Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO

Biochemistry. 1998 Aug 4;37(31):10906-19. doi: 10.1021/bi980810b.

Abstract

The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Carbon Monoxide / chemistry*
  • Crystallography, X-Ray
  • Hemoglobins / chemistry*
  • Hydrogen
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular
  • Polychaeta
  • Protein Conformation*
  • Protein Structure, Secondary
  • Solutions
  • Thermodynamics*

Substances

  • Hemoglobins
  • Macromolecular Substances
  • Nitrogen Isotopes
  • Solutions
  • Carbon Monoxide
  • Hydrogen
  • hemoglobin IV

Associated data

  • PDB/1VRE
  • PDB/1VRF