Enzyme secondary structure

Ellipsometry and nonlinear optics have proven their sensitivity in studying monolayer thickness and molecular orientation, but generally the anisotropic nature of the interface makes results rather difficult to interpret [20-22], In many cases, these methods were limited in their potential to supply information about biophysical issues such as head group structure, enzyme secondary structure, and the orientation of ordered regions. 

Characterization of protein (enzyme) secondary structure and stability upon pH, temperature, denaturizing agents etc... 

The shape of a large protein is influenced by many factors including of course Its primary and secondary structure The disulfide bond shown m Figure 27 18 links Cys 138 of carboxypeptidase A to Cys 161 and contributes to the tertiary structure Car boxypeptidase A contains a Zn " ion which is essential to the catalytic activity of the enzyme and its presence influences the tertiary structure The Zn ion lies near the cen ter of the enzyme where it is coordinated to the imidazole nitrogens of two histidine residues (His 69 His 196) and to the carboxylate side chain of Glu 72... 

As a result of the micellar environment, enzymes and proteins acquire novel conformational and/or dynamic properties, which has led to an interesting research perspective from both the biophysical and the biotechnological points of view [173-175], From the comparison of some properties of catalase and horseradish peroxidase solubilized in wa-ter/AOT/n-heptane microemulsions with those in an aqueous solution of AOT it was ascertained that the secondary structure of catalase significantly changes in the presence of an aqueous micellar solution of AOT, whereas in AOT/n-heptane reverse micelles it does not change. On the other hand, AOT has no effect on horseradish peroxidase in aqueous solution, whereas slight changes in the secondary structure of horseradish peroxidase in AOT/n-heptane reverse micelles occur [176],... 

Loops are regions that contain residues beyond the minimum number necessary to connect adjacent regions of secondary structure. Irregular in conformation, loops nevertheless serve key biologic roles. For many enzymes, the loops that bridge domains responsible for binding substrates often contain aminoacyl residues... 

Propiolactone is one example. It will alkylate amino, imino, hydroxyl and carboxyl groups, all of which occur in proteins, and react also with thiol and disulphide groups responsible for the secondary structure of proteins and the activity of some enzymes. 

The CD spectrum of the C188S mutant is essentially the same as that of the wild-type enzyme, which reflects that the tertiary structure of this mutant changed little compared to that of the wild-type enzyme. Calculation of the content of secondary structure of the mutant enzyme based on J-600S Secondary Structure Estimation system (JASCO) also showed that there is no significant change in the secondary structure of the mutant. The fact that the k value of this mutant is extremely small despite little change in conformation clearly indicates that Cysl88 is located in the active site. 

Fig. 4.12(a). An outline structure of a protein (here the enzyme phospholipase A2), showing a-helical runs of amino acids as cylinders (A-E) and anti-parallel P-sheet runs as heavy black arrows. Disulfide cross-links are shown (the enzyme is extracellular), and runs of no a/p secondary structure appear as thin lines. The structure is relatively immobile, and binds calcium in a constrained loop. (Reproduced with permission from Professor J. Drenth.)... 

C). In addition, enzymes often combine a high specificity for the recognized substrates with a large tolerance for secondary structure. Alternatively, noble metal transformations offer reaction conditions that are also mild enough to be compatible with sensitive, doubly lipidated peptides. 

RNA amplification by PCR has been facilitated by the use of a single heat-stable enzyme. Thus, DNA polymerase from Thermus thermophilus, which has enhanced reverse transcriptase (rT) activity in presence of manganese, can be used with one buffer system. The high temperature used for rT (70°C) to produce a complementary DNA copy from RNA, and the subsequent amplification of DNA at 60°C, increases efficiency by destabilizing secondary structures in the RNA template. This procedure has been used for the amplification of hepatitis C viral RNA (Yl). 

The torsion angles around the bonds of the sugar-phosphate DNA backbone are of decisive importance for the secondary structure of DNA as well as for base-base recognition. [44] For antisense agents to be effective inhibitors of protein expression in vivo, they have to resist the action of DNA-degrading enzymes and bind to their... 

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