Long-range NOE

Eor a macromolecule such as a large protein, the steps in characterization involve, first, identification of the spin systems present, using correlated spectroscopy, and identification of neighboring amino acids. The long range noes are then assigned, and three bond coupling constants ate deterrnined. 

Fig. 2. 32 Parallel hairpin formation in a j3-peptide by incorporation of a D-Pro-DADME turn segment [195]. Summary of the long-range NOE observed by NMR in CD3OH which is consistent with a hairpin conformation together with the structure of 123 in the...

What conclusions can be drawn from the paucity of long-range NOEs is not clear. Whereas two protons must be separated by a short distance (<5 A) to give rise to an NOE, they must also retain a relatively fixed spatial relationship for 1 ns or longer. Therefore, extensive contact between widely separated chain segments would go undetected if such structure were highly dynamic, with contacts lasting only 10-100 ps. 

Because of the intrinsic flexibility and poor resonance dispersion of unfolded and partly folded proteins, long-range NOEs are generally very difficult to observe and assign. While observation of a long-range NOE between two protons provides a definitive indication that they are in close proximity in at least some structures in the conformational ensemble, determination of the nature of the folded structures is difficult unless an extensive network of NOEs can be observed. This has so far been achieved in only one case (Mok et al., 1999). 

The helix-turn-helix scaffold is designed to dimerize into a four-helix bundle. Modification of the peptide with the nicotinoyl functionality did not significantly perturb the peptide structure. CD spectroscopy showed no loss in helici-ty from the parent peptide and NMR spectroscopy confirmed successful incorporation of the nicotinoyl group as well as maintenance of crucial NOE connectivities. In particular, the presence of long-range NOE signals between the side chains of phenylalanine 38 and leucine 12 or isoleucine 9, which lie near the C- and AT-termini, respectively, demonstrate that the supersecondary structure of the motif has been conserved. 

Fig. 5. The aromatic cluster of the hydrophobic core of GTD-43, a helrx-loop-helrx dimer, and some of the assigned long-range NOEs that demonstrate the interactions of the aromatic side chains in the folded motif The formation of aromatic clusters has been observed in several designed proteins. Reproduced with permission from J Am Chem Soc (1997) 119 8598. ( 1997 ACS)...

An NMR structure determination has also been reported of a helix-loop-helix motif where the fold is controlled by the formation of an intramolecular disulfide bridge. The long-range NOEs were limited to residues in close proxi-... 

Solution structures of RNA and DNA are more difficult to determine, compared to those of proteins, due to the lack of medium and long range NOEs. Long range constraints can be provided by the pseudocontact shifts obtained in the presence... 

Figure 8. Key long range nOe correlations of patellamide C in CDCI3...

We recently characterized undecamer 6 using NOESY (Fig. 10), which revealed numerous amide-side chain NOEs that were fully consistent with a three-center hydrogen bond rigidified backbone [52]. Three sets of long-range NOEs (indicated in Fig. 10a), which were not detected in the NOESY spectrum of a hexamer that was about half of 6, suggest that 6 did indeed adopt a helical conformation. 

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