Since part of the biochemical preference of an enzyme for a given substrate may be determined by residues surrounding the post-translational modification (PTM) site, this specific pattern of residues formed by the protein or peptide sequence is called a motif. Motif analysis can provide useful sequence pattern information for all identified PTM proteins/peptides and help identify important motifs. On the other hand, motif analysis can ideally help to identify relevant enzymes based on known substrate specificity. Creative Proteomics is proud to offer PTM site motif analysis service based on popular tools, such as Motif-x, PhosphoMotif, and iceLogo. Based on our experienced bioinformatics team and advanced tools, we can help our global customers explore existing motifs or discover novel motifs.
The significance of studying motifs
A motif is a typical sequence or structure. Specifically, a motif is a short sequence with characteristic features, which is generally considered to be a conserved sequence possessing a biological function and may contain characteristic binding sites or regions of sequence with commonality involving a particular biological process. Motifs are not limited to genomic DNA sequences or RNA sequences, but can also be extracted from protein sequences. By parsing the sequence information, we can further explore the codes of biological processes. Based on the extraction of motif sequences, we can predict the potential binding sites, etc., which can help us to further understand the biological significance involved in each biological process. For instance, the identification and study of motifs (conserved motifs) of modified proteins are important for the prediction of PTM sites and the discovery of signaling pathways.
Fig.1 Motif analysis of the SUMO binding regions. (Li, Yaoyong, et al, 2019)
PTM site motif analysis service
Based on our experienced bioinformatics team and advanced tools, we were able to perform motif analysis and statistics on differential modifications, providing important motif structural information to facilitate researchers' understanding of the complex regulatory mechanisms of the relevant enzymes. We mainly used the Motif-x method to analyze and characterize the potential motifs of the modification sites. Our results can be further classified by analyzing the hydrophobicity, acidity, and sequence secondary structure of the amino acid residues corresponding to the conserved motifs to better explore new substrates for relevant enzymatic actions and to develop new functions of the enzymes. In addition, exploring the species specificity, condition specificity, and enzyme specificity of motifs is an important guide to finding the conservation and specificity of protein PTMs.
In recent years, the available data on PTMs have increased dramatically due to the development of mass spectrometry (MS)-based detection and other experimental methods. To simplify the analysis of complex PTM data and to improve our clients' understanding of various PTMs in different organisms, Creative Proteomics offers PTM bioinformatics analysis services. Our bioinformatics team has done a lot of work on the identification of PTM results and has developed our own platform for quality control, data processing, and analysis. With the development of biological MS-based methods and MS-specific PTM related tools, our PTM data calculation methods are also being further developed. Please use our contact form for general inquiries. We will then forward your request to the correct contact.
Related services
References
- Li, Yaoyong, Elisa Aguilar-Martinez, and Andrew D. Sharrocks. "Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions." Journal of integrative bioinformatics 16.3 (2019).
- Schwartz, Daniel, Michael F. Chou, and George M. Church. "Predicting protein post-translational modifications using meta-analysis of proteome scale data sets." Molecular & Cellular Proteomics 8.2 (2009): 365-379.
Our products and services are for research use only.
