Classification of common functional loops of kinase super‐families

Abstract

A structural classification of loops has been obtained from a set of 141 protein structures classified as kinases. A total of 1813 loops was classified into 133 subclasses (9 betabeta(links), 15 betabeta(hairpins), 31 alpha-alpha, 46 alpha-beta and 32 beta-alpha). Functional information and specific features relating subclasses and function were included in the classification. Functional loops such as the P-loop (shared by different folds) or the Gly-rich-loop, among others, were classified into structural motifs. As a result, a common mechanism of catalysis and substrate binding was proved for most kinases. Additionally, the multiple-alignment of loop sequences made within each subclass was shown to be useful for comparative modeling of kinase loops. The classification is summarized in a kinase loop database located at http://sbi.imim.es/archki.

Local Protein Structures

“…Consensus sequences were then binding was sustained for most kinases [220]. ArchDB has also been used in prediction process with excellent results [221], the dataset used was based on SCOP 40 of the 1.61…”

Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts

“…Secondly, only the proteins were selected with super secondary structures information in ArchDB40 (Fernandez-Fuentes et al, 2004). Finally, the PISCES program (Wang and Dunbrack, 2005) was utilized to removing similar sequences.…”

“…In this paper, we concentrate on the former. At present, there are five kinds of simple super secondary structures in ArchDB40 (Fernandez-Fuentes et al, 2004), namely, α-loop-α HH ð Þ, α-loop-β HE ð Þ, β-loop-α EH ð Þ, β-loop-β-hairpin EE ð Þ and β-loop-β-link EE1 ð Þ. These structural motifs play an important role in protein folding and stability, because a large number of motifs exist in protein spatial structure.…”

Application of HMM to the Study of Three-Dimensional Protein Structure

“…(Fetrow, 1995;Fernandez-Fuentes et al, 2004). The HMM-SA was optimised in terms of 3D local description of proteins and resulted in precise and detailed description of 3D conformations into 27 SLs: 18 SLs being focused on loop description.…”