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The molecular basis of Rubisco's specificity is investigated in terms of the structure and kinetics of the enzyme. We propose that the rates of the conformational changes (closing/opening) of the binding niche exert a crucial influence on apparent binding rates and the enzyme's specificity. An extended reaction scheme for binding and conformational kinetics is presented and expressed in a mathematical model. The closed conformation, known from X-ray structures, is assumed to be necessary for binding of the gaseous substrates (carbon dioxide and oxygen) and for catalysis. Opening the niche interrupts catalysis and enables a fast exchange of those molecules between the internal cavity and the surrounding solvent. Our model predicts that specificity of Rubisco for CO(2) increases with the rate by which the niche opens. This is due to the fact that binding of the carbon dioxide is faster than oxygen binding, which is hampered by spin inversion. The apparent rate of carbon dioxide binding correlates with the repetition rate of the conformational change, and the rate of oxygen binding with the probability of the closed state. |
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