Time resolved optical spectroscopy with nanosecond lasers and molecular dynamics calculations have been employed to investigate ligand rebinding and conformational changes in hemoglobin subsequent to photodissociation of the carbon monoxide complex. In order to precisely measure the time course of the changes in the conformation of the deoxy photoproduct, which produce small spectral changes, as well as to determine the kinetics of ligand rebinding, as automated, sensitive nanosecond spectrometer has been developed to measure time-resolved spectra. The spectra have been analyzed using singular value decomposition to produce a set of orthonormal basis spectra and the time course of their amplitudes. With these techniques the kinetics of ligand rebinding and conformational changes have been studied with hemoglobins initially in the R and T quaternary structure. The R to T quaternary transition is observed for the completely unliganded R state molecule to occur at about 0.02 ms, while both R and T state molecules show tertiary conformational relaxations at about 50 ns and 500 ns. The 50 ns relaxation is simultaneous with geminate rebinding, suggesting that it is caused by motion of the ligand out of the heme pocket. Using the simplest kinetic model, a comparison of the geminate kinetics for R and T state molecules indicate that the difference in the factor of about 50 in the overall rate of ligand binding to the R and T states can be explained by differences in binding rates to the heme from within the heme pocket. Changes in the barriers to motion of the ligand inside the protein or between the protein and the solvent appear to play a minor role in determining the difference in overall rates. The photodissociation process is being simulated using the technique of molecular dynamics, which describes the motion of the individual atoms. Calculations on a complete tetramer in vacuo show that the heme conformation change is a sub- picosecond process and that the excess vibrational energy of the heme is deposited in the surrounding protein in about 20 ps. The trajectories are being analyzed to determine the response of the globin conformation to the change in heme conformation.
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