Análisis estructural, funcional y filogenético in silico de la proteína ARNasa H2A de reptiles y aves
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Date
2022
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Universidad Nacional de Trujillo
Abstract
La presente investigación tuvo como objetivo analizar in silico la estructura, función y filogenia de la ARNasa H2A de reptiles y aves. Las secuencias fueron tomadas del NCBI y procesadas con la herramienta BLAST; así mismo, se usaron diferentes softwares como MEGA X para generar el árbol filogenético y servidores como Protparam para determinar las propiedades fisicoquímicas, Fuel-mLoc, BaCelLo y Euk-mPloc para la ubicación subcelular, CFSSP para determinar las probabilidades de tipos de estructura secundaria, Phyre2 para el modelamiento 3D, el software VMD para visualizar y evaluar la calidad de los modelos 3D, la base de datos STRING para la red de interacción proteica y el servidor Pprint para la identificación de los residuos que interactúan con el ARN. Los Resultados indican que la ARNasa H2A relaciona filogenéticamente a los Arcosaurios con los Testudines, distanciando a los Squamata; las ARNasas H2A de reptiles y aves tienen puntos isoeléctricos ácidos, pesos moleculares alrededor de 32.00 kDa, longitudes de 211 a 358 aminoácidos, el índice de inestabilidad en reptiles es inferior a 40 y en aves es superior, las ARNasas H2A son proteínas termoestables e hidrofílicas, se componen principalmente de alanina, valina y leucina, se encuentran en el núcleo y/o citoplasma, presentan estructuras secundarias del tipo alfa y beta principalmente, su núcleo catalítico está compuesto por hojas beta y rodeado por hélices alfa en su estructura 3D, interactúan con las proteínas ARNasa H1, ARNasa H2B y PCNA, y reconoce a su sustrato mediante aminoácidos polares y apolares. En conclusión, las ARNasas H2A de reptiles y aves muestran diferencias y similitudes estructurales y funcionales que permite comparar filogenéticamente ambos grupos.
The aim of this research was to analyze in silico the structure, function and phylogeny of RNase H2A from reptiles and birds. The sequences were retrieved from the NCBI and processed with the BLAST tool; Likewise, different software such as MEGA X were used to generate the phylogenetic tree and servers such as Protparam to determine the physicochemical properties, Fuel-mLoc, BaCelLo and Euk-mPloc for the subcellular location, CFSSP to determine the forms of types of secondary structure , Phyre2 for 3D modeling, VMD software to visualize and evaluate the quality of 3D models, STRING database for protein interaction network, and Pprint server for identification of RNA-interacting residues. The results indicate that RNase H2A is phylogenetically related to the Archosaurs with the Testudines, distancing themselves from the Squamata; RNAses H2A from reptiles and birds have acidic isoelectric points, molecular weights around 32.00 kDa, lengths from 211 to 358 amino acids, the instability index in reptiles is less than 40 and in birds it is higher, RNAses H2A are thermostable and hydrophilic proteins, they are mainly composed of alanine, valine and leucine, they are found in the nucleus and/or cytoplasm, they present secondary structures of the alpha and beta type mainly, their catalytic nucleus is composed of beta sheets and surrounded by alpha helixes in their 3D structure, they interact with RNase H1, RNase H2B, and PCNA proteins, and recognize their substrate by polar and nonpolar amino acids. In conclusion, the H2A RNAses of reptiles and birds show structural and functional differences and similarities that allow both groups to be compared phylogenetically.
The aim of this research was to analyze in silico the structure, function and phylogeny of RNase H2A from reptiles and birds. The sequences were retrieved from the NCBI and processed with the BLAST tool; Likewise, different software such as MEGA X were used to generate the phylogenetic tree and servers such as Protparam to determine the physicochemical properties, Fuel-mLoc, BaCelLo and Euk-mPloc for the subcellular location, CFSSP to determine the forms of types of secondary structure , Phyre2 for 3D modeling, VMD software to visualize and evaluate the quality of 3D models, STRING database for protein interaction network, and Pprint server for identification of RNA-interacting residues. The results indicate that RNase H2A is phylogenetically related to the Archosaurs with the Testudines, distancing themselves from the Squamata; RNAses H2A from reptiles and birds have acidic isoelectric points, molecular weights around 32.00 kDa, lengths from 211 to 358 amino acids, the instability index in reptiles is less than 40 and in birds it is higher, RNAses H2A are thermostable and hydrophilic proteins, they are mainly composed of alanine, valine and leucine, they are found in the nucleus and/or cytoplasm, they present secondary structures of the alpha and beta type mainly, their catalytic nucleus is composed of beta sheets and surrounded by alpha helixes in their 3D structure, they interact with RNase H1, RNase H2B, and PCNA proteins, and recognize their substrate by polar and nonpolar amino acids. In conclusion, the H2A RNAses of reptiles and birds show structural and functional differences and similarities that allow both groups to be compared phylogenetically.
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Keywords
In silico, estructura, función, filogenia, ARNasa H2A, reptiles y aves