Designing a methodology to estimate complexity of protein structures

Authors:
Alejandro Balbín;Eugenio Andrade
Affiliations:
Grupo de Biología Molecular, Teórica y Evolutiva., Departamento de Biología, Universidad Nacional de Colombia, Bogotá;Grupo de Biología Molecular, Teórica y Evolutiva., Departamento de Biología, Universidad Nacional de Colombia, Bogotá
Venue:
ECAL'07 Proceedings of the 9th European conference on Advances in artificial life
Year:
2007

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Abstract

This paper proposes a methodology to estimate the information content of protein structures by using: an alphabet of local microenvironments obtained from a set of protein domains with equivalent function, a modification of the physical complexity concept [1], the measures of mutual information (I(seq; str)) and conditional entropy (H(str|seq)). between sequence and structure. The kinase domain catalytic subunit was used as a specific example. Our results are in accord with the hypothesis that proteins are information gathering and using systems [3], and suggest that protein structure depends less on protein sequence than biologists have historically supposed.