Alignment of 700 globin sequences: Extent of amino acid substitution and its correlation with variation in volume

Abstract

Seven-hundred globin sequences, including 146 nonvertebrate sequences, were aligned on the basis of conservation of secondary structure and the avoidance of gap penalties. Of the 182 positions needed to accommodate all the globin sequences, only 84 are common to all, including the absolutely conserved PheCD1 and HisF8. The mean number of amino acid substitutions per position ranges from 8 to 13 for all globins and 5 to 9 for internal positions. Although the total sequence volumes have a variation -2-3%, the variation in volume per position ranges from -13% for the internal to -21% for the surface positions. Plausible correlations exist between amino acid substitution and the variation in volume per position for the 84 common and the internal but not the surface positions. The amino acid substitution matrix derived from the 84 common positions was used to evaluate sequence similarity within the globins and between the globins and phycocyanins C and colicins A, via calculation of pairwise similarity scores. The scores for globin-globin comparisons over the 84 common positions overlap the globinphycocyanin and globin-colicin scores, with the former being intermediate. For the subset of internal positions, overlap is minimal between the three groups of scores. These results imply a continuum of amino acid sequences able to assume the common three-on-three a-helical structure and suggest that the determinants of the latter include sites other than those inaccessible to solvent.

A TyrCD1/TrpG8 hydrogen bond network and a TyrB10—TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O

“…Remarkably, residue CD1, which is invariably Phe in (non)vertebrate Hbs and Mbs, as well as in trHbs from groups I and III, is Tyr in trHbO and in other trHbs from group II. As observed for all currently known group II and III trHbs, trHbO displays a Trp residue at the G8 site, where smaller apolar residues (Val, Leu, or Ile) are constantly found in group I trHbs, as well as in (non)vertebrate Hbs͞Mbs, flavohemoglobins, and plant Hbs (1,4,10,(18)(19)(20). Resonance Raman data indicate that in trHbO, a hydrogen-bonded network stabilizes the hemebound O 2 and CO ligands, as evidenced by frequencies of the Fe-O 2 and Fe-CO stretching modes (13).…”

“…In addition to TyrB10-23 and TyrCD1-36, the trHbO distal site pocket is characterized by residues AlaE7-44 and TrpG8-88, which can also be defined as quite unusual for the heme distal pocket, both in trHbs and generally in 3-on-3 folded globins (18,19). AlaE7-44 substitutes for a residue (either His or Gln), often providing the main H bonding capabilities to the heme distal ligand in Hbs and Mbs.…”

Genome‐Wide Analysis of the Globin Gene Family of C. elegans

“…First, sequences that matched the globin motifs with Evalues 4 10 75 or shorter than 100 aa were discarded and the remaining sequences were checked employing the WormBase Release WS123 (http://www.wormbase.org). Orthologous sequences were manually aligned following the procedure used earlier in the alignment of over 700 globins (26). This procedure is designed to fit the putative sequences to the myoglobin fold (1,27), the pattern of 32 conserved, hydrophobic, intra-helical residues A8, A11, A12, A15, B9, B10, B13, B14, E4, E11,E12, E15, E18, E19, F1, F4, G5, G8, G11, G12, G13, G15, G16, H7, H8, H11, H12, H15, and H19, the two conserved, hydrophobic inter-helical residues at CD1 and FG4 and the invariant His at F8 (26,28).…”

“…Orthologous sequences were manually aligned following the procedure used earlier in the alignment of over 700 globins (26). This procedure is designed to fit the putative sequences to the myoglobin fold (1,27), the pattern of 32 conserved, hydrophobic, intra-helical residues A8, A11, A12, A15, B9, B10, B13, B14, E4, E11,E12, E15, E18, E19, F1, F4, G5, G8, G11, G12, G13, G15, G16, H7, H8, H11, H12, H15, and H19, the two conserved, hydrophobic inter-helical residues at CD1 and FG4 and the invariant His at F8 (26,28). The alignment is based on the crystal-structure-based alignment of the 56 known globin crystal structures available from the Protein Data Bank (29).…”

An electrospray ionization mass spectrometric study of the subunit structure of the giant hemoglobin from the leech Nephelopsis oscura

“…These giant complexes were found to have masses of ϳ3500 kDa and to consist of two types of polypeptide chains: heme-containing 16 -17 kDa globin chains and non-globin, linker chains of 24 -32 kDa containing 9 to 12 cysteines [4]. The amino acid sequences of the globin chains are clearly related to vertebrate and invertebrate globins [5] and they form disulfide-bonded dimer, trimer and tetramer subunits as well as noncovalent subassemblies, ranging from dimer to dodecamer [4].…”