in Biology | DNA Electron Transport Dynamics
Understanding the process of O2 binding to hemoglobin and myoglobin
is of importance in biology since these molecules are responsible
for the oxygen transportation and storage in mammalian cells.
Molecular recognition by biological macromolecules involves many
elementary steps, usually convoluted by diffusion processes. However,
details are difficult to determine due to the complex nature of
the protein structure. Synthetic model porphyrins are used to
mimic the structure and function of the proteins so to obtain
insights of the correlation between structure and function. Studies
of the dynamics, from the femtosecond to the microsecond time
scale, of the different elementary processes involved in the bimolecular
recognition of a protein mimic, cobalt picket-fence porphyrin,
were carried out by transient absorption with varying oxygen concentration
at controlled temperatures.
transfer, bond breakage, with initial O2 release occuring
in 1.9 ps, and thermal “on” (recombination) and “off”
(dissociation) reactions are the different processes involved.
for the reported thermodynamics, kinetics and dynamics was achieved
by a two-step recognition model, with reversibility being part
of both steps. The transient intermediates are configurations
defined by the contact between oxygen (diatomic) and the picket-fence
porphyrin (macromolecule), without formation of a strong ligand-metal
bond. This intermediate is critical in the description of the
potential energy landscape, and both enthalpic and entropic contributions
to the free energy are important. Most of the diffusion-controlled
encounters which lead to the formation of the intermediate do
not result in a final bound state, resulting in an effective recombination
rate which is much slower than the theoretical (Smoluchowski)
diffusion controlled rate. The formation of intermediate structure(s)
actually facilitates the final recognition on the global energy
landscape which must involve both the diffusion in the solvent
and the intramolecular rearrangement of the porphyrin structure.
This two-step mechanism is relevant to macromolecular biological
processes of enzymes and DNA/drug recognition. It is remarkable
that the process in the initial femtosecond/picosecond O2
liberation is similar to that observed for the CO/myoglobin system.
*The text above has been adapted from the following publications.
RNA-Protein Recognition: Single-Residue Ultrafast Dynamical
Control of Structural Specificity and Function,
T. Xia, C. Wan, R. W. Roberts, A. H. Zewail, Proc. Natl. Acad. Sci.
USA 2005, 102, 13013.
The RNA-Protein Complex: Direct Probing of the Interfacial
Recognition Dynamics and Its Correlation with Biological Functions,
T. Xia, H.-C. Becker, C. Wan, A. Frankel, R. W. Roberts, A. H.
Zewail, Proc. Natl. Acad. Sci. USA 2003, 100, 8119.
Molecular Recognition of Oxygen by Protein Mimics: Dynamics
on the Femtosecond to Microsecond Time Scale, S. Z. Zou,
Baskin, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2002, 99, 9625.
Femtosecond Dynamics of Dioxygen-Picket-Fence Cobalt Porphyrins:
Ultrafast Release of O2 and the Nature of Dative Bonding,
B. Steiger, J. S. Baskin, F. C. Anson, A. H. Zewail, Angew. Chem.,
Int. Ed. 2000, 39, 257.