Molecular modelling of Trematomus newnesi Hb 1: insights for a lowered oxygen affinity and lack of root effect.
Three-dimensional structural models of the hemoglobin (Hb 1) of the Antarctic fish Trematomus newnesi were built by homology modelling, using as template the X-ray crystallographic structures of Trematomus (previously named Pagothenia) bernacchii Hb 1, both in R and T state. The Hbs of these two fishes, although showing remarkably different oxygen binding properties, differ only by 4 residues in the alpha chain (142 aa) and 10 residues in the beta chain (146 aa). T. newnesi Hb1 R-state model, essentially performed as a quality control of the adopted modelling procedure, showed a good correspondence with the crystallographic one. Modelling of T. newnesi Hb1 in the T state was performed taking into account that the proton uptake by aspartate residues, proposed to be responsible for half of the Root effect in T. bernacchii Hb 1 (showing sharp pH dependent oxygen affinity and T-state overstabilization at low pH, i. e. Bohr and Root effect), does not occur in T. newnesi Hb1 (having nearly pH-independent lower oxygen affinity). Comparison with the template structure (submitted to the same minimization procedure) indicates that, in T. newnesi Hb1 T-state model, the substitution of Ile for Thr in 41 C6, in central position of the switch region, induces at the alpha(1)beta(2) interface structural modifications able to hamper the protonation. Similar modifications are also found in T. bernacchii Hb 1 modelled in the T state with the single substitution Thr-->Ile in 41alpha. These models also suggest that the lower oxygen affinity observed in T. newnesi Hb1 is related to structural differences at the alpha(1)beta(2) interface leading to a more stable low-affinity T state. Proteins 2000;39:155-165.
D'Avino
R
R
Institute of Protein Biochemistry and Enzymology, C.N.R., Naples, Italy. davino@dafne.ibpe.na.cnr.it
De Luca
R
R
D000465:Algorithms; D000494:Allosteric Regulation; D019943:Amino Acid Substitution; D000818:Animals; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D005069:Evaluation Studies as Topic; D005399:Fishes / Q000097:blood*; D006454:Hemoglobins / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010100:Oxygen / Q000378:metabolism; D010108:Oxyhemoglobins / Q000378:metabolism; D020836:Protein Structure, Quaternary; D011522:Protons; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
D006454:Hemoglobins; D010108:Oxyhemoglobins; D011522:Protons; D010100:Oxygen