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

Is the protein folding an aim-oriented process? 241• The Accessible Surface Area (ASA) taking a probe radius of 1.4 Å. ASA wascalculated using surface racer programme (Tsodikov et al., 2002).• The radius of gyration (R g ), which was calculated using the following equation(Flory, 1953):1R r r( N + 1)( )N−1N2g=2 i− j(5)i= 1 j= i+1where N is the number of residues, r iand r jare the coordinates of C atomof ith and jth residue, respectively.• The distances between the geometric centre of the molecule and sequential C atomsin the polypeptide chain (D centre-Cα ).• RMSD-C calculation using the native form of haemoglobin as a referencestructure. Structure alignments and RMSD calculations were done using VMD(Humphrey et al., 1996).• The distances between haem iron atom and sequential C atoms of haemoglobinresidues.• The axis angles between adjoining helices. The axis angle is defined as the anglebetween the two helix vectors that correspond to the vector from the N-terminusatom to the C-terminus atom in two helices under consideration.2.8 Hydrophobicity scaleThe hydrophobicity scale is necessary to apply the presented model. Many scales forresidue hydrophobicity are available. Some of them are based on analysis of knownprotein 3D structures (Kyte and Dooloittle, 1982; Eisenberg et al., 1982; Engelman et al.,1986; Hopp and Woods, 1981; Janin, 1979; Rose et al., 1985), while the others arederived from the physicochemical properties of amino-acid side chains (Wimley andWhite, 1996; Wolfender et al., 1981). The hydrophobicity scale including parametersfor haem has been created using the relative position in fuzzy-oil-drop applied tosingle-domain proteins in PDB and particularly those being complexed with haem.The position found in this way was transformed into the hydrophobicity scaleguaranteeing the unification of all amino acids and haem. Haem was dividedinto five fragments: haem_A, haem_B, haem_C, haem_D and haem_Fe (Figure 1).The calculation of hydrophobicity parameters was done utilising the set of 1353structures of haem–protein complexes found in PDB No. 2004 (Berman et al., 2000).The complete hydrophobicity scale was calculated for all 20 amino acids and haem tomake the scale consistent (Table 1).