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Protein signatures using electrostatic molecular surfaces in harmonic space

C. S. Carvalho, D. Vlachakis, G. Tsiliki, V. Megalooikonomou, S. Kossida

Abstract
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the molecular electrostatic potential, whose three-dimensional coordinates have been either experimentally or theoretically determined. Thus we achieve a reduction of the initial three-dimensional information on the molecular surface to the one-dimensional information on pairs of points at a fixed scale apart. Consequently, the similarity search in our method is computationally less demanding and significantly faster than shape comparison methods. As proof of principle, we applied our method to a training set of viral proteins that are involved in major diseases such as Hepatitis C, Dengue fever, Yellow fever, Bovine viral diarrhea and West Nile fever. The training set contains proteins of four different protein families, as well as a mammalian representative enzyme. We found that the power spectrum successfully assigns a unique signature to each protein included in our training set, thus providing a direct probe of functional similarity among proteins. The results agree with established biological data from conventional structural biochemistry analyses.

Keywords
Drug: design - Electrostatic: potentials - Harmonic: space - Protein: similarity: search - Structural: biology

PeerJ
Volume 1, Page e185_1
2013 October

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Instituto de Astrofísica e Ciências do Espaço Universidade do Porto Faculdade de Ciências da Universidade de Lisboa
Fundação para a Ciência e a Tecnologia COMPETE 2020 PORTUGAL 2020 União Europeia