Peptides conformational analysis

The recognition that short chain / -peptides can form regular secondary structures initially came from detailed conformational analysis of y9 -peptides 1 and 66 (which incorporates a central (2S,3S)-3-amino-2-methylbutanoic acid residue) by NMR in pyridine-d5 and CD3OH [10, 103, 164] and homooUgomers (as short as four residues) of trons-2-amino-cyclohexanecarboxyhc acid (trans-ACHC) (e.g. hex-amer 2 for the (S,S) series) by NMR and X-ray diffraction [6, 126, 159]. 

Detailed NMR conformational analysis of y -peptides 139-141 (Fig. 2.35) in pyri-dine-d5 revealed that y-peptides as short as four residues adopt a 2.6-hehcal fold stabilized by H-bonds between C=0 and NH +3 which close 14-membered pseudocycles [200, 201]. The 2.614-helical structure of a low energy conformer of y-hex-apeptide 141 as determined from NMR measurements in pyridine-d5 [200], is shown in Fig. 2.36A and B). Determination of the structure of y" -peptides in CD3OH was hampered by the much lower dispersion of the diasterotopic H-C(a) protons compared to their dispersion in pyridine-d5. However, the characteristic and properly resolved i/ir-2 NOE crosspeacks between H-C(y) and NH +2 in the NH/H-C(y) region of the ROESY spectrum were an indication that the 2.6-helical structure is at least partially populated in CD3OH. 

Wilkes BC, Schiller PW. Theoretical conformational analysis of a p-selective cyclic opioid peptide analog. Biopolymers 1987 26 1431-1444. 

However, 2D NOE studies are invaluable in structure determination, in particular of peptides and proteins here the NOEs give invaluable information for conformational analysis and the determination of the tertiary structures of proteins. 

Scarsdale, J. N., C. Van Alsenoy, V. J. Klimkowski, L. Schafer, and F. A. Momany. 1983. Ab Initio Studies of Molecular Geometries. 27. Optimized Molecular Structures and Conformational Analysis of N-Acetyl-N-methylalaninamide and Comparison with Peptide Crystal Data and Empirical Calculations. J. Am. Chem. Soc. 105,3438-3445. 

Schafer, L., C. Van Alsenoy, and J. N. Scarsdale. 1982. Ab Initio Studies of Structural Features Not Easily Amenable to Experiment. 23. Molecular Structures and Conformational Analysis of the Dipeptide N-acetyl-N -methyl Glycyl Amide and the Significance of Local Geometries for Peptide Structures. J. Chem. Phys. 76, 1439-1444. 

Ouyang, H., Vander Velde, D. G., Borchardt, R. T., Synthesis and conformational analysis of a coumarinic acid-based cyclic prodrag of an opioid peptide with modified sensitivity to esterase-catalyzed bioconversion. J. Peptide Res. 2002, 59, 183-195. 

Application of the analytical techniques discussed thus far focuses upon detection of proteinaceous impurities. A variety of additional tests are undertaken that focus upon the active substance itself. These tests aim to confirm that the presumed active substance observed by electrophoresis, HPLC, etc. is indeed the active substance, and that its primary sequence (and, to a lesser extent, higher orders of structure) conform to licensed product specification. Tests performed to verify the product identity include amino acid analysis, peptide mapping, N-terminal sequencing and spectrophotometric analyses. 

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

Tight turns were first recognized from a theoretical conformational analysis by Venkatachalam (1968). He considered what conformations were available to a system of three linked peptide units (or four successive residues) that could be stabilized by a backbone hydrogen bond between the CO of residue n and the NH of residue n + 3. He... 

A. G. Beck-Sickinger G. Jung, Synthesis and Conformational Analysis of Lantibiotic Leader-, Pro-, and Pre-Peptides. In Nisin and Novel Lantibiotics G. Jung, H.-G. Sahl, Eds. ESCOM Leiden, 1991 pp 218-230. 

I. L. Karie, X-ray Analysis Conformation of Peptides in the Crystalline State. In The Peptides. Analysis, Synthesis,... 

Conformational analysis can be performed using a variety of methods.1161 Most important are X-ray analysis and NMR spectroscopic techniques, which allow detailed insights into the topology of the peptides. NMR combined with molecular dynamic calculations provides the spatial structure of the peptide, but also its dynamics in solution.13643491 Additional information can be obtained from FTIR,15,4521 CD,151,53-551 or Raman spectroscopy. 56,571 The results derived from such conformational analysis of cyclic peptides have a considerable impact on the study of the bioactive conformations of peptides and on the design of cyclic peptides as proteinomimetics.124,58,59,6301... 

In principle every compound with an amino and a carboxy group can be used for such purpose ranging from simple co-amino acids [e.g., 5-aminopentanoic acid (6-aminovaleric acid) (1, n = 3)]1541 or 6-aminohexanoic acid (e-aminocaproic acid) (1, n = 4)]135,57,4 791 and related derivatives of 3-aminobenzoic acid 14801 or more sophisticated structures. A few examples (1-6) are shown in Scheme 28. Numerous cyclic turn mimetics have been developed in the past years and for details on this subject the reader is directed to Vol. E 22c, Section 12. To explore the rigidification introduced by nonnatural amino acids or equivalent structures into cyclic peptides, a careful NMR conformational analysis is required, since frequently the so-called p-turn mimetics do not enable such turns to be established, conversely other secondary structure elements may be induced.14811... 

A few words about conformational analysis are given in Section 7.5.3. In Section 7.5.1 the NMR of peptides in general is discussed. Reviews of NMR spectroscopy of peptides can be found in the literature. 16-18 ... 

It is beyond the scope of this section to describe the conformational analysis of peptides and the reader is directed to the literature.[16 181... 

After a-helices, P-sheets are the most prominent secondary structure feature in globular proteins. However, the most widely used tool for secondary analysis, ultraviolet ECD, is so dominated by its sensitivity to the a-helix that, at best, it can only poorly characterize ( -sheet content. IR on the other hand has a good differential sensitivity to the p-sheet because of the large frequency shift ( 30 cm-1) from the helical band and because the extinction coefficient for model extended sheets is often higher than for other conformations. However, study of the p-sheet conformation with peptide models has long been hindered by their natural tendency to aggregate. Furthermore, no (or very few) peptide models of parallel sheets are available, to our knowledge. 

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