Polyamino acids helical

Go et al. (1968) have recently shown how the data of Sections IXB and IXD may be used to compute the parameters [e.g. a and s of Zimm and Bragg (1959)] of the helix-coil transition in polyamino acids. Heretofore, it had been necessary to rely on a comparison of the results of the statistical mechanical theory with experimental data in order to obtain these parameters. However, with the aid of the aforementioned calculations of the conformational energies of dipeptides and helices, it has been possible to formulate a theory for computing a and s. It remains to be seen how well the computed values of these parameters agree with those evaluated from experimental data on the melting of polyamino acid helices. 

The tendencies of the amino acids to stabilize or destabilize a-helices are different in typical proteins than in polyamino acids. The occurrence of the common amino acids in helices is summarized in Table 6.1. Notably, proline (and hydroxyproline) act as helix breakers due to their unique structure, which fixes the value of the —N—C bond angle. Helices can be formed from either... 

Indeed, 13C spin-lattice relaxation times can also reflect conformational changes of a protein, i.e. helix to random coil transitions. This was demonstrated with models of polyamino acids [178-180], in which definite conformations can be generated, e.g. by addition of chemicals or by changes in temperature. Thus effective molecular correlation times tc determined from spin-lattice relaxation times and the NOE factors were 24-32 ns/rad for the a carbons of poly-(/f-benzyl L-glutamate) in the more rigid helical form and about 0.8 ms/rad for the more flexible random coil form [180],... 

Recently, studies of the conformation of oligomers were extended to peptides derived from /3-methyl-L-aspartates. Their synthesis (n = 2 up to 14) was described by Goodman and Boardman (82), and later the specific rotations of their solutions in dimethyl formamide, dichloro-acetic acid and in chloroform were determined (83). The oligomers exist in a random-coil form in the first two solvents, but helices become stable in chloroform for n — 11 and 14. These peptides are unusual since their L-amino-acid residues produce a left-hand helix (84, 85) whereas most of the investigated polyamino acids crystallise as a right-hand helix (86). 

Similar calculations have been carried out for a variety of other homopolymer helices (Ooi et al., 1967 Scheraga et dl., 1966b, 1967b Scheraga, 1967a, c Yan et al., 1968), each of which has presented an interesting structural problem in polyamino acid chemistry. The energy contributions included in all of these calculations were torsional, nonbonded,... 

From the above examples, it is clear that the nature of the side chain influences the helical sense of polyamino acids. The side-chain-to-side-... 

The development of VCD as a peptide conformational probe proceeded in a manner similar to the one followed earlier by researchers in CD spectroscopy [38], Homo-polyamino acids, such as poly-L-Tyr or poly-L-Lys, for which the secondary structure is well known and can be varied as a function of solvent acidity, were studied via VCD, and distinct results for the established conformations were observed. These results are summarized in Figures 4 and 5. In poly-L-Tyr [41], for example, the a-heli-cal conformation exhibits a distinct, sharp and near-conservative positive / negative couplet in the amide I region. In the context of this discussion, "conservative couplet" implies equal positive and negative VCD intensities, and a description of positive / negative couplet always implies low to high wavenumber. The a-helical conformation is assumed by poly-L-Tyr in acidified DMSO solution (80% 20% by volume of DMSO... 

We have carried out a computational and experimental study on the "random coil" conformation of poly-L-Tyr to answer the question about the local order in the "random coil" conformation which had been addressed before by researchers in a number of fields [39,40]. This study was made possible by our successful application of the DECO model (cf. Section 3) to interpret VCD spectra of model compounds. Our efforts to deduce a structure for the "random coil conformation of (homo)-polyamino acids was prompted by the observation by us and others [41] that the "random coil" in systems (such as poly-L-Tyr) produces VCD features which are nearly equal in magnitude, and opposite in sign, to those produced by the a-helical conformation (cf. Figure... 

Finally, the shift toward higher wavenumbers of the zero crossing of the negative-positive VCD spectrum is better reproduced by the extended helix than the left-handed a-helix. Thus, we favor the interpretation that the observed spectra of the "random coil" conformation can best be described by an extended helical structure, and that a truly random coil peptide will exhibit virtually no VCD. Dukor and Keiderling [39] reached very similar conclusions about the nature of the "random coil" conformation of homo-polyamino acids based on an extensive study of a number of left- and right handed helical segments, and fully supports the conclusion reached earlier by Krimm [42,43] about the extended helix discussed above. All evidence points to the fact... 

Predict which of the following polyamino acids will form a helices and which will form no ordered structures in solution at room temperature. 

Polyamino acids can be considered as models for conformational studies, providing an atomistic description of the secondary structural motifs typically found in proteins [30-39]. Two-dimensional hydrogen-bonded layers and columns in the structures of crystalline amino acids can mimic S-sheets and helices in proteins and amyloids [40 5], and can be compared with two-dimensional crystalline layers at interfaces [46-58]. Nano-porous structures of small peptides can mimic cavities in proteins [24, 59-63]. One can also prepare crystals in which selected functional groups and side chains are located with respect to each other in the same way, as at recognition sites of substrate-receptor complexes, and use the systems to simulate the mutual adaptation of components of the complex responsible for recognition. 

Surface Viscosity of Protein Monolayers. Figure 2 shows the surface viscosity ( H g) of a number of proteins and one polyamino acid as a function of H ( ), The extremely high surface viscoelasticity of protein monolayers appears to be more characteristic of an interacting random chain system than an array of rigid helices. The theory of surface viscosity of Moore and Eyring ), based on the Theory of Absolute Reaction Rates, postulates that the flow of a monolayer consists of movements of flow units, normally molecules, from one equilibrium position to another, over an intermediate activation energy barrier. The equation derived for the coefficient of surface viscosity ( g)... 

Electronic spectra yield valuable information on the presence or absence of chromophores and functional groups, but have rather limited use in the elucidation of the three dimensional structure in peptides. Infrared spectroscopy has been applied for the detection of helices and )8-sheets, yet the spectra are usually meaningful only when the molecules are somewhat ordered as, for instance, in stretched films of polyamino acids. The scope of investigations seems to broad-... 

Such measurements on polyamino acids such as poly(L-glutamic acid) and poly(benzyl-L-glutamate) are of particular interest because the character of the absorption is different for the helical and random coil configurations which are found in different solvents. ... 

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