The RESID Database of protein structure modifications

Garavelli, John S.

doi:10.1093/nar/27.1.198

Cited by 8 publications

(7 citation statements)

References 6 publications

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“…Protein aspects as diverse as three‐dimensional structure and function, degradation and cellular localization are partly controlled by posttranslational modifications (PTMs) altering the structure of targeted amino acids. Higher eukaryotes in particular hold an extended repertoire of molecules, ions and enzymes that evoke and manage this type of dynamic proteome diversity 1–3. Only in the past few years have improved analytical instruments enabled researchers to globally map this wealth of PTMs 4…”

mentioning

confidence: 99%

Improved tandem mass spectrometric characterization of 3‐nitrotyrosine sites in peptides

Ghesquière

Goethals

Damme

et al. 2006

Rapid Comm Mass Spectrometry

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Nitrated tyrosines are easily converted into their aminotyrosine equivalents by a reduction step. We here show that this conversion can be exploited to readily discern 3-aminotyrosine peptides in a background of non-nitrated peptides. Furthermore, aminotyrosine peptides are more stable in single mass spectrometry (MS) mode rendering peptide mass maps easier to interpret. One significant caveat of both 3-nitrotyrosine and 3-aminotyrosine peptides is their lack of efficient fragmentation upon collision-induced dissociation (CID) which, in the case of the latter peptides, also produces unexpected, deviating isotopic patterns of fragment ions containing the aminotyrosine residue. The net result is that sequence database searching becomes daunting as the correct peptide is frequently missed since insufficient and/or inaccurate peptide fragments are used. We show that a simple acetylation step, blocking all amines (including aminotyrosine), produces peptides that undergo extensive backbone fragmentation by CID and are thus easily identifiable in databases. Our procedure is additionally illustrated by doubling the number of nitration events mapped in tetranitromethane-nitrated bovine serum albumin (BSA) as compared to a direct analysis of the nitrated peptides using the same amount of material. In conclusion, we here illustrate that this two-step process, heme-mediated reduction and acetylation, can be used for more efficient characterization of protein-bound nitrated tyrosines.

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mentioning

confidence: 99%

Improved tandem mass spectrometric characterization of 3‐nitrotyrosine sites in peptides

Ghesquière

Goethals

Damme

et al. 2006

Rapid Comm Mass Spectrometry

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“…They may also be involved in disease processes. We have mapped Protein Modifications (PMs) in the PDB to the RESID database of PMs (18,19) and the associated Protein Modifications Ontology PSI-MOD (20). PM definitions and the software to identify them are available from the BioJava project (21) (https://github.com/biojava/biojava/tree/master/biojava-modfinder).…”

Section: New Website Featuresmentioning

confidence: 99%

OUP accepted manuscript

Rose

Prlić

Altunkaya

et al. 2016

Nucleic Acids Research

543

233

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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

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“…First, the forced distinction between lowercase and uppercase character sets puts undesirable constraints on the implementation hardware/software; likewise the use of Greek characters to indicate degeneracy of amino acids with similar physical properties in minimotif definitions can also be problematic due to machine-specific character encoding. Second, this minimotif syntax is not extensible to all of the approximately 500 known posttranslational modifications, several of which have established roles in minimotif function [ 14 , 18 ]. For example, myristoylated residues and cis-proline bonds can not be enumerated using the Seefeld Convention.…”

Section: Introductionmentioning

confidence: 99%

A proposed syntax for Minimotif Semantics, version 1

et al. 2009

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BackgroundOne of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.ResultsHerein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established minimotif sequence definitions was implemented using a relational database management system (RDBMS). To assess the usefulness of our standardized semantics, a series of database queries and stored procedures were used to classify SH3 domain binding minimotifs into 10 groups spanning 700 unique binding sequences.ConclusionOur derived minimotif syntax is currently being used to normalize minimotif covalent chemistry and functional definitions within the MnM database. Analysis of SH3 binding minimotif data spanning many different studies within our database reveals unique attributes and frequencies which can be used to classify different types of binding minimotifs. Implementation of the syntax in the relational database enables the application of many different analysis protocols of minimotif data and is an important tool that will help to better understand specificity of minimotif-driven molecular interactions with proteins.

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The RESID Database of protein structure modifications

Cited by 8 publications

References 6 publications

Improved tandem mass spectrometric characterization of 3‐nitrotyrosine sites in peptides

Improved tandem mass spectrometric characterization of 3‐nitrotyrosine sites in peptides

OUP accepted manuscript

A proposed syntax for Minimotif Semantics, version 1

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