Peptide standards conformation

Figure 2.10. (Top) Graphical construction of a dipeptide. Once the second peptide unit is located (see Figure 2.12), it is rotated through an angle of 33° clockwise to generate a dipeptide in the standard conformation, with < ) = 180° and / = 180°.

The free energy differences obtained from our constrained simulations refer to strictly specified states, defined by single points in the 14-dimensional dihedral space. Standard concepts of a molecular conformation include some region, or volume in that space, explored by thermal fluctuations around a transient equilibrium structure. To obtain the free energy differences between conformers of the unconstrained peptide, a correction for the thermodynamic state is needed. The volume of explored conformational space may be estimated from the covariance matrix of the coordinates of interest, = ((Ci [13, lOj. For each of the four selected conform-... 

The use of PIR compounds to study protein interactions is a significant advance over the use of standard homobifunctional crosslinkers. The unique design of the PIR reagent facilitates deconvolution of putative protein interaction complexes through a simplified mass spec analysis. The software can ignore all irrelevant peak data and just focus analysis on the two labeled peptide peaks, which accompany the reporter signal of appropriate mass. This greatly simplifies the bioinformatics of data analysis and provides definitive conformation of protein-protein crosslinks. 

Alternatively, if the dehydroamino acid is C-terminal or is central in the peptide chain, then the oxazolone precursor to the dehydropeptide must be in position two in order to apply this methodology (Scheme 7.165). The requisite unsaturated 5(4//)-oxazolone intermediate 518 is obtained from the appropriate precursors following standard cyclization procedures and avoiding experimental conditions that would epimerize the chiral center. This methodology has been applied to access analogues of important peptides including dehydroaspartame, somatostatin, and dermorphin. In these cases, a dehydroamino acid was incorporated into the peptide backbone to study the relationship between conformational restriction and biological properties of the modified peptide. 

Several methods have been developed for the incorporation of thioamide bonds at defined positions into linear peptides (for details see Vol. E 22c, Section 10.9.1) 498,499 The resulting linear precursors can be cyclized by standard procedures, although the thioamide bond should not be located in penultimate position, since activation of the carboxy group leads to thia-zolone formation as outlined in Scheme 31.1500-502 The cyclization yield of thioamide-containing peptides is generally rather low. This effect results from the additional local steric restrictions exerted by the thioamide bond, which leads to decreased conformational flexibility 488 ... 

Analogously, the fluorescence quantum yield of an extrinsic fluorescent probe contained in a peptide can be measured by comparison with an appropriate standard. If the fluorescent peptide exists in a conformational equilibrium, the fluorophore may be located in a number of different environments and may have a distinct quantum yield (ip,) in each environment. In this case the determined fluorescence quantum yield represents a population-weighted average of the individual [Pg.700]

The RGD sequence was thus constrained into a variety of sheet or /3-turn structures, which were unequivocally determined for each peptide. The biological activity of 18 cyclic peptides was then compared with that of a linear standard, GRGDS, in inhibition assays of tumour cell adhesion. An increase in activity of up to 100-fold was observed for just two cyclic pentapeptides, all others showing a decrease in activity. This identified the required conformation of the RGD backbone. 

An A -methyl-amino-oxy amino acid has also been incorporated into peptides using standard SPPS procedures. Reaction of these peptides with native reducing sugars yields neoglycopeptides via a chemoselective reaction with the amino-oxy side chains, maintaining the linked sugars in their cyclic conformations and... 

In order to show that HIT-1 was a-helix compatible and induces a-helical conformations in short peptides from the N- and C-terminus as well as from internal positions, template-linked peptides have been compared to nonconstrained reference peptides. In the N- and C-cap projects a hydrophobic 12-mer peptide was used as a standard reference. The 12-mer reference peptide 104 was originally developed for host guest experiments to evaluate the a-helix propensities of unnatural amino acids (see Section II.A) and had later been used to confirm N-cap induced helix formation.141,202,214 In the C-cap series and for position-independent templates the same reference peptide could be used after minor modification of the terminal protection groups. The suitably protected reference peptide and the corresponding template-linked model peptides used for the evaluation of N-terminal, C-terminal, and internal helix induction are depicted in Figure 39. 

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