Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps.
Reconstructing protein structure based on contact maps leads to two types of models: properly oriented models and mirror models. This is due to the fact that contact maps do not include information on protein chirality. Therefore, both types of model orientations share the same contact map and are geometrically allowed. In this work, we verified the hypothesis that some of the energy terms calculated by PyRosetta could be useful to distinguish between properly oriented and mirror models. We studied 440 models of all-alpha protein domains reconstructed manually from their contact maps, where 50% of the models were properly oriented and 50% had mirror orientation. We showed that dihedral angles and energy terms, based on the probability of specific geometrical arrangement of the residues, differed significantly for properly oriented and mirror models.
Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
Monika
M
Kurczynska
Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.|Biotechnology Center, Dresden University of Technology, Tatzberg 47/49, 01307, Dresden, Germany.
Ewa
E
Kania
Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
Bogumil M
BM
Konopka
Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland. malgorzata.kotulska@pwr.edu.pl.
Malgorzata
M
Kotulska
D008958:Models, Molecular; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins
Contact maps; Energy terms; Mirror images; Protein structure; Protein structure reconstruction