Other species in the aqueous environment of a peptide can invert its intrinsic solvated polyproline II/beta propensity: Implications for amyloid formation

As we have previously shown, the predominance of the polyproline II conformation in the circular dichroism spectra of aqueous polypeptides is related to its lower energy than that of the beta conformation. To test whether this is still the case in the presence of additional components in the medium, we have calculated the energy difference between these two conformations in an alanine‐dipeptide/12‐water system without and with the addition of an HCl molecule. We find in the latter case that the beta conformer is of lower energy than the polyproline II. Energy profiles near the minima in both cases also permit conclusions about the relative entropies of these structures. These results emphasize the importance of considering the peptide‐plus‐medium state as the relevant entity in determining the structural properties of such systems. Such an inversion could be relevant to the formation of amyloid and could thus lead to new strategies for studying its role in the development of neurodegenerative diseases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 305–311, 2016.     

Phase determination of x-ray reflections for membrane-type systems with constant fluid density.

A new technique for phase determination of X-ray reflections from symmetric structures is presented. This method, involving comparison of intensity data from structures with variable fluid layer thickness and constant fluid electron density, permits computation of phase angles, scaling factors, and origin reflection values independently. Possible sources of error inherent in other methods of phase determination are thereby eliminated. Results of the application of this method to model structures and to myelin data are reported. Advantages of the technique, which tests all possible phase angle combinations in a rapid fashion, are discussed.     

Vibrational analysis of peptides, polypeptides and proteins. XXVII. Structure of gramicidin S from normal mode analyses of low-energy conformations

Normal mode calculations have been carried out on three low-energy structures of gramicidin S obtained from conformational energy calculations. When the results on the amide modes are compared with observed bands in the infrared and Raman spectra of crystalline gramicidin S and its N-deuterated derivative, one of the structures is clearly disfavored. Of the other two, one is slightly favored, and it corresponds to the lowest-energy structure obtained from the energy calculations. Spectra from solutions in DMSO and CH3 OH suggest that the molecular conformation is essentially retained in these solvents.     

Vibrational analysis of conformation in peptides,polypeptides, and proteins

A vibrational force field for the polypeptide chain has been developed for normal-mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm^?1. We review the application of this technique to conformational problems in peptides (β-turns and their model compounds), polypeptides [the α_II-helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).