Creation and visualization of secondary structure consensus for
protein families

k 2019

Creation and visualization of secondary structure consensus for protein families

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA et. al.

Základní údaje

Originální název

Creation and visualization of secondary structure consensus for protein families

Autoři

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

Vydání

XX. setkání biochemiků a molekulárních biologů, 2019

Další údaje

Jazyk

angličtina

Typ výsledku

Prezentace na konferencích

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Přírodovědecká fakulta

Změněno: 22. 1. 2020 13:53, Mgr. et Mgr. Adam Midlik, Ph.D.

Anotace

V originále

Protein structural data, deposited in the Protein Data Bank, are a valuable source of information and their amount is continuously growing (currently more than 150 000 structures). Furthermore, most protein structures can be classified into protein families based on their similarity [1]. Systematic study of these families is gaining importance and can yield interesting research results. Every protein family has a set of characteristic secondary structure elements (SSEs, namely helices and β-strands). Their arrangement is well defined and consistent throughout the whole family. However, there will always be some differences between the members of the family and a single structure is not enough to represent the whole family of structures, just as a single amino acid sequence is not enough to represent the whole family of sequences. For sequences, this problem is solved by multiple sequence alignment, which produces the consensus sequence and can be visualized by a sequence logo [2] – this extracts the essential features of the family and shows the similarities and differences within the family. For secondary structure, such an approach is currently missing. In this work, we introduce computational methods for extracting and visualizing the secondary structure consensus for a given protein family. Apart from giving an overview of the family, this consensus can also be used as an annotation template for our previously developed program SecStrAnnotator [3]. This allows annotation of SSEs in any family and unlocks the possibility of automated annotation of the key regions (e.g. active sites and channels) based on their position relative to the SSEs. [1] Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 45(D1):D289-D295. https://doi.org/10.1093/nar/gkw1098

Citovat

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA, Karel BERKA a Radka SVOBODOVÁ VAŘEKOVÁ. Creation and visualization of secondary structure consensus for protein families. In XX. setkání biochemiků a molekulárních biologů. 2019.

@proceedings{1608525,
   author = {Midlik, Adam and Hutařová Vařeková, Ivana and Hutař, Jan and Navrátilová, Veronika and Koča, Jaroslav and Berka, Karel and Svobodová Vařeková, Radka},
   booktitle = {XX. setkání biochemiků a molekulárních biologů},
   language = {eng},
   title = {Creation and visualization of secondary structure consensus for protein families},
   url = {https://setkanibmb.webnode.cz/},
   year = {2019}
}

TY  - CONF
ID  - 1608525
AU  - Midlik, Adam - Hutařová Vařeková, Ivana - Hutař, Jan - Navrátilová, Veronika - Koča, Jaroslav - Berka, Karel - Svobodová Vařeková, Radka
PY  - 2019
TI  - Creation and visualization of secondary structure consensus for protein families
UR  - https://setkanibmb.webnode.cz/
N2  - Protein structural data, deposited in the Protein Data Bank, are a valuable source of information and their amount is continuously growing (currently more than 150 000 structures). Furthermore, most protein structures can be classified into protein families based on their similarity [1]. Systematic study of these families is gaining importance and can yield interesting research results. Every protein family has a set of characteristic secondary structure elements (SSEs, namely helices and β-strands). Their arrangement is well defined and consistent throughout the whole family. However, there will always be some differences between the members of the family and a single structure is not enough to represent the whole family of structures, just as a single amino acid sequence is not enough to represent the whole family of sequences. For sequences, this problem is solved by multiple sequence alignment, which produces the consensus sequence and can be visualized by a sequence logo [2] – this extracts the essential features of the family and shows the similarities and differences within the family. For secondary structure, such an approach is currently missing. In this work, we introduce computational methods for extracting and visualizing the secondary structure consensus for a given protein family. Apart from giving an overview of the family, this consensus can also be used as an annotation template for our previously developed program SecStrAnnotator [3]. This allows annotation of SSEs in any family and unlocks the possibility of automated annotation of the key regions (e.g. active sites and channels) based on their position relative to the SSEs. [1] Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 45(D1):D289-D295. https://doi.org/10.1093/nar/gkw1098
ER  -

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA, Karel BERKA a Radka SVOBODOVÁ VAŘEKOVÁ. Creation and visualization of secondary structure consensus for protein families. In \textit{XX. setkání biochemiků a molekulárních biologů}. 2019.

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