Protein signatures using electrostatic molecular surfaces in harmonic space

PeerJ

Georgia Tsiliki¹  Dimitrios Vlachakis¹  Sophia Kossida¹  C. Sofia Carvalho²  Vasileios Megalooikonomou³ 

[1] Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Athens, Greece;Centro de Astronomia e Astrofísica da Universidade de Lisboa, Tapada da Ajuda, Lisbon, Portugal;Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece;

关键词: Protein similarity search;    Structural biology;    Harmonic space;    Electrostatic potentials;    Drug design;   

DOI  :  10.7717/peerj.185

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown