Conformation, peptide

Simmerling C and R Elber 1995. Computer Determination of Peptide Conformations in Water Differei Roads to Stracture. Proceedings of the National Academy of Sciences USA 92 3190-3193. 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

The effect of C ,C -disubstituted amino acids (aaAAs) on peptide secondary structure has been studied in recent years.2a d While longer side-chain C ,C -di-n-alkyl amino acids promote extended peptide conformation,23 alicyclic aaAAs, in which the Ca carbon forms a cyclic bridge with itself, such a 1-aminocyclopentane-l-carboxylic acid (Ac5c) and 1-aminocyclohexane-l-carboxylic acid (Ac6c), have helix-forming characteristics similar to those of 1 -aminoisobutyric acid (Aib).2ax... 

The strange amino-acid (4) is a fat version of phenylalanine (5) having a side chain which is rigid and inert, but which is also space filling rather than flat. Optically active (4) was needed to study peptide conformation and the biological activity of drugs. 

The partial double-bond character of the bond that links the carbonyl carbon and the nitrogen of a peptide renders four atoms of the peptide bond coplanar and restricts the number of possible peptide conformations. 

Kessler, H. Peptide conformations. 19. Conformation and biological activity of cyclic peptides. Angew. Chem. Int. Ed. 

Kessler, H., Griesinger, C., Wagner, K. Peptide conformations. 42. Conformation of side chains in peptides using heteronudear coupling constants obtained by two-dimensional NMR spectroscopy. J. Am. Chem. Soc. 1987, 109, 6927-6933. 

PPII helix-forming propensities have been measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and T. P. Creamer (unpublished results). In the simulations the peptide backbone was constrained to be in the PPII conformation, defined as (0,VO = ( — 75 25°, +145 25°), using constraint potentials described previously (Yun and Hermans, 1991 Creamer and Rose, 1994). The AMBER/ OPLS potential (Jorgensen and Tirado-Rives, 1988 Jorgensen and Severance, 1990) was employed at a temperature of 298° K, with solvent treated as a dielectric continuum of s = 78. After an initial equilibration period of 1 x 104 cycles, simulations were run for 2 x 106 cycles. Each cycle consisted of a number of attempted rotations about dihedrals equal to the total number of rotatable bonds in the peptide. Conformations were saved for analysis every 100 cycles. Solvent-accessible surface areas were calculated using the method of Richmond (1984) and a probe of 1.40 A radius. 

Barone, V., F. Fratemali, and P. L. Cristinziano. 1990. Sensitivity of Peptide Conformation to Methods and Geometrical Parameters. A Comparative Ab Initio and Molecular Mechanics Study of Oligomers of a-Aminoisobutyric Acid. Macromolecules 23, 2038-2044. 

Perczel, A., J. G. Angyan, M. Kajtar, W. Viviani, J.-L. Rivail, J.-F. Marcoccia, and I. G. Csizmadia. 1991a. Peptide Models. 1. Topology of Selected Peptide Conformational... 

Perczel, A., W. Viviani, and I. G. Csizmadia. 1992. Peptide Conformational Potential Energy Surfaces and Their Relevance to Protein Folding in Molecular Aspects of Biotechnology Computational Models and Theories, Bertran, J., ed., Kluwer Academic Publishers, 39-82. 

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

Bartels, C. Karplus, M., Multidimensional adaptive umbrella sampling applications to main chain and side chain peptide conformations, J. Comput. Chem. 1997, 18, 1450-1462... 

Ytreberg, F. M. Zuckerman, D. M., Peptide conformational equilibria computed via a single-stage shifting protocol, J. Phys. Chem. B 2005,109, 9096-9103... 

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...

Protein structures are so diverse that it is sometimes difficult to assign them unambiguously to particular structural classes. Such borderline cases are, in fact, useful in that they mandate precise definition of the structural classes. In the present context, several proteins have been called //-helical although, in a strict sense, they do not fit the definitions of //-helices or //-solenoids. For example, Perutz et al. (2002) proposed a water-filled nanotube model for amyloid fibrils formed as polymers of the Asp2Glni5Lys2 peptide. This model has been called //-helical (Kishimoto et al., 2004 Merlino et al., 2006), but it differs from known //-helices in that (i) it has circular coils formed by uniform deformation of the peptide //-conformation with no turns or linear //-strands, as are usually observed in //-solenoids and (ii) it envisages a tubular structure with a water-filled axial lumen instead of the water-excluding core with tightly packed side chains that is characteristic of //-solenoids. 

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. 

H. Kessler K. Wagner M. Mill, Analysis of Peptides Conformation by NMR Spectroscopy. Proceedings of the 9th International Symposium on Medicinal Chemistry, Berlin, 1986 pp 143-157. 

These NMR structures reveal that the A isomer conforms to the design hypothesis, whereas the less regular peptide conformation of the A isomer forms an alternate structure. 

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