Predicción computacional de la estructura terciaria de la iduronato 2-sulfato sulfatasa humana

Sáenz, Homero; Lareo, Leonardo; Poutou, Raúl A.; Sosa, Angela; Barrera, Luis Alejandro

doi:10.7705/biomedica.v27i1.229

Cited by 16 publications

(9 citation statements)

References 55 publications

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“…A: Pig aspartate aminotransferase (EC 2.6.1.2; UniprotKB AC: P13119, PDB ID: AATM-PIG; constructed by homology modeling for this study). B: Human iduronate 2-sulfate sulfatase (EC 3.1.6.13; UniprotKB AC: P22304, PDB ID: IDS_HUMAN; model developed by Sáenz et al, 2007). C: Human alcohol dehydrogenase (EC 1.1.1.1; UniprotKB AC: P00325; PDB ID: 1DEH).…”

Section: Resultsmentioning

confidence: 99%

“…Three-dimensional models of five proteins were employed, and 3D models of four proteins were constructed by homology modeling (Chen et al, 2014;Seddigh and Darabi, 2014) with the assistance of the protein-modeling tools ProMod and Swissmodel (Peitsch, 1996). In contrast, a previously developed 3D model was employed for IDS ( Figure 1) (Sáenz et al, 2007). There are two reasons to expect that this approach could produce realistic models.…”

Section: D Theoretical Structure Retrievalmentioning

confidence: 99%

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Prediction of glycation sites: new insights from protein structural analysis

Suarez¹,

Poutou-Piñales²,

Santos³

et al. 2016

Turk J Biol

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Glycation of proteins is a nonenzymatic process in which proteins react with reducing sugar molecules. This process takes place at ε-amino (ε-NH +) groups of lysine or hydroxylysine residues as well as α-amino groups of N-terminal residues. In the present study glycation of ε-NH + groups of lysines was computationally analyzed for 26 proteins based on their 3D structures. We determined the spatial relationship with acidic or basic residues and correlated them with the glycation prediction algorithm Netglycate 1.0 software, which employed primary structure exclusively for glycation site prediction. Of the lysines from 19 of the 20 proteins employed to build the Netglycate 1.0 algorithm 87.80% depicted a spatial relationship with acidic or basic residues. For the remaining seven proteins that were not included in the algorithm, 95.23% of the lysines exhibited a spatial relationship with acidic or basic residues. For these seven proteins, Netglycate 1.0 predicted only 52.38% of the lysines with a previously reported experimental glycation as potential glycation sites. In all cases, distances between residues were less than or equal to 9.78 Å. These results suggest that it is the spatial relationship of lysines with acidic or basic residues in the 3D conformation of a protein that determines the glycation target site, rather than a specific sequence of the primary structure.

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Section: Resultsmentioning

confidence: 99%

Section: D Theoretical Structure Retrievalmentioning

confidence: 99%

Prediction of glycation sites: new insights from protein structural analysis

Suarez¹,

Poutou-Piñales²,

Santos³

et al. 2016

Turk J Biol

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“…A predicted tertiary structure has been reported for human IDS (Sáenz et al 2007), which shows strong similarities with other human sulfatases: GALNS (Rivera-Colón et al (2012)); ARSA (Chruszcz et al 2003) and STS (Hernandez-Guzman et al 2003). …”

Section: Introductionmentioning

confidence: 68%

Comparative studies of vertebrate iduronate 2-sulfatase (IDS) genes and proteins: evolution of A mammalian X-linked gene

Holmes

2017

3 Biotech

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IDS is responsible for the lysosomal degradation of heparan sulfate and dermatan sulfate and linked to an X-linked lysosomal storage disease, mucopolysaccharidosis 2 (MPS2), resulting in neurological damage and early death. Comparative IDS amino acid sequences and structures and IDS gene locations were examined using data from several vertebrate genome projects. Vertebrate IDS sequences shared 60–99% identities with each other. Human IDS showed 47% sequence identity with fruit fly (Drosophila melanogaster) IDS. Sequence alignments, key amino acid residues, N-glycosylation sites and conserved predicted secondary and tertiary structures were also studied, including signal peptide, propeptide and active site residues. Mammalian IDS genes usually contained 9 coding exons. The human IDS gene promoter contained a large CpG island (CpG46) and 5 transcription factor binding sites, whereas the 3′-UTR region contained 5 miRNA target sites. These may contribute to IDS gene regulation of expression in the brain and other neural tissues of the body. An IDS pseudogene (IDSP1) was located proximally to the IDS gene on the X-chromosome in primate genomes. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate IDS gene. These suggested that IDS has originated in an invertebrate ancestral genome and retained throughout vertebrate evolution and conserved on marsupial and eutherian X-chromosomes, with the exception of rat Ids on chromosome 8.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0595-3) contains supplementary material, which is available to authorized users.

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“…Sin embargo, en la literatura científica no existen reportes acerca de las estructuras secundaria, terciaria y cuaternaria de las proteínas alfa-B cristalina, Hsp27 y HspB8. Ante la ausencia de conocimientos obtenidos experimentalmente, sobre la conformación nativa de estas moléculas, la elaboración de modelos computacionales para las proteínas normales y mutadas ofrece la posibilidad de tener buenas aproximaciones a las estructuras tridimensionales (37,38,39). A partir de estos modelos se puede obtener información por predicción computacional de algunas de sus propiedades químicas e inferir implicaciones en su comportamiento.…”

Section: Discussionunclassified

“…A partir de estos modelos se puede obtener información por predicción computacional de algunas de sus propiedades químicas e inferir implicaciones en su comportamiento. La comparación de las estructuras normales y mutadas obtenidas de esta forma, permite conocer la influencia de cada mutación sobre la estructura y función de la molécula normalmente expresada y abre la posibilidad de establecer correlaciones genotipofenotipo (37).…”

Section: Discussionunclassified

Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8

Sáenz-Suárez

Lareo²,

Oribio-Quinto

et al. 2011

Univ. Sci.

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Objective: To make computational predictions of the structure of the human proteins Hsp27, αB-crystalline and HspB8. Materials and methods. The prediction of the secondary structure was obtained by a consensus of the programs for secondary prediction GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN and Psi-Pred. The models of tertiary structure were built from fragments homologous to proteins with tertiary known structure that were obtained by multiple alignments. Using the primary sequence we obtained the antigenicity profiles of native proteins and we analyzed the profiles of hydrophobicity, polarity, flexibility and accessibility of both native and mutant proteins. Results. Predictions of the secondary and tertiary structures of the studied proteins show that in the three cases, more than 65% are coil regions, 20-25 % are folded sheet and less than 10% are alpha helix. Analyses of the primary structure show that at least one of the studied profiles in every mutation is altered. Conclusions. The comparative analyses of structure suggest that mutations affect the solubility of the mutated proteins and hence affect their function as molecular chaperones Key words: Hsp27, αB-cristalline, HspB8, prediction of secondary structure, computational model of tertiary structure

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Predicción computacional de la estructura terciaria de la iduronato 2-sulfato sulfatasa humana

Cited by 16 publications

References 55 publications

Prediction of glycation sites: new insights from protein structural analysis

Prediction of glycation sites: new insights from protein structural analysis

Comparative studies of vertebrate iduronate 2-sulfatase (IDS) genes and proteins: evolution of A mammalian X-linked gene

Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8

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