Enzyme function, perturbation

The topic of low-barrier hydrogen bonds (LBHBs) and the question of how they are involved in enzyme function has been discussed heavily in the literature recently. Hydrogen bonds between two bases of nearly matched proton affinity often exhibit strongly perturbed bond lengths and spectroscopic parameters it remains somewhat unclear exactly how the spectroscopic parameters reflect total energy or reactivity. In this study, we report H NMR chemical shift data and surveys of structural preferences for the well-studied 0-H---0 systems, and also for less studied, but biologically important N-H-0 systems, in particular the imidazole and imidazolium functionality. The H shifts also show interesting trends in comparison with O-H-O motifs, which will require further scrutiny. 

TBT and TFT are membrane-active molecules, and their mechanism of action appears to be strongly dependent on organotin(IV) lipophilicity. They function as ionophores and produce hemolysis, release Ca(II) from sarcoplasmic reticulum, alter phosphatodylseiine-induced histamine release, alter mitochondrial membrane permeability and perturb membrane enzymes. Organotin(IV) compounds have been shown to affect cell signaling they activate protein kinase and increase free arachidonic acid through the activation of phospholipase... 

The enzymatic activities of O -chymotrypsin in solution and adsorbed at the different surfaces are presented in Fig. 11, where the specific enzymatic activity (defined as activity per unit mass of protein) is plotted as a function of temperature. The enzyme loses activity due to adsorption. On the hydrophobic Teflon and PS surfaces, the activity is completely gone, whereas on the hydrophilic silica surface, or-chymotrypsin has retained most of its biological function. These differences are in agreement with the adsorption isotherms and the circular dichroism spectra. The influence of the hydrophobicity of the sorbent surface on the affinity of the protein for the sorbent surface, as judged from the rising parts of the adsorption isotherms (Fig. 8), suggests that the proteins are more perturbed and, hence, less biologically active when adsorbed at hydrophobic surfaces. Also, the CD spectra indicate that adsorption-induced structural perturbations are more severe at hydrophobic surfaces. 

Figure 5.36 Mechanism of the receptor-mediated induction of CYP4A by a chemical such as the drug clofibrate. The inducer-receptor (PPAR) complex enters the nucleus, binds with RXR, and the complex binds to the receptor response elements in the CYP gene. This induces the production of CYP4A mRNA, which leads to the production of CYP4A protein and functional enzyme. Alternatively, the drug may perturb lipid metabolism leading to increases in a lipid(s), which will bind to the receptor and cause the same response. Abbreviations PPAR, peroxisome proliterator-activated receptor RXR, retinoid X receptor.

Theoretical titration curves for enzymes can be calculated from known crystal structures and first principles of electrostatics. Key amino acids at the active site have significantly perturbed pK values and unusual regions in which they are partially protonated over a wide pH region.3 In principle, such titration calculations can identify the active site of a protein whose structure is known, but whose function is not. 

As noted earlier, protein structure is stabilised by a series of weak forces which often give rise to the properties which are functionally important (models of active sites and substrate binding are discussed above). On the other hand, because active sites involve a set of subtle molecular interactions involving weak forces, they are vulnerable and can be transformed into less active configurations by small perturbations in environmental conditions. It is therefore not surprising that a multitude of physical and chemical parameters may cause perturbations in native protein-geometry and structure. Thus, enzyme deactivation rates are usually multi-factorial, e.g. enzyme sensitivity to temperature varies with pH and/or ionic strength of the medium. 

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