Protein Repeats From First Principles

PARRA, R. GONZALO; ESPADA, ROCÍO; FERREIRO, DIEGO; TURJANSKI, PABLO; BECHER, VERÓNICA

Buenos Aires

Otro; 30º edición de la Escuela de Ciencias Informáticas; 2016

FCEyN-UBA

Repeat proteins are composed of tandem copies of structural motifs of similar amino acid stretches, that usually fold up into elongated structures and due to their repetitive structure, their sequences seem less random than sequences from their globular counterparts. These proteins are useful models where to study the sequences-structures-functions relationships in proteins. There are many Repeat Protein Families that have been defined: Ankyrins, Leucine Rich, Heat, TPR, Armadillo, Beta-Propellers, among others. Definition of "What is a protein family?" is usually based on subjective definitions of substitution matrices, similarity functions, sequence alignments, hidden markov models and others. This non-objectivity leads to fuzzy limits in between families. This is evident at the Pfam database where fine tuning for sequence detection parameters using ad-hoc profiles are needed to generate non overlapping clusters of sequences that constitute the families.In this work we mathematize the notion of repeat protein families and show that sequences from repeat proteins (and maybe proteins in general) are repetitive in terms of exact maximal repetitions, when considering the families where they come from.