Bioinformatics Bioinformatics Server Protein Structure

Motivated Proteins

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Motivated Proteins is a web facility devoted to a wide range of small hydrogen-bonded motifs, such as Beta Turns, Schellman Loops and Beta Bulges, which are common constituents of the three-dimensional structure of proteins. 

The ‘Motif Glossary’ contains the available motifs and provides a comprehensive definition of each of them. The ‘Introduction’ section gives illustrations of the facilities available, bibliographic and author information, and links to software and data downloads.

Most users will be interested either in a particular protein or a particular motif. For any of the 430 proteins in the database we can search for individual or overlapping motifs in that protein, and motifs near ligands or active sites. If we are interested in a particular motif, ‘Specific Motifs’ gives us access to all the examples of that motif in the database.

A key feature of Motivated Proteins is the ability to view the three-dimensional structure of motifs and their hydrogen bonding. 

The February 2019 update of the web application provides a more extensive classification of Beta Bulges, details of which are in the Motif Glossary.

Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they consist between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are;

  • αβ-motifs
  • asx-motifs
  • asx-turns
  • β-bulges
  • β-bulge loops
  • β-turns, nests
  • niches
  • Schellmann loops
  • ST-motifs
  • ST-staples
  • ST-turns

Motivated Proteins provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or subcategories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. 

Results

  • The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. 
  • Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. 
  • Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. 

Summary information for the motifs are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. 

Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.

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