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In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature
Author(s) -
Prymula Katarzyna,
Piwowar Monika,
Kochanczyk Marek,
Flis Lukasz,
Malawski Maciej,
Szepieniec Tomasz,
Evangelista Giovanni,
Minervini Giuseppe,
Polticelli Fabio,
Wiśniowski Zdzisław,
Sałapa Kinga,
Matczyńska Ewa,
Roterman Irena
Publication year - 2009
Publication title -
chemistry and biodiversity
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.427
H-Index - 70
eISSN - 1612-1880
pISSN - 1612-1872
DOI - 10.1002/cbdv.200800338
Subject(s) - in silico , structural similarity , threading (protein sequence) , computational biology , sequence (biology) , similarity (geometry) , homology modeling , biological system , protein structure , chemistry , homology (biology) , amino acid , computer science , biology , biochemistry , artificial intelligence , gene , image (mathematics) , enzyme
The three‐dimensional structures of a set of ‘never born proteins’ (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the ‘fuzzy‐oil‐drop’ (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three‐dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS‐D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be ‘unfoldable’ for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions.