Peptides structural analysis

Mikhailiuk PK, Afonin S, Chemega AN, Rusanov EB, Platonov MO, Dubinina GG, Ber-ditsch M, Ulrich AS, Komarov IV (2006) Conformationally rigid trifluoromethyl-substituted alpha-amino acid designed for peptide structure analysis by solid-state F-19 NMR spectroscopy. Angew Chem Int Edit 45 5659-5661... 

Infrared spectroscopy has been an important part of peptide structural analysis for 50 years now. From a rather basic beginning, applications have blossomed to encompass secondary structure analysis, polarization phenomena, membrane conformation, and orientation, and have extended to time-dependent conformational folding mechanisms. Questions have evolved from basic polymer chemistry to issues centered on peptides involved in socially... 

Table 18.1 Comparison of selected NMR labels used for peptide structure analysis...

Mikhailiuk, P. K., Afonin, S., Chemega, A. N., et al. (2006) Conformationally rigid trifluoro-methyl-substituted a-amino acid designed for peptide structure analysis by solid-state 19F NMR spectroscopy. Angewandte Chemie International Edition, 45, 5659-5661. 

Peptide CD structure analysis differs firom that of proteins as peptides are usually a combination of a particular secondary structure and random coil (i.e. unordered) residues. Proteins seldom if ever have random coils, so the CD of the proteins in the basis set of the protein anal3rsis program has no random coil component. Further, the analysis of the CD of a peptide is not under-determined, and so does not require a flexible method like Variable Selection. A Convex Constraint Analysis (22) that extracts the component spectra has been developed into a peptide structure analysis program by Greenfield (14). 

Hoveyda and coworkers [142] developed the Cu-catalyzed allylic substitutions of phosphonate derivatives with pyridinyl peptide structures as efficient ligands. The structure of the ligands was chosen through synthesis, and analysis of libraries. Optimized compounds were used as ligands for the... 

Applications of Molecular Dynamics for Structural Analysis of Proteins and Peptides... 

The hybrid approach enhances the speed and efficiency of primary structure analysis and the range of proteins that can be sequenced. It also circumvents obstacles such as the presence of an amino-terminal blocking group or the lack of a key overlap peptide. Only a few segments of primary strucmre must be determined by Edman analysis. 

Swiderek, K. M. Alpert, A. J. Heckendorf, A. Nugent, K. Patterson, S. D. Structural analysis of proteins and peptides in the presence of detergents Tricks of the trade. ABRF News 1997. 

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. 

Keywords Solid-state NMR structure analysis 19F-labeling Membrane-active peptides Native biomembranes Oriented membrane models Antimicrobial peptides... 

Fig. 1 Solid-state NMR structure analysis relies on the 19F-labelled peptides being uniformly embedded in a macroscopically oriented membrane sample, (a) The angle (0) of the 19F-labelled group (e.g. a CF3-moiety) on the peptide backbone (shown here as a cylinder) relative to the static magnetic field is directly reflected in the NMR parameter measured (e.g. DD, see Fig. 2c). (b) The value of the experimental NMR parameter varies along the peptide sequence with a periodicity that is characteristic for distinct peptide conformations, (c) From such wave plot the alignment of the peptide with respect to the lipid bilayer normal (n) can then be evaluated in terms of its tilt angle (x) and azimuthal rotation (p). Whole-body wobbling can be described by an order parameter, S rtlo. (d) The combined data from several individual 19F-labelled peptide analogues thus yields a 3D structural model of the peptide and how it is oriented in the lipid bilayer...

For the orientation-based structure analysis of MAPs, uniformly oriented lipid bilayers are typically prepared on solid supports as illustrated in Fig. 2 [23, 47, 55]. These mechanically oriented membranes are advantageous for static ssNMR experiments, as they provide a robust way to orient a sample with any desired lipid composition, peptide concentration, and at any desired temperature. The lipids... 

Fig. 3 Important 19F-labelled amino acids, (a) Compounds that are wo-steric to native amino acids can be incorporated into proteins biosynthetically, but they possess too many degrees of torsional freedom to be useful for ssNMR structure analysis, (b) In these artificial amino acids the 19F-reporter group is rigidly attached to the peptide backbone. They can be incorporated by solid-phase peptide synthesis, but some problems can arise due to racemisation (4F-Phg, 4CF3-Phg), steric hindrance of coupling (F3-Aib) or HF elimination (fluoro-Ala, F3-Ala). 4F-Phg is additionally problematic due to an ambiguity of the side-chain rotamer. The preferred 19F-labels for ssNMR structure analysis are CF3-Bpg and CF3-Phg (as suitable substitutes for Leu, lie, Met, Val and Ala), as well as F3-Aib and CF3-MePro...

Wadhwani P, Strandherg E (2009) Structure analysis of membrane-active peptides using 19F-labeled amino acids and solid-state NMR. In Ojima I (ed) Fluorine in medicinal chemistry and chemical biology. Wiley, Chichester, pp 463-493... 

Wadhwani P, Tremouilhac P, Strandberg E, Afonin S, Grage S, Ieronimo M, Berditsch M, Ulrich AS (2007) Using fluorinated amino acids for structure analysis of membrane-active peptides by solid-state 19F-NMR. In Soloshonok V, Mikami K, Yamazaki T, Welch JT, Honek J (eds) Current fluoroorganic chemistry (ACS symposium series). American Chemical Society, Washington, pp 431 146... 

Afonin S, Glaser RW, Berditchevskaia M, Wadhwani P, Guhrs KH, Mollmann U, Pemer A, Ulrich AS (2003) 4-Fluorophenylglycine as a label for F-19 NMR structure analysis of membrane-associated peptides. ChemBioChem 4 1151-1163... 

Afonin S, Mikhailiuk PK, Komarov IV, Ulrich AS (2007) Evaluating the amino acid CF3-bicyclopentylglycine as a new label for solid-state F-19-NMR structure analysis of membrane-bound peptides. J Pept Sci 13 614-623... 

Afonin S, Durr UHN, Wadhwani P, Salgado J, Ulrich AS (2008) Solid state NMR structure analysis of the antimicrobial peptide gramicidin S in lipid membranes concentration-depen-dent re-alignment and self-assembly as a beta-barrel. Top Curr Chem 273 139-154... 

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