1VRE

SOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC HEMOGLOBIN-CO

Summary for 1VRE

• Entry DOI: 10.2210/pdb1vre/pdb
• Descriptor: PROTEIN (GLOBIN, MONOMERIC COMPONENT M-IV), PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE (3 entities in total)
• Functional Keywords: heme protein, globin, oxygen transport
• Biological source: Glycera dibranchiata
• Total number of polymer chains: 1
• Total formula weight: 15693.57

Authors

Volkman, B.F.,Alam, S.L.,Satterlee, J.D.,Markley, J.L. (deposition date: 1999-03-25, release date: 1999-04-02, Last modification date: 2023-12-27)

Primary citation

Volkman, B.F.,Alam, S.L.,Satterlee, J.D.,Markley, J.L.
Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.
Biochemistry, 37:10906-10919, 1998

PubMed 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measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results).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.

PubMed: 9692983
DOI: 10.1021/bi980810b

Experimental method

SOLUTION NMR