Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

Abstract

Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

“…The second option has been added to follow the remarks of users interested in multifunctional peptides. Another modification was the replacement of the "aromatic" version of SMILES representations of aromatic amino acids (fulfilling formal aromaticity rule) by the Kekulé version according to recent recommendations [21,22]. For instance, SMILES strings N…”

In Silico Analysis of Individual Fractions of Bovine Casein as Precursors of Bioactive Peptides—Influence of Post-Translational Modifications

“…There are datasets of non-proteinogenic and modified amino acids, such as the SwissSideChain database [21] and Norine list of monomers [14]. New codes allowing the extension of space of annotated amino acids have been recently proposed [22][23][24][25]. Recent trends in encoding of biopolymers (e.g., peptides) have been recently discussed by David et al [26].…”

New Advances in Short Peptides: Looking Forward

“…This was reflected in the first edition of the Special Issue Advances in Research of Short Peptides . The issue received a large number of truly impressive and gratifying contributions, each of which reveals still open problems or challenges [ 1 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]; therefore, it seems advisable to the Editors to extend a follow-up collection of articles providing the newest results of research on short peptides with a more flexible approach worth being further developed toward applications in bio-medicine. As we move forward to new advances and look back on the studies on short peptides, the aim remains the same—reaching their full potential.…”