Mapping and 2D visualization of secondary structure elements in cytochromes

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Radka SVOBODOVÁ VAŘEKOVÁ a Karel BERKA. Mapping and 2D visualization of secondary structure elements in cytochromes. In ISMB/ECCB, Prague. 2017.

Základní údaje

• Originální název: Mapping and 2D visualization of secondary structure elements in cytochromes
• Autoři: HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Radka SVOBODOVÁ VAŘEKOVÁ a Karel BERKA.
• Vydání: ISMB/ECCB, Prague, 2017.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Konferenční abstrakt
• Obor: 10201 Computer sciences, information science, bioinformatics
• Stát vydavatele: Česká republika
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Organizační jednotka: Fakulta informatiky
• Příznaky: Mezinárodní význam

Anotace

Secondary structure elements (SSEs) such as helices and sheets are important parts of protein structure. Their composition and organization is often characteristic for proteins from a certain protein family and they participate in formation of protein fold. Thanks to advanced structure determination techniques, we have a lot of structural data about individual protein families with variations originating from different organisms, binding various ligands and containing diverse mutations. Mapping and 2D visualization of their SSEs could provide a very useful insight, e.g. visualization of their differences, identification of conserved or other key regions, etc.. Unfortunately, current approaches focused on SSE 2D visualization (e.g., PROMOTIF, Pro-Origami, Hera) do not take into account an information about real distances of SSEs or common protein family fold. Therefore, even when two proteins from the same family differ only slightly, their SSE 2D diagrams can be totally different. In our approach, the analysis of SSEs is provided within a protein set with the detection of the conserved (“skeleton”) SSEs forming the conserved fold. Afterwards, it can perform SSE 2D visualization such a way, that structural information is kept. An applicability of this approach is shown in a case study focused on cytochromes P450. This protein family, which is important for drug design, has currently available more than 580 structures from about 30 organisms and each cytochrome contains more than 20 SSEs. Our approach can be extended to most of other protein structural families which will allow family-wide annotations and comparisons in a simple visual manner.