Polypeptides a-helical

Torii, H., and M. Tasumi. 1993. Infrared Intensities of Vibrational Modes of an a-helical Polypeptide Calculations Based on the Equilibrium Charge/Charge Flux (ECCF) Model. J. Mol. Struct. 300,171-179. 

The long side chains of a homopolypeptide have remarkable motional freedom about multiple bonds, while the main chain forms the secondary regular conformation such as a-helix, /1-sheet, and turn, which are rigid structures. The macroscopic properties of the rigid a-helical polypeptide, therefore, highly depends on the dynamic structure of the side chains so that a lot of studies on the side chain dynamics of the a-helical polypeptides have been carried out in the solid and solution states.12,14,29 66... 

The a-helix CD spectrum is remarkably insensitive to solvent. One apparent exception is poly(Ala) in HFIP.1471 The CD amplitude for poly(Ala) in HFIP is only about half that of typical a-helical polypeptides, the CD bands are shifted several nm to the blue, and the long-wavelength njr band is observed as a shoulder rather than a discrete band. These features are unique to poly(Ala), as other helix-forming polypeptides exhibit normal CD spectra in... 

Since Robinson [1] discovered cholesteric liquid-crystal phases in concentrated a-helical polypeptide solutions, lyotropic liquid crystallinity has been reported for such polymers as aromatic polyamides, heterocyclic polymers, DNA, cellulose and its derivatives, and some helical polysaccharides. These polymers have a structural feature in common, which is elongated (or asymmetric) shape or chain stiffness characterized by a relatively large persistence length. The minimum persistence length required for lyotropic liquid crystallinity is several nanometers1. 

An individual polypeptide in the a-keratin coiled coil has a relatively simple tertiary structure, dominated by an a-helical secondary structure with its helical axis twisted in a left-handed superhelix. The intertwining of the two a-helical polypeptides is an example of quaternary structure. Coiled coils of this type are common structural elements in filamentous proteins and in the muscle protein myosin (see Fig. 5-29). The quaternary structure of a-keratin can be quite complex. Many coiled coils can be assembled into large supramolecular complexes, such as the arrangement of a-keratin to form the intermediate filament of hair (Fig. 4-1 lb). 

Figure 25-17 Representation of the quaternary structure of a-keratin showing (a) three a-helical polypeptide strands coiled into a rope and (b) eleven units of the three-stranded rope arranged to form one microfibril...

A photoresponsive amphiphilic helical polypeptide (a helical polypeptide in which all the polar residues are located on one side of the helical cylinder and all the hydrophobic residues on the opposite side) was prepared by Higuchi et al., using a simple and unique technique.1117-1211 The polypeptide XXI was first placed at a... 

The a-helical polypeptide chains, presumably polymerized head-to-tail, interact laterally to form dimers. This is made possible by each polypeptide chain assuming a slightly distorted shape referred to as a "coiled coil." The dimer is referred to as a 2-nm protofilament, because it has a diameter of about 2 nm. It is believed that the dimer consists of one type 1 and one type 2 polypeptide chain. There are a couple of possibilities for the next level of organization either two 2-... 

The matter has been carried further in the studies of Gratzer et al. (1961) with measurements of the absorption of polarized radiation by oriented films of a-helical polypeptides. Their polarization spectra of poly-L-ala-nine, and of poly-7-methyl-L-glutamate (Fig. 8) clearly show the predicted opposite polarization for the two peptide absorption bands of the -helix. Taking these band positions as 1910 and 2060 A, we obtain a band separation of 3800 cm . [The value of 2700 cm in the paper of Gratzer et al. 

Fig. 4. Typical flow curves of an a-helical polypeptide in m-cresol at 25°C. The experimental points at t > 10 dynes cm were omitted in the plot. Concentrations O, 0,379% A, 0.502% X, 0.621% A, 0.776% , 0.918%. Reproduced from Yang (1959).

Fig. 5. Shearing stress dependence of the intrinsic viscosities of three a-helical polypeptides. The lines are theoretical curves (broken lines to the right of the arrows being extrapolated theoretical curves) 1, ijiiQ/T = 0.76 3, riaO/T = 0.054 2, calculated on the basis of three parts curve 1 and one part curve 3. Reproduced from Yang (1959).

As stated earlier, lipases act at the interface between hydrophobic and hydrophilic regions, a characteristic that distinguishes lipases from esterases. Similar to serine proteases, lipases share the nucleophile-histidine-acidic residue catalytic triad that manifests itself as either a Ser-His-Asp triad or a Ser-His-Glu triad. The enzyme s catalytic site often is buried within the protein structure, surrounded by relatively hydrophobic residues. An a-helical polypeptide structure acts as a cover, making the site inaccessible to solvents and substrates. For the lipase to be active, the a-helical lid structure has to open so that the active site is accessible to the substrate. The phenomenon of interfacial activation is often associated with reorientation of the lid, increasing the hydrophobicity of the surface in the vicinity of the active site and exposing it. The opening of the lid structure may be initiated on interaction with an oiFwater interface. 

Experiments on liquid crystallinity exhibited by solutions of a-helical polypeptides have been especially illuminating (see Chapter 2 by Uematsu and Uematsu). Principal results are summarized and compared with theory in Table 2. Most of the measurements presented were carried out by visual observation between crossed... 

This conclusion was reached, tentatively, by Frenkel, Shaltyko and Elyashevich A phenomenological analysis presented by Pincus and de Gennes predicted a first-order phase transition even in the absence of cooperativity in the conformational transition. These authors relied on the Maier-Saupe theory for representation of the interactions between rodlike particles. Orientation-dependent interactions of this type are attenuated by dilution in lyotropic systems generally. In the case of a-helical polypeptides they should be negligible owing to the small anisotropy of the polarizability of the peptide unit (cf. seq.). Moreover, the universally important steric interactions between the helices, regarded as hard rods, are not included in the Maier-... 

Another class of polymers equipped with azobenzene moieties comprises a-helical polypeptides, in particular pQly(L-glutamate)s and poIy(L-lysine)s. In solution, these azobenzene-modified polypeptides can undergo photoinduced helix-coil transitions. Polypeptides partially (30 to 50%) substituted with azobenzene moieties are surface active and form stable monolayers. Because of the partial substitution, there is sufficient free volume, and the azobenzene moieties can be isomerized in the monolayer. The photoisomerization changes the area per molecule, and the monolayer shows a photomechanical effect. LBK films of a photosensitive poly(L-lysine) with 31 mol... 

Figure 9 presents exponents a for both models as a function of temperature. The Go-like model exhibits a much sharper transition to a white noise spectrum than the BLN model as the temperature departs from the transition temperature. This finding also mirrors the results obtained from the Allan variance where the Go-model exhibits a sharp transition to nonstationarity around the transition temperature, while this transition is diffuse in the case of the BLN model. It was also shown [64,65] in a two-state-like helix-coil transition of a helical polypeptide that a 1//-noise structure of the potential energy fluctuations... 

It is worth noting from Table XIII that the approximate force field gives a good reproduction of the frequencies and eigenvectors of the non-CHs modes of the side-chain point-mass model of the a helix. This approximation should therefore be satisfactory for reproducing the amide modes of an a-helical polypeptide chain in, for example, a globular protein. 

It might be expected that amide and backbone bands in the spectra of a-(Ala) would be representative of frequencies to be found in all a-helical polypeptides. Evidence has suggested, however, that the amide-III frequencies are sensitive to side-chain composition (Hsu et al., 1976). It is, therefore, important that a detailed analysis of another a-helical polypeptide be available so that the influence of this factor can be assessed. 

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