thermophilic interface detail

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes

2.3. Identification of interface residues

Interface residues were defined as those residues that show a change in solvent accessibility area upon monomer association. Those residues for which the change was more than 90% were defined as composing the core interface (Bahadur et al., 2003). Solvent accessibility computation was performed with the program NACCESS (Hubbard and Thornton, 1993). The change in solvent accessibility area for each residue in the monomeric state and in the oligomeric state was calculated using a Perl script.

The structural similarity of the subunit interfaces within each protein family was evaluated on the basis of the multiple structure alignment. To ensure that the interface was structurally conserved within each family and the selected structural data comparable, the interface C_α carbons of each mesophilic member were superimposed to the equivalent atoms from the thermophilic homolog. 

Only interfaces showing RMSD ≤ 1.3 Å were considered similar. This threshold is within the expected structural variation corresponding to the range of sequence similarities of the multiple structure alignments (Chothia and Lesk, 1986). Indeed, the expected value of RMSD for a pair of homologous proteins whose sequence identity is 30% is equal to 1.42 Å. RMSDs were calculated using DeepView-Swiss-PdbViewer “iterative magic fit” tool (Guex and Peitsch, 1997) and the InsightII package (version 2005; Accelrys, San Diego, CA 92121, USA).