Enzymes electrostatic effects

Most transition states involve charged intermediates, which are stabilized within the active site of an enzyme via ionic bonds in pockets or holes bearing a matching opposite charge. Such charges are derived from acidic or basic amino acid side chains (such as Lys, Arg, Asp, or Glu) ° or are provided by (Lewis acid-type) metal ions, typically Zn +. Computer simulations studies suggested that in enzymes electrostatic effects provide the largest contribution to catalysis [107]. As a prominent example, the tetrahedral intermediate of carboxyl ester hydrolysis is stabilized in serine hydrolases by the so-called oxyanion hole (Scheme 2.1). 

Destabilization of the ES complex can involve structural strain, desolvation, or electrostatic effects. Destabilization by strain or distortion is usually just a consequence of the fact (noted previously) that the enzyme is designed to bind the transition state more strongly than the substrate. When the substrate binds, the imperfect nature of the fit results in distortion or strain in the substrate, the enzyme, or both. This means that the amino acid residues that make up the active site are oriented to coordinate the transition-state structure precisely, but will interact with the substrate or product less effectively. 

The approach taken above estimates the effect of the metal by simply considering its electrostatic effect (subjected, of course, to the correct steric constraint as dictated by the metal van der Waals parameters). To examine the validity of this approach for other systems let s consider the reaction of the enzyme carbonic anhydrase, whose active site is shown in Fig. 8.6. The reaction of this enzyme involves the hydration of C02, which can be described as (Ref. 5)... 

In view of the arguments presented in this chapter, as well as in previous chapters, it seems that electrostatic effects are the most important factors in enzyme catalysis. Entropic factors might also be important in some cases but cannot contribute to the increase of kcJKM. Furthermore, as much as the correlation between structure and catalysis is concerned, it seems that the complimentarity between the electrostatic potential of the enzyme and the change in charges during the reaction will remain the best correlator. Finally, even in cases where the source of the catalytic activity of a given enzyme is hard to elucidate, it is expected that the methods presented in this book will provide the crucial ability to examine different hypothesis in a reliable way. 

Lower and coworkers [199] have investigated the adsorption of T4 lysozyme on colloidal silica. It was observed that the enzymatic activity decreased upon adsorption due to the differences in adsorbed enzyme structure and orientation as well as the electrostatic effects. 

The enzyme-resistant residue left after ribonuclease action is not dialyz-able and was believed to have a high molecular weight. This has now been shown to be due not to molecular size but to electrostatic effects, and in the presence of salts the enzyme-resistant core readily dialyzes.212 Moreover, it consists of a mixture of relatively small oligonucleotides containing some di- and tri-nucleotides.96 Some of these oligonucleotides have been charac-... 

There is no scrambling in the absence of the acceptor because it is required to cause a conformational change in the enzyme, or to exert an electrostatic effect on the reaction (i.e., the acceptor is a promoter). 

Effective concentration 65-72 entropy and 68-72 in general-acid-base catalysis 66 in nucleophilic catalysis 66 Elastase 26-30, 40 acylenzyme 27, 40 binding energies of subsites 356, 357 binding site 26-30 kinetic constants for peptide hydrolysis 357 specificity 27 Electrophiles 276 Electrophilic catalysis 61 metal ions 74-77 pyridoxal phosphate 79-82 Schiff bases 77-82 thiamine pyrophosphate 82-84 Electrostatic catalysis 61, 73, 74,498 Electrostatic effects on enzyme-substrate association rates 159-161... 

One may suggest that the enzyme has a smaller dielectric effect than the one deduced from the above exercise and that this leads to a large electrostatic effect. Unfortunately, Asp52 would not be ionized in an active... 

Diffusive and electrostatic effects with insolu-bilized enzymes (with M.L. Schuler and H.M. Tsuchiya). J. Theor. Biol. 35, 67-76 (1972). 

Although the contribution of the purine and pyrimidine bases is considered to be relatively minor compared to the electrostatic effects of the phosphates, the enzymic subsites must clearly be able to preferentially distinguish and discriminate the various bases. For example, Mikulski et al. have shown that the nature of the base in the / position exerts a dominant role in the susceptibility of hydrolysis of dinucleotides a clear preference is demonstrated for A and T (22). Also consistent with this are the observations that 5 -mononucleotide binding shows a clear preference for A and T (3, 63), that poly A is more rapidly hydrolyzed than poly C or poly U (3), and that Tp are preferentially released during the early phases of RNA and DNA hydrolysis. 

Enfolding a substrate in this way can serve to maximize the favorable entropy change associated with removing a hydrophobic substrate molecule from water. It also allows the enzyme to control the electrostatic effects that promote formation of the transition state. The substrate is forced to respond to the directed electrostatic fields from the enzyme s functional groups, instead of the disordered fields from the solvent. 

Another of Conant s students was Frank Westheimer (b. 1912), who, after postdoctoral work with Hammett at Columbia, held a post at the University of Chicago (1936-1954) and then returned to Harvard. Westheimer worked in several areas of physical organic chemistry and engaged in other chemistry-based activities, as revealed in an interview conducted in 1995 by Istvan Hargittai.233 For much of his career, Westheimer was essentially a physical organic chemist working in biochemistry and he has himself written reflectively on the discovery of the mechanisms of enzyme action over the period 1947-1963234 and on the application of physical organic chemistry to biochemical problems.235 Westheimer has also contributed, as Tetrahedron Perspective Number 4, an article on Coincidences, decarboxylation, and electrostatic effects , which, he writes, ...allows me to review some of my past .236... 

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