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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