Secondary Structure Elements-Annotations and Schematic 2D
Visualizations Stable for Individual Protein Families

a 2018

Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families

SVOBODOVÁ VAŘEKOVÁ, Radka, Adam MIDLIK, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ et. al.

Základní údaje

Originální název

Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families

Autoři

SVOBODOVÁ VAŘEKOVÁ, Radka, Adam MIDLIK, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA a Karel BERKA

Vydání

Biophysical Society 62nd Annual Meeting, San Francisco, California, 2018

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.665

Organizační jednotka

Přírodovědecká fakulta

ISSN

DOI

http://dx.doi.org/10.1016/j.bpj.2017.11.307

UT WoS

000429315800242

Příznaky

Mezinárodní význam

Změněno: 1. 7. 2020 12:21, Mgr. Marie Šípková, DiS.

Anotace

V originále

Composition and organization of secondary structure elements (SSEs), such as alpha-helices and beta-sheets, are characteristic for protein families and they participate in formation of protein fold. They are however often influenced by the sequence variability and ligand binding. For this reason, identification of similarities and differences between SSEs can help us in the analysis of individual proteins within a protein family. To utilize the SSEs for research of individual protein families, we need to have the SSEs easily and automatically intercomparable within one protein family. Specifically, the corresponding SSEs should have the same name (annotation) and there should be a transparent schema of their localization in the protein structures. Unfortunately, SSE annotations are still performed mainly manually and universal automatic approach to assign SSE names is not available yet. Moreover, current methods focused on 2D visualization of SSEs (e.g., PROMOTIF, Pro-origami, HERA) do not consider information about real distances of SSEs. Therefore, even when two proteins from the same family differ only slightly, their SSE 2D diagrams can be totally different. For this reason, we developed a tool set which can perform SSE annotation and 2D visualization in such a way that structural information is kept. Applicability of this approach is shown in a case study focused on cytochromes P450. This protein family of drug-metabolizing enzymes has currently available more than 750 structures from about 30 organisms and each cytochrome P450 contains more than 20 SSEs for which there is a stable annotation used through the community. Our approach can be further extended to other protein structural families, which will allow family-wide SSE annotations and comparisons in a simple visual manner.

Návaznosti

MUNI/A/1194/2016, interní kód MU

Název: Statistické a deterministické modelování (Akronym: StaDeMo)

Investor: Masarykova univerzita, Statistické a deterministické modelování, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

SVOBODOVÁ VAŘEKOVÁ, Radka, Adam MIDLIK, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA a Karel BERKA. Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. In Biophysical Society 62nd Annual Meeting, San Francisco, California. 2018. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2017.11.307.

@proceedings{1455876,
   author = {Svobodová Vařeková, Radka and Midlik, Adam and Hutařová Vařeková, Ivana and Hutař, Jan and Navrátilová, Veronika and Koča, Jaroslav and Berka, Karel},
   booktitle = {Biophysical Society 62nd Annual Meeting, San Francisco, California},
   doi = {http://dx.doi.org/10.1016/j.bpj.2017.11.307},
   language = {eng},
   title = {Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families},
   url = {https://www.cell.com/biophysj/fulltext/S0006-3495(17)31539-4},
   year = {2018}
}

TY  - CONF
ID  - 1455876
AU  - Svobodová Vařeková, Radka - Midlik, Adam - Hutařová Vařeková, Ivana - Hutař, Jan - Navrátilová, Veronika - Koča, Jaroslav - Berka, Karel
PY  - 2018
TI  - Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families
UR  - https://www.cell.com/biophysj/fulltext/S0006-3495(17)31539-4
N2  - Composition and organization of secondary structure elements (SSEs), such as alpha-helices and beta-sheets, are characteristic for protein families and they participate in formation of protein fold. They are however often influenced by the sequence variability and ligand binding. For this reason, identification of similarities and differences between SSEs can help us in the analysis of individual proteins within a protein family. To utilize the SSEs for research of individual protein families, we need to have the SSEs easily and automatically intercomparable within one protein family. Specifically, the corresponding SSEs should have the same name (annotation) and there should be a transparent schema of their localization in the protein structures. Unfortunately, SSE annotations are still performed mainly manually and universal automatic approach to assign SSE names is not available yet. Moreover, current methods focused on 2D visualization of SSEs (e.g., PROMOTIF, Pro-origami, HERA) do not consider information about real distances of SSEs. Therefore, even when two proteins from the same family differ only slightly, their SSE 2D diagrams can be totally different. For this reason, we developed a tool set which can perform SSE annotation and 2D visualization in such a way that structural information is kept. Applicability of this approach is shown in a case study focused on cytochromes P450. This protein family of drug-metabolizing enzymes has currently available more than 750 structures from about 30 organisms and each cytochrome P450 contains more than 20 SSEs for which there is a stable annotation used through the community. Our approach can be further extended to other protein structural families, which will allow family-wide SSE annotations and comparisons in a simple visual manner.
ER  -

SVOBODOVÁ VAŘEKOVÁ, Radka, Adam MIDLIK, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA a Karel BERKA. Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. In \textit{Biophysical Society 62nd Annual Meeting, San Francisco, California}. 2018. ISSN~0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2017.11.307.

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