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Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study

Cong Zhao1, Bingbing Zhang, Weihong Du

  • 1Department of Chemistry, Renmin University of China, Beijing, 100872, China.

Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry
|September 17, 2013
PubMed

Insights

Distal mutations in cytoglobin (Cgb) significantly alter protein dynamics and heme pocket structure. The E7 residue is critical for regulating CgbCO

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Dynamics

Background:

  • Cytoglobin (Cgb) is a hexacoordinate globin with diverse physiological roles.
  • The distal His(81)(E7) residue is vital for ligand binding and heme pocket stability in globins.
  • The specific role of E7 in Cgb dynamics remains understudied compared to other globins.

Purpose of the Study:

  • To investigate the structural dynamic features of carbon monoxide-ligated cytoglobin (CgbCO).
  • To examine the impact of distal E7 residue mutations (H81Q, H81L, H81V) on CgbCO dynamics.
  • To elucidate the role of the E7 residue in CgbCO's structural and dynamic properties.

Main Methods:

  • Molecular dynamics (MD) simulations were performed on CgbCO and three distal mutants (H81QCgbCO, H81LCgbCO, H81VCgbCO).
  • Analysis focused on dynamic properties, loop region fluctuations, and heme pocket rearrangements.
  • Key residue dynamics and cavity formation were assessed.

Main Results:

  • Distal mutations significantly altered the dynamic properties of Cgb's CD-D-E and EF loop regions.
  • Mutations induced distinct fluctuations and new inner cavities, indicating heme pocket rearrangements.
  • The E7 residue critically influenced CgbCO dynamics, affecting loop fluctuations, cavity rearrangement, and heme motion.

Conclusions:

  • The distal E7 residue is a crucial determinant of CgbCO's dynamic behavior.
  • Distal mutations in Cgb lead to significant rearrangements in the heme pocket and surrounding loops.
  • Cgb exhibits a distinct heme motion mechanism compared to neuroglobin, influenced by E7 dynamics.

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