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Home / Equine Research Bank / J Mol Biol / High-resolution study of the three-dimensional structure of ...
Journal of molecular biology1990; 213(4); 885-897; doi: 10.1016/S0022-2836(05)80270-0

High-resolution study of the three-dimensional structure of horse heart metmyoglobin.

Abstract: The three-dimensional structure of horse heart metmyoglobin has been refined to a final R-factor of 15.5% for all observed data in the 6.0 to 1.9 A resolution range. The final model consists of 1242 non-hydrogen protein atoms, 154 water molecules and one sulfate ion. This structure has nearly ideal bonding and bond angle geometry. A Luzzati plot of the variation in R-factor with resolution yields an estimated mean co-ordinate error of 0.18 A. An extensive analysis of the pattern of hydrogen bonds formed in horse heart metmyoglobin has been completed. Over 80% of the polypeptide chain is involved in eight helical segments, of which seven are composed mainly of alpha-helical (3.6(13))-type hydrogen bonds; the remaining helix is composed entirely of 3(10) hydrogen bonds. Altogether, of 102 hydrogen bonds between main-chain atoms only six are not involved in helical structures, and four of these six occur within beta-turns. The majority of water molecules in horse heart metmyoglobin are found in solvent networks that range in size from two to 35 members. The size of water molecule networks can be rationalized on the basis of three factors: the number of hydrogen bonds to the protein surface, the presence of charged side-chain atoms, and the ability to bridge to neighboring molecules in the crystal lattice. Bridging water networks form the dominant intermolecular interactions. The backbone conformation of horse heart metmyoglobin is very similar to sperm whale metmyoglobin, with significant differences in secondary structure occurring only near residues 119 and 120, where residues 120 to 123 in sperm whale form a distorted type I reverse turn and the horse heart protein has a type II turn at residues 119 to 122. Nearly all of the hydrogen bonds between main-chain atoms (occurring mainly in helical regions) are common to both proteins, and more than half of the hydrogen bonds involving side-chain atoms observed in horse heart are also found in sperm whale metmyoglobin. Unlike sperm whale metmyoglobin, the heme iron atom in horse heart metmyoglobin is not significantly displaced from the plane of the heme group.
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Publication Date: 1990-06-20 PubMed ID: 2359126DOI: 10.1016/S0022-2836(05)80270-0Google Scholar: Lookup
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Summary

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The research article details a high-resolution investigation into the three-dimensional structure of horse heart metmyoglobin, detailing its atomic composition, bonding geometry, hydrogen bond patterns, water molecule networks, and comparing it to the structure of sperm whale metmyoglobin.

Three-Dimensional Structure of Metmyoglobin

  • Using technological approaches, the authors were able to refine the observation of metmyoglobin’s three-dimensional structure to a considerable degree, with an R-factor of 15.5% across all observed data in a specific resolution range.
  • The final structural model comprises 1242 non-hydrogen protein atoms, a single sulfate ion, and 154 water molecules, displaying a bonding and bond angle geometry that approaches an ideal state.
  • The researchers suggest an estimated mean co-ordinate error of 0.18 A based on a Luzzati plot analysis of R-factor variation by resolution.

Hydrogen Bond Patterns and Helical Segments

  • Extensive hydrogen bond pattern analysis revealed that around 80% of the polypeptide chain forms eight helical segments. Seven of these feature mainly alpha-helical (3.6(13))-type hydrogen bonds, with the residual helix comprising entirely of 3(10) hydrogen bonds.
  • The overarching hydrogen bonds between the main-chain atoms, totaling 102, are predominantly involved in helical structures, with four out of the remaining six found within beta-turns.

Water Molecule Networks

  • The majority of water molecules in horse heart metmyoglobin appear in solvent networks that vary in size from two to 35 members.
  • These water molecule network sizes are justified based on the numbers of hydrogen bonds connecting to the protein surface, the presence of charged side-chain atoms, and the ability to bridge to neighbouring molecules existing in the crystal lattice, thus forming intermolecular interactions.

Comparative Analysis with Sperm Whale Metmyoglobin

  • The backbone conformation of horse heart metmyoglobin shows similarities to that of sperm whale metmyoglobin, with significant structural differences only identified near residues 119 and 120.
  • A high proportion of the hydrogen bonds between main-chain atoms and those involving side-chain atoms observed in horse heart metmyoglobin are also evident in the structure of sperm whale metmyoglobin, despite their different organismal origins.
  • Differentiating the two, the heme iron atom in horse heart metmyoglobin doesn’t significantly displace from the plane of the heme group as it does in sperm whale metmyoglobin.

Cite This Article

APA
Evans SV, Brayer GD. (1990). High-resolution study of the three-dimensional structure of horse heart metmyoglobin. J Mol Biol, 213(4), 885-897. https://doi.org/10.1016/S0022-2836(05)80270-0

Publication

Journal of molecular biology
ISSN: 0022-2836
NlmUniqueID: 2985088R
Country: Netherlands
Language: English
Volume: 213
Issue: 4
Pages: 885-897

Researcher Affiliations

Evans, S V
  • Department of Biochemistry, University of British Columbia, Vancouver, Canada.
Brayer, G D

    MeSH Terms

    • Animals
    • Heme
    • Hemeproteins
    • Horses
    • Hydrogen Bonding
    • Metmyoglobin
    • Myocardium / analysis
    • Protein Conformation
    • X-Ray Diffraction

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