Cytochrome P450 structure anatomy – recognition and analysis of secondary structure elements

MIDLIK, Adam, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika NAVRÁTILOVÁ, Karel BERKA and Jaroslav KOČA. Cytochrome P450 structure anatomy – recognition and analysis of secondary structure elements. In ISMB/ECCB, Prague. 2017.

Basic information

• Original name: Cytochrome P450 structure anatomy – recognition and analysis of secondary structure elements
• Authors: MIDLIK, Adam, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika NAVRÁTILOVÁ, Karel BERKA and Jaroslav KOČA.
• Edition: ISMB/ECCB, Prague, 2017.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science
• Tags: International impact

Abstract

Nowadays, structural bioinformatics faces an enormous growth in the number of available protein structures. Moreover, structurally similar proteins form protein families and these families represent rich datasets. In order to understand their molecular function we must focus on the key structural regions (binding sites, channels, allosteric sites, etc.), which involve both conserved and variable regions. Number and position of secondary structure elements (helices and sheets) is usually highly conserved within each protein family, thus they can serve as a firm point for identification of these key regions. Cytochromes P450 are proteins responsible for degradation of drugs and other xenobiotic substances in the organism and thus understanding of their function is crucial in drug design. They are an example of a protein family where the secondary structure elements are traditionally annotated with fixed names, facilitating description and comparison of their structures in the literature. In the last few years, the number of resolved cytochrome P450 structures has grown markedly and currently there are available more than 700 structures originating from more than 50 different organisms. Conserved annotation motivated us to analyze secondary structure elements across the whole cytochrome P450 family. During this process, we first developed an algorithm for automated annotation of secondary structure elements based on a template protein annotation. Secondly, we described the general anatomy and variability of cytochromes P450, based on this annotation. Specifically, we report features of their secondary structure elements such as frequency of occurrence, typical length, amino acid composition, and relation to the source organism.