-type inhibitors as antihemostatic factors

“…9A). Disulfide linkages are strongly conserved throughout evolution in proteins of related structure and function, and the TAP/BPTI pair is considered a paradigmatic example of distant homologs that are detectable by their identical S-S bonding pattern (van Vlijmen et al, 2004). Perhaps more importantly, two independently determined NMR solution structures of TAP showed the same major structural elements that define the Kunitz fold: two antiparallel b-strands and a C-terminal a-helix (refs.…”

Prediction of disulfide connectivity in proteins with support vector machine

“…The overall Q p of the SVM model on the dataset SP39-PDB, which was also used in previous studies (Baldi et al, 2005;Vullo and Frasconi, 2004), can reach 59%. Moreover, comparing with the CSP method proposed previously (Chuang et al, 2003;van Vlijmen et al, 2004;Zhao et al, 2005), in which the distribution of cysteine residues in a protein sequence was considered as important information for predicting the disulfide connectivity, our SVM model still generates better results by learning from the profile information only.…”

“…Besides encoding information of amino acids as features, some other possible values such as the length of protein sequence can also be used. In this study, we further explored the usage of sequential distances between cysteines, which may contain knowledge for disulfide bonding patterns (Chuang et al, 2003;Harrison and Sternberg, 1994;van Vlijmen et al, 2004;Zhao et al, 2005). Hence, a data entry for our model can be expressed as follows: label : window i ; window j ; distanceði; jÞ ðo ptionalÞ;…”

“…Other than machine learning techniques, a simpler method based on cysteine separation profiles (CSPs) was originally proposed by Chuang et al (2003) and van Vlijmen et al (2004). This method was further developed in our previous work to predict the disulfide connectivity pattern of proteins (Zhao et al, 2005).…”

Homology between DUF784, DUF1278 domains and the plant prolamin superfamily typifies evolutionary changes of disulfide bonding patterns

“…2), in which both gain and loss of Cys-Cys pairs or disulfide bond were utilized to generate a series of different domain facets with gained or lost together within the protein family. [14][15][16][17] The gain of a disulfide bond can be exemplified by the evolutionary changes of Cys-Cys pairs between members of the prolamin superfamily (Figs. 1 and 2).…”