Codon number shapes peptide redundancy in the universal proteome composition.

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• The UniRef100 database contains a comprehensive collection of protein sequences.
• Understanding the frequency and distribution of short amino acid motifs like pentapeptides is crucial for deciphering protein structure-function relationships.

Purpose of the Study:

• To investigate the occurrence patterns and redundancy of pentapeptides across the entire known proteome.
• To identify factors influencing the frequency of specific pentapeptides in protein sequences.

Main Methods:

• Collected and analyzed all proteomes from the UniRef100 database.
• Quantified the frequency of all possible pentapeptides.
• Correlated pentapeptide frequencies with physico-chemical and biological parameters, including codon number, bulkiness, hydrophobicity, and heat of formation.

Main Results:

• Observed significant variation in pentapeptide redundancy, with some occurring once and others over 50,000 times.
• Identified 417 theoretically possible pentapeptides that are absent in the known proteome.
• Pentapeptide frequency distribution approximates a quasi-Gaussian curve.
• Found that the number of codons encoding amino acids is the primary driver of pentapeptide frequency, more so than bulkiness or hydrophobicity.

Conclusions:

• Pentapeptide composition in the universal proteome is strongly influenced by the genetic code's degeneracy.
• Amino acid composition and codon usage bias are key determinants of pentapeptide prevalence.
• Physico-chemical properties like bulkiness and hydrophobicity play a lesser role in shaping pentapeptide frequencies.