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Abstract:

Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www. embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis". © 2015 Lorenzo et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Registro:

Documento: Artículo
Título:Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder
Autor:Lorenzo, J.R.; Alonso, L.G.; Sánchez, I.E.
Filiación:Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Buenos Aires, Argentina
Palabras clave:asparagine; beta interferon; protein bcl xl; superoxide dismutase; trastuzumab; amide; asparagine; intrinsically disordered protein; protein bcl x; Saccharomyces cerevisiae protein; superoxide dismutase; amino acid sequence; Article; deamination; DNA damage; glycosylation; learning algorithm; molecular dynamics; NGOME; protein analysis; protein degradation; protein folding; protein metabolism; protein modification; protein purification; protein secondary structure; protein stability; racemization; receiver operating characteristic; sequence analysis; yeast; amino acid sequence; animal; chemistry; human; metabolism; molecular genetics; procedures; protein processing; protein secondary structure; software; Amides; Amino Acid Sequence; Animals; Asparagine; bcl-X Protein; Humans; Interferon-beta; Intrinsically Disordered Proteins; Molecular Sequence Data; Protein Processing, Post-Translational; Protein Structure, Secondary; Saccharomyces cerevisiae Proteins; Sequence Analysis, Protein; Software; Superoxide Dismutase
Año:2015
Volumen:10
Número:12
DOI: http://dx.doi.org/10.1371/journal.pone.0145186
Título revista:PLoS ONE
Título revista abreviado:PLoS ONE
ISSN:19326203
CODEN:POLNC
CAS:asparagine, 70-47-3, 7006-34-0; protein bcl xl, 151033-38-4; superoxide dismutase, 37294-21-6, 9016-01-7, 9054-89-1; trastuzumab, 180288-69-1; amide, 17655-31-1; Amides; Asparagine; bcl-X Protein; Interferon-beta; Intrinsically Disordered Proteins; Saccharomyces cerevisiae Proteins; Superoxide Dismutase
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v10_n12_p_Lorenzo

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Citas:

---------- APA ----------
Lorenzo, J.R., Alonso, L.G. & Sánchez, I.E. (2015) . Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder. PLoS ONE, 10(12).
http://dx.doi.org/10.1371/journal.pone.0145186
---------- CHICAGO ----------
Lorenzo, J.R., Alonso, L.G., Sánchez, I.E. "Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder" . PLoS ONE 10, no. 12 (2015).
http://dx.doi.org/10.1371/journal.pone.0145186
---------- MLA ----------
Lorenzo, J.R., Alonso, L.G., Sánchez, I.E. "Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder" . PLoS ONE, vol. 10, no. 12, 2015.
http://dx.doi.org/10.1371/journal.pone.0145186
---------- VANCOUVER ----------
Lorenzo, J.R., Alonso, L.G., Sánchez, I.E. Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder. PLoS ONE. 2015;10(12).
http://dx.doi.org/10.1371/journal.pone.0145186