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Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels

Author(s): Maria S Shadrina

Atomistic molecular dynamics simulations of diffusion of O2 from the hemes to the external solvent in the a- and ß-subunits of the human hemoglobin (HbA) tetramer reveal transient gas tunnels that are not seen in crystal structures. We find here that the tu...

Article GUID: 26226318
O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7

Author(s): Maria S Shadrina

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the rel...

Article GUID: 26226401
Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study

Author(s): Maria S Shadrina

Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per...

Article GUID: 26938707
Title:Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels
Authors:Maria S Shadrina
Link:https://pubmed.ncbi.nlm.nih.gov/26226318/
DOI:10.1021/acs.biochem.5b00368
Category:
PMID:26226318
Dept Affiliation: CERMM
1 Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada.

Description:

Atomistic molecular dynamics simulations of diffusion of O2 from the hemes to the external solvent in the a- and ß-subunits of the human hemoglobin (HbA) tetramer reveal transient gas tunnels that are not seen in crystal structures. We find here that the tunnel topology, which encompasses the reported experimental Xe binding cavities, is identical in HbA's T, R, and R2 quaternary states. However, the O2 population in the cavities and the preferred O2 escape portals vary significantly with...