ArticleBiophysical journal2002
New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 55 citations in OpenAlex.
- Article
- Methemoglobin formation in mutant hemoglobin α chains: electron transfer parameters and rates.Biophysical journal · 2021Article
- Article
- Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations.Scientific reports · 2017Article
- Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin.Scientific reports · 2015Article
- Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.Scientific reports · 2014Article
- Collective dynamics underlying allosteric transitions in hemoglobin.PLoS computational biology · 2013Article
- Unsuspected pathway of the allosteric transition in hemoglobin.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation.PLoS computational biology · 2010Article
- Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.Biophysical journal · 2008Article
- Protein dynamics explain the allosteric behaviors of hemoglobin.Biochimica et biophysica acta · 2008Review
- Effects of active site mutations in haemoglobin I from Lucina pectinata: a molecular dynamic study.Molecular simulation · 2008Article
- Article
- Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics.Biophysical journal · 2008Article
- A quantum-chemical picture of hemoglobin affinity.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Molecular dynamics simulation of deoxy and carboxy murine neuroglobin in water.Biophysical journal · 2007Article
- A comparative NMR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmonoxy forms.Biochemistry · 2007Article
- Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility.Biophysical journal · 2006Article
- Exploring the common dynamics of homologous proteins. Application to the globin family.Biophysical journal · 2005Article
- High frequency dynamics in hemoglobin measured by magnetic relaxation dispersion.Biophysical journal · 2005Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is still difficult to obtain a precise structural description of the transition between the deoxy T-state and oxy R-state conformations of human hemoglobin, despite a large number of experimental studies. We used molecular dynamics with the Path Exploration with Distance Constraints (PEDC) method to provide new insights into the allosteric mechanism at the atomic level, by simulating the T-to-R transition. The T-state molecule in the absence of ligands was seen to have a natural propensity for dimer rotation, which nevertheless would be hampered by steric hindrance in the "joint" region. The binding of a ligand to the alpha subunit would prevent such hindrance due to the coupling between this region and the alpha proximal histidine, and thus facilitate completion of the dimer rotation. Near the end of this quaternary transition, the "switch" region adopts the R conformation, resulting in a shift of the beta proximal histidine. This leads to a sliding of the beta-heme, the effect of which is to open the beta-heme's distal side, increasing the accessibility of the Fe atom and thereby the affinity of the protein. Our simulations are globally consistent with the Perutz strereochemical mechanism.
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