Helical secondary structure, effect

Effect of pH on the Conformation of a-Helical Secondary Structures The unfolding of the a helix of a polypeptide to a randomly coiled conformation is accompanied by a large decrease in a property called its specific rotation, a measure of a solution s capacity to rotate plane-polarized light. Polyglutamate, a polypeptide made up of only l-G1u residues,... 

The effect of several polyols on the Tn, of thrombin and trypsin have also been reported (Boctor and Mehta, 1992). For example, the Tn, of trypsin (pH 6.5) was observed to increase with increasing glycerol concentration (up to 50%) from 52°C to 60°C, resulting in a ATn, = 8.0°C. Similar increases in thermal stability were observed for thrombin, were the AT = 9.8°C when comparing purely aqueous conditions with 50% glycerol. The effect of glycerol on myoglobin (pH 7.4) was more subtle, in which the overall tertiary structure was destabilized, but the overall a-helical secondary structure was stabilized (Barter et ah, 1996). 

Zwitterionic PLCllu 15-/>PLLys,5 in water (Fig. lc) can self-assemble into unilamellar vesicles with a hydrodynamic radius of greater than 100 nm (SANS), as shown by Rodriguez-Hernandez and Lecommandoux [24], A change of the pH from 3 to 12 induced an inversion of the structure of the membrane (NMR) and was accompanied by an increase of the size of vesicles from 110 to 175 nm (DLS). Whether the formation of vesicles was controlled by a secondary structure effect or simply by copolymer composition (geometry) remains an open question. Spectroscopic data supporting an a-helical conformation of the polypeptide in the hydrophobic part of the membrane, as speculated by the authors, were not provided. It appears that, however, the peptide segments could be too short to form a stable a-helix. 

Nonionic block copolypeptides made of PEGylated L-lysine and L-leucine residues, PELLys- -PLLeu (Fig. lOh) have also been described [52], The copolymers adopted a rod-like conformation, due to the strong tendency of both segments to form a-helices (CD spectroscopy), and produced a variety of self-assembled structures in aqueous solution. Micrometer vesicles and sheet-like membranes could be obtained for copolymers with fractions of the hydrophobic leucine ranging from 10 to 30mol%. Conventional uncharged block copolymers of this composition would be expected to form spherical or cylindrical micelles. The assembly into bilayers was related to a secondary structure effect, as illustrated in Fig. 12. Accordingly, samples with the same composition but nonhelical chain conformation (CD),... 

We prepared three bifunctional redox protein maquettes based on 12 16-, and 20-mer three-helix bundles. In each case, the helix was capped with a Co(III) tris-bipyridyl electron acceptor and also functionalized with a C-terminal viologen (l-ethyl-V-ethyl-4,4 -bipyridinium) donor. Electron transfer (ET) was initiated by pulse radiolysis and flash photolysis and followed spectrometrically to determine average, concentration-independent, first-order rates for the 16-mer and 20-mer maquettes. For the 16-mer bundle, the a-helical content was adjusted by the addition of urea or trifluoroethanol to solutions containing the metal-loprotein. This conformational flexibility under different solvent conditions was exploited to probe the effects of helical secondary structure on ET rates. In addition to describing experimental results from these helical systems, this chapter discusses several additional metalloprotein models from the recent literature. 

The influence of secondary structure on reactions of deamidation has been confirmed in a number of studies. Thus, deamidation was inversely proportional to the extent of a-helicity in model peptides [120], Similarly, a-hel-ices and /3-turns were found to stabilize asparagine residues against deamidation, whereas the effect of /3-sheets was unclear [114], The tertiary structure of proteins is also a major determinant of chemical stability, in particular against deamidation [121], on the basis of several factors such as the stabilization of elements of secondary structure and restrictions to local flexibility, as also discussed for the reactivity of aspartic acid residues (Sect. 6.3.3). Furthermore, deamidation is markedly decreased in regions of low polarity in the interior of proteins because the formation of cyclic imides (Fig. 6.29, Pathway e) is favored by deprotonation of the nucleophilic backbone N-atom, which is markedly reduced in solvents of low polarity [100][112],... 

There is a correlation between the backbone conformations which commonly flank disulfides and the frequency with which disulfides occur in the different types of overall protein structure (see Section III,A for explanation of structure types), although it is unclear which preference is the cause and which the effect. There are very few disulfides in the antiparallel helical bundle proteins and none in proteins based on pure parallel /3 sheet (except for active-site disulfides such as in glutathione reductase). Antiparallel /3 sheet, mixed /8 sheet, and the miscellaneous a proteins have a half-cystine content of 0-5%. Small proteins with low secondary-structure content often have up to 15-20% half-cystine. Figure 52 shows the structure of insulin, one of the small proteins in which disulfides appear to play a major role in the organization and stability of the overall structure. 

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