Backbone torsion angles

Examination of the backbone torsion angles in a number of crystal stractures of /9-alanine-containing peptides reveals that the conformation around the C(a)-C(/9) bond of /9-alanine residues is essentially gauche or trans (anti) with values close to 60° or 180°, respectively [158]. Populating the gauche conformation of /9-ami-... 

Examination of the backbone torsion angles in the crystal structure of 101 (Tab. 2.6) shows that for residues 1-7, the 9 value is between -87.8 and -113.3° with a mean value of -96 ° (the somewhat larger 9 value for residue 8 is mainly due to fraying of the hehx at the C-terminus). 

Tab. 2.7 Comparaison of selected backbone torsion angles for strand segments in antiparallel sheet-forming jff-peptides 117-119, 121, 122 [109, 154, 191-194]...

As a consequence of their different turn geometry a 10-membered turn closed by H-bonds between NH and C=0 +i and a 12-membered turn closed by Id-bonds between C=0 and NH +3, antiparallel hairpins formed by y9-peptides 121 and 122 display opposite sheet polarities (see Fig. 2.30A and B). Comparison of backbone torsion angles (X-ray and NMR) for selected y9-amino acids residues within extended strand segments of peptides 117-122 are shown in Tab. 2.7. The observed values are close to ideal values for y9-peptide pleated sheets =-120° (or 120°), 01 = 180°, (/ =120°(or-120°). 

Tab. 2.8 Comparison of selected backbone torsion angles characteristic of the y-peptide 2.5-heli-cal backbone extracted from NMR solution structure of y -hexapeptide 141 and solid-state structure of y -tetrapeptide 146 [200, 205, 207]...

Several mathematical techniques have been used to obtain atomic coordinates for nucleic acid structures. They incorporate several different approaches. (a) Systematic rotations about all backbone torsional angles are performed and those conformations which form helicies and have adjacent bases parallel or in a given orientation are selected (59 6o). (b) Least squares techniques are used to re-... 

The molecular structure of the amyloid fibrils formed by fragment 105-115 of transthyretin (TTR10sns, YTIAALLSPTS) has been characterized by solid-state NMR. The fibril backbone structure was first established based on the TALOS analysis of the 15N and 13C chemical shifts [89]. Using the correlation experiments of Hn(0-N(0—CV-H0 , Ha(0-Ca(0-N(i.+1)-HN(i+1), and N -Tco-N, a total of 41 constraints on 19 backbone torsion angles have been obtained in a... 

Figure 2.5 Maps of absolute value of unit twist t as function of backbone torsion angles 0, and 62 for (a) isotactic and (b) syndiotactic polymers.27 Curves corresponding to t = 180°, 160°, 140°, 120°, 100° are reported. (Reproduced with permission from Ref. 27. Copyright 1992 by the Society Chimica Italiana.)...

Calculations of the conformational energy are performed according to the equivalence principle and, as a consequence, a succession of backbone torsion angles. .. 0i020i 20i 2- is generally assumed for isotactic polymers. 

Figure 2.10 Maps of conformational energy of various isotactic polymers as function of backbone torsion angles 0i and 02 (a) Isotactic polystyrene, (b) polypropylene, (c) poly(l-butene), and (d) poly(4-methyl-l-pentene). Succession of torsion angles. .. 0i020i02 [s(M/N) symmetry] has been assumed. Isoenergetic curves are reported every 10 (a,c,d) or 5 (b) kJ/mol of monomeric units with respect to absolute minimum of each map assumed as zero.

Figure 2.14 Maps of conformational energy as function of backbone torsion angles 9i and 02 of a chain of isotactic poly((S)-3-methyl-l-pentene) for (a,b) left-handed helix and (c) right-handed helix.29 For each pair of Oi and 02, reported energy corresponds to minimum obtained by varying torsion angles of lateral group 03 and 04. Curves are reported at intervals of 0.5 kcal/mol of monomeric unit. Values of energies corresponding to minima are also indicated. (Reprinted with permission from Ref. 29. Copyright 1976 by Elsevier Science.)...

Fig. 16.6 Theoretical curves of the dipole-dipole CCR rate and the di-pole-CSA CCR rate as a function of the peptide backbone torsion angle y/. The sterically allowed regions are indicated by a gray background.

Recently, we studied by trNOE and trCCR the interaction of a peptide derived from lKKj8 which is reported to interact with NEMO by trNOE and trCCR. The experimental data as well as the strategy to obtain the backbone torsion angles of this peptide is presented here in detail. 

Fig. 5 Dependence of the CCR-rates on the peptide backbone torsion angles //(N-Ca-C -N) and 0(C -N-Ca-C ). The thin curve corresponds to the dipole-CSA CCR-rate (/nhc )> the thick curve to the dipole-dipole CCR-rate (Fnhch) [9] and the grey curve to the dipole-dipole CSA-rate (Thnnhnhq ) [47]. The allowed regions for and (j> are indicated a indicates a-helix, ar is left-handed helix, f) is /3-sheet...

A suitable CCR-rate to determine the backbone torsion angle 0 by CCR is the /NHCHcf dipole-dipole CCR-rate that conveniently can be measured by an HNCA-derived experiment [44]. Alternatively, like for the torsion angle 0, the FcuaCii-i) dipole-CSA CCR can be measured by a triple-resonance experiment that is derived from a combination of HNCA and HNCO experiments [45]. Also, CCR experiments for which the rate depends on 0 and

dipole-dipole CCR experiment can be used [46]. Unfortunately for the peptide under investigation, we were not able to successfully record any of these spectra, possibly due to the relatively strong auto relaxation. 

Using 18 trNOE-derived distance restraints and 13 trCCR-derived backbone torsion angle restraints, structure calculations using distance geometry and simulated annealing [48] resulted in a well-defined structure of the IKK/1-derived peptide bound to NEMO. The backbone structure is displayed in Fig. 7B and is compared with the result of the calculation carried out using the trNOE-derived distance restraints alone. It is obvious from Eig. 7 that only the combination of the trNOE- and trCCR-derived restraints results in the structure elucidation of the bound conformation of this peptide. 

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