Peptide backbone, modeling

Fig. 39. (A) The ribbon diagram of subunit c and (B) peptide backbone model of a dodecameric ring of c-subunits of E. coli Fq viewd toward the membrane from the F, side. The C-terminal a-heiices are arranged in the inner ring and the N-terminal a-heiices in the peripheral ring. Residue Asp-61 located in the middle of the C-terminal sequence is indicated by a dot. Figure source (A) Fillingame, Girvin and Zhang (1995) Correlations of structure and function in subunit c of Escherichia coli FqF, ATP synthase. Biochem Soc Trans 23 763 (B) Groth and Walker (1997) Model of the c-subunit oligomer in the membrane domain ofF-A TPases. FEBS Lett 410 118.

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

However, all of these studies were performed using model components in vitro—none have examined formaldehyde-induced modifications in vivo. Further, while modification sites have been mapped by MS/MS, intact cross-linked peptide species have not been observed in such experiments.49 This possibly indicates that the covalent bonds of the formaldehyde cross-links are not as strong as those of the peptide backbone. The resulting fragment ion spectra are similar to that of the unmodified peptide with the exception of 12Da or 30Da additions at modifications sites. Thirty Dalton modifications correspond to the addition of formaldehyde while 12 Da modifications indicate water elimination. 

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...

Fig. 8. Peptide backbone structure of the designed triple-stranded monomeric /1-sheet Betanova in band and liquorice model representation, coordinates taken from high-resolution NMR structure [9]...

Peptide dithioesters have been used as model compounds to study the conformations of dithioacyl enzyme complexes. 1 3 Dithioesters are also used as thioacylating agents that introduce the thioamide bonds into the peptide backbone in order to study the structures of endothiopeptidesJ4,5 ... 

FIGURE 4. Molecular model of the peptide backbone of silicatein a (221 amino acid residues, constrained by three intramolecular disulfide cross-links), determined as described in the text. Locations of the putative catalytically active serine (at position 26) and histidine (at position 165) in juxtaposition on both sides of the active-site (substrate binding) cleft are identified. These features are very similar to those in the homologous protease (hydrolytic enzyme)... 

Relevant to the conflicting reports of copper versns nickel reqnirements for enzyme activity,biochemical stndies demonstrated the existence of a labile nickel associated with the a snbnnit of ACS/CODH. Very recently, model stndies on a metal-ion captnre of a peptide-backbone, nonlabile [MN2S2] (26) nnit have established the capability of snch a nickel dithiolate to bind exogeneons metals. A qualitative ranking of the binding ability of complex (26) with Zn +, Cn+, and Ni + was established by a metal-ion displacement experiment (Zn + < < Cn+), as shown in Scheme 9. ... 

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