Is the protein folding an aim-oriented process ... - IngentaConnect

Is the protein folding an aim-oriented process? 249Figure 6The time profiles of parameters monitored during folding process: the radiusof gyration [Å] (A), the total number of non-bonding interactions (B)and solvent-accessible surface area (ASA) [Å 2 ] (C). The simulations with haemmolecule absent and present in folding process are represented by grey and black lines,respectively. In all plots, the constant dotted line pinpoints the quantity of a probedparameter (R g , NB or ASA) calculated for native structure. ES denotes early stagetreated as starting one for simulation and LS – late stage treated as final one forsimulation3.2.3 The non-bonding contacts and RMSD calculationThe comparison of non-bonding contact maps is used commonly to verify thecorrectness of obtained structures. These maps for all discussed structural forms areshown in Figure 7. Table 2 presents also the percentage of native non-bonding contacts infinal structures obtained according to the adopted model, together with RMSD-C usingthe native forms as reference structures. Noticeable better results are seen for chain ofhaemoglobin.