Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder
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 presen...
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2015
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v10_n12_p_Lorenzo http://hdl.handle.net/20.500.12110/paper_19326203_v10_n12_p_Lorenzo |
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paper:paper_19326203_v10_n12_p_Lorenzo2023-06-08T16:30:27Z Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder 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 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. 2015 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v10_n12_p_Lorenzo http://hdl.handle.net/20.500.12110/paper_19326203_v10_n12_p_Lorenzo |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
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 |
| spellingShingle |
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 Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| topic_facet |
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 |
| description |
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. |
| title |
Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| title_short |
Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| title_full |
Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| title_fullStr |
Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| title_full_unstemmed |
Prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| title_sort |
prediction of spontaneous protein deamidation from sequence-derived secondary structure and intrinsic disorder |
| publishDate |
2015 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v10_n12_p_Lorenzo http://hdl.handle.net/20.500.12110/paper_19326203_v10_n12_p_Lorenzo |
| _version_ |
1768542147264380928 |