Conformational Analysis of Structural Motifs of α-α-Corner in the Computational Experiment of Molecular Dynamics
Rudnev V.R., Pankratov A.N., Kulikova L.I., Dedus F.F., Tikhonov D.A., Efimov A.V.
Institite of Mathematical Problems of Biology of the Russian Academy of Sciences
Institite of Protein Research of the Russian Academy of Sciences
Abstract. The problem of recognition of structural motifs of proteins is considered in this work. The motif of the type α-α-corner is taken as an example which has been analyzed by both an analytical description of the main chain of the protein globule and the spectral method for detecting repetitions. The verification of the found structures is performed by the conformational pattern, which is characterized by the limited φ,ψ-values on the Ramachandran plot. It is shown by the molecular dynamics method that α-α-corners are rather stable as autonomous structural units in the aqueous medium.
Key words: pattern recognition, conformational analysis of protein structures, Ramachandran plot, molecular dynamics.