Polyproline peptide

Section 7.3.1 describes the experimental apparatus for collecting and analyzing fluorescence lifetime data vs temperature. Section 7.3.2 presents the results of lifetime measurements of polyproline peptides and MD simulations to (a) relate fluorescence quenching rates to specific conformational fluctuations, and (b) calculate the implications of intramolecular electrostatic interactions for the quenching mechanism. 

Talbot FO, Rullo A, Yao H, Jockusch RA (2010) FluOTescence resonance energy transfer in gaseous, mass-selected polyproline peptides. J Am Chem Soc 132 16156-16164... 

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Jardetzky, T.5., Wiley, D.C. Crystallographic analysis of endogenous peptides associated with HLA-DRl suggests a common, polyproline Il-like conformation for hound peptides. Proc. Natl. Acad. Sci. USA 93 734-728, 1996. 

Neuropeptide Y (NPY) is a 36 amino acid polypqrtide with tyrosine residues at both ends of the molecule. It is characterised structurally by a PP-fold consisting of an extended polyproline helix and an a-helix connected by a (3-tum [1]. Based on structural and evolutionary criteria, NPY is closely related to peptide YY (PYY) and pancreatic polypeptide (PP). 

Each polytripeptide chain is twisted around a threefold screw axis and exists in a secondary structure, analogous to the left-handed polyproline II-helix, i.e. with transposition of the peptide bond (pitch 8.4 A, 3 amino acids) (Figs. 2,3). 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

T. P. Creamer (unpublished results). A plot of estimated (ASA) against %PPII content is given in Figure 5. At first glance, it would appear that there is little correlation between the two properties. However, three residues—proline, glycine, and glutamine—can be considered outliers, each for a specific reason. Proline has a high %PPII content in the polyproline-based host peptide used by Kelly et al. (2001) as a result of its unique properties as an imine. As discussed above, a proline that is followed in sequence by a second proline is restricted to the PPII conformation by steric interactions. 

Experimental and theoretical approaches are now converging on the polyproline II backbone conformation as the most stable structure for short alanine peptides in water. It becomes of urgent importance to determine the energy differences between polyproline II and other possible backbone conformations, as well as to determine how amino acid composition and sequence affect backbone conformation. 

Mykhailiuk PK, Afonin S, Palamarchuk GV, Shishkin OV, Ulrich AS, Komarov IV (2008) Synthesis of trifluoromethyl-substituted proline analogues as F-19 NMR labels for peptides in the polyproline II conformation. Angew Chem Int Edit 47 5765-5767... 

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