A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin.
The distribution of carbon monoxide after photodissociation in the myoglobin haem pocket has been investigated using molecular dynamics simulations at 300 K. The results show that both intermediates (one close to the haem iron and one further away) observed in recent low temperature X-ray studies of photodissociated CO have a high probability of occurrence, even at ambient temperatures. The fact that the O of CO is oriented toward the haem iron in the closer intermediate provides an explanation for the slow rate of CO geminate rebinding. A refinement against X-ray data generated from the molecular dynamics simulations indicates that the CO has a broader distribution in the haem pocket than is apparent from the experimental electron density. This effect is likely to be general for systems containing highly mobile groups.
Vitkup
D
D
Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254, USA.
Petsko
G A
GA
Karplus
M
M
D000465:Algorithms; D001665:Binding Sites; D002248:Carbon Monoxide / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D006418:Heme; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry* / Q000378:metabolism; D010782:Photolysis; D011336:Probability; D011487:Protein Conformation; D012984:Software; D013816:Thermodynamics
D009211:Myoglobin; C018013:carboxymyoglobin; D006418:Heme; D002248:Carbon Monoxide