Binding-unbinding reaction

In the present section some applications of the previously outlined theoretical framework, recently reported in literature [24,25], will be illustrated. In particular we will focus our attention on two benchmark reactions of computational-theoretical chemistry, namely the carbon monoxide (CO) binding-unbinding reaction in myoglobin (Mb) and the unimolecular tautomeric proton transfer in aqueous malonaldehyde. 

The principal concept was already described in the early 70 s by the first paper on this topic by Magde et al. (2J. A real renaissance arrived in 1993 with the introduction of the confocal illumination scheme for FCS by Rigler et al. fSJ, Since then FCS has been developed towards probably the most important technique for single molecule detection (SMD). FCS allows measuring rates of binding/unbinding reactions SJ, coefficients of translational and rotational diffusion (6, 7, 8, 9J, conformational states and a manifold of photophysical parameters (JO, II, 12) of the induced fluorescent process. 

FFS retrieves essential information about biomolecules by analyzing the fluctuations of the fluorescence intensity /(/) during a short time interval T. Typical sources for these fluctuations are particle motions through the sampling volume via diffusion and flow, the stochastic nature of the photophysical response of the fluorophores, for instance singlet or triplet transitions, and variations of the quantum yield with the molecular environment or binding/unbinding reactions. 

Analogous to the treatment of the antiporter in Section 7.1.2, the mechanism of Figure 7.5 assumes that the binding and unbinding steps are lumped into single reactions. This assumption is reasonable if the binding and unbinding reaction are maintained in rapid equilibrium ex = [Na+J3[Ca2+]< i/A / and e- = [Na+]3[Ca ]e4/A. These relationships allow us to simplify Equation (7.23) to... 

The kinetics of pH are governed by proton binding and unbinding as well as the consumption and generation of protons via chemical reactions. For a general system of Nr reactants, and considering [H+], [Mg2+], and [K+] binding, the total... 

A possible mechanism for this antiport reaction is illustrated in the right panel of Figure 7.2. Here the binding and unbinding of reactants to the antiporter protein are lumped into single reactions ... 

Transition metal salts and complexes also serve as homogeneous catalysts. In the Monsanto process, rhodium salts plus iodide convert methanol and carbon monoxide into an industrially useful carboxylic acid, acetic acid. The rhodium metal serves as the primary reaction site it binds the reactants and subsequently unbinds the products. The key reactions at the metal reaction site are called oxidative addition and reductive elimination. 

In far-from-equilibrium situations, the two binding partners are rapidly separated after unbinding and there is practically no recomplexation, that is, back-reaction. off(0) = off (/) relates the kinetic off-rate at a force f, kosif) to the off-rate at zero force, A off(0) by (6). 

The closed complex is quite unstable as compared with the open one (McClure 1985) a polymerase binds and unbinds several times to the promoter before forming the open complex. This means that the rates corresponding to the chemical reaction in (8.1) are much larger than those corresponding to the reaction in (8.2) kM < k, kp. 

Being promoter binding and unbinding by a polymerase the fastest processes of gene expression, we can make a quasi-stationary approximation similar the ones we have done in the previous sections. As a result we get a reduced system schematically represented in Fig. 8.1. The chemical reactions governing the dynamics of this system are then as follows ... 

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