7V5R

The dimeric structure of G80A/H81A/L137D myoglobin

Summary for 7V5R

• Entry DOI: 10.2210/pdb7v5r/pdb
• Descriptor: Myoglobin, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: oxygen storage, oxygen binding
• Biological source: Equus caballus (Horse)
• Total number of polymer chains: 2
• Total formula weight: 35097.77

Authors

Xie, C.,Komori, H.,Hirota, S. (deposition date: 2021-08-17, release date: 2022-06-29, Last modification date: 2023-11-29)

Primary citation

Xie, C.,Shimoyama, H.,Yamanaka, M.,Nagao, S.,Komori, H.,Shibata, N.,Higuchi, Y.,Shigeta, Y.,Hirota, S.
Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.
Rsc Adv, 11:37604-37611, 2021

PubMed Abstract: Various factors, such as helical propensity and hydrogen bonds, control protein structures. A frequently used model protein, myoglobin (Mb), can perform 3D domain swapping, in which the loop at the hinge region is converted to a helical structure in the dimer. We have previously succeeded in obtaining monomer-dimer equilibrium in the native state by introducing a high α-helical propensity residue, Ala, to the hinge region. In this study, we focused on another factor that governs the protein structure, hydrogen bonding. X-ray crystal structures and thermodynamic studies showed that the myoglobin dimer was stabilized over the monomer when keeping His82 to interact with Lys79 and Asp141 through water moleclues and mutating Leu137, which was located close to the H-bond network at the dimer hinge region, to a hydrophilic amino acid (Glu or Asp). Molecular dynamics simulation studies confirmed that the number of H-bonds increased and the α-helices at the hinge region became more rigid for mutants with a tighter H-bond network, supporting the hypothesis that the myoglobin dimer is stabilized when the H-bond network at the hinge region is enhanced. This demonstrates the importance and utility of hydrogen bonds for designing a protein dimer from its monomer with 3D domain swapping.

PubMed: 35496441
DOI: 10.1039/d1ra06888a

Experimental method

X-RAY DIFFRACTION (1.39 Å)