Structure Determination by NMR

The upper size limitation for complete structure determination is not well defined. Structures of proteins that are less than 30 kDa should be obtainable by NMR methods. However, it is certainly possible to obtain some degree of structural information on much larger proteins (e.g., 30-80 kDa). The five different types of constraints that are commonly used in structure determination by NMR spectroscopy are listed below. The first two are the most common forms of constraints for the generation of structures from the NMR data. 

In the case of partially deuterated proteins, the number of available distance constraints is reduced due to the presence of the deuterons. Consequently, it is usually only possible to measure inter-proton distances between amide protons as well as the distance between amides and methyl protons. In the case of fully deuterated proteins, it is only possible to measure inter-proton distances between amides. Although these distances are more accurate in deuterated proteins they are insufficient in number to produce a reasonably high-resolution structure. 

The amount of time required to complete a structure by NMR spectroscopy is difficult to estimate. The assignment of peaks in the various NOESY spectra may require 1 to 3 months, depending on the degree of automation utilized. The actual 

---

Figure 3 Model building by Modeller [31], First, spatial restraints in the form of atomic distances and dihedral angles are extracted from the template stmcture(s). The alignment is used to determine equivalent residues between the target and the template. The restraints are combined into an objective function. Finally, the model for the target is optimized until a model that best satisfies the spatial restraints is obtained. This procedure is technically similar to the one used in structure determination by NMR.

EXAFS data are in agreement with the structure determined by NMR with two carbons at relatively short distances (not resolved at 1.79 A), corresponding to the (= CHtBu) and (= CtBu) ligands, another carbon and an... 

K. Wuthrich, Six years of protein structure determination by NMR spectroscopy What have we learned in Protein Conformation. Ciba Foundation Symposium 161, John Wiley Sons, Chichester, 1991, pp. 136-149. 

Saaby S, Knudsen KR, Ladlow M, Ley SV (2005) The Use of a Continuous Flow-Reactor Employing a Mixed Flydrogen-Liquid Flow Stream for the Efficient Reduction of Imines to Amines. Chem Commun 23 2909-2911 Seebach D, Overhand M, Kilhnle FNM, Martinoni D, Oberer L, Hommel U, Widmer H (1996) Beta-Peptides Synthesis by Arndt-Eistert Homologation with Concomitant Peptide Coupling. Structure Determination by NMR and CD Spectroscopy and by X-ray Crystallography. Helical Secondary Structure of a Beta-Hexapeptide in Solution and its Stability Towards Pepsin. Helv Chim Acta 79 913-941... 

Figure 1 Peptide pheromone structures determined by NMR. (a) Structure of peptide pheromone (PinA) from Lactobacillus plantarum required for piantaricin biosynthesis. (b) Structure of peptide pheromone (ComC) from Streptococcus pneumonia required for competence deveiopment. ...

Duus J0, Gotfredsen CH, Bock K (2000) Carbohydrate Structural Determination by NMR Spectroscopy Modem Methods and Limitations. Chem Rev 100 4589 Agrawal PK, Pathak AK (1996) Nuclear Magnetic Resonance Spectroscopic Approaches for the Determination of friterglycosidic Linkage and Sequence in Oligosaccharides. Phytochem Anal 7 113... 

Novel biomarkers, i.e. tracer derivatives from unknown natural products, are sometimes encountered in geological or environmental samples, typically as hydrocarbons. The detection and determination of these compounds are usually based on the interpretation of mass spectra in GC-MS analyses. The proofs of chemical structures are based on the proposed interpretation of the MS data, separation and purification of the unknown compounds, exact structure determination by NMR methods or X-ray crystallography (if the compound is a solid that can be crystallized), and finally, comparison with a synthetic standard. The next question concerns the biological source of the biomarker precursor compound. Many biomarkers still have no proven natural product precursors nor known biological sources (e.g. perylene, tricyclic terpanes). " ... 

Piperidines (629) can be made from butadienes and benzaldimines, by use of palladium(II) nitrate and triphenylphosphine in DMF for the case where R1 = Me, R2 = Ph, four stereoisomers were isolated by GLC and the structures determined by NMR, the major products being (2r,3-trans-6-cis) (45% of total isomers), and (2r,3-cis-6-cis) (40%) (74CC506). 

NMR spectroscopy has proven to be an invaluable tool in structure determination of hydrogenated fullerenes ever since the first synthesis of C60H36 (Haufler et al. 1990) and the first structure determination by NMR was reported for C60H2 by Henderson and Cahill in 1993 (Henderson and Cahill 1993). Today, a multitude of both one- and two-dimensional NMR experiments are available for this purpose. Recent developments in NMR technology with higher magnetic field strengths and cryoprobes have dramatically increased the sensitivity and improved the usefulness of NMR in this field even further. 

Further addition of Br2 to the double bond is not observed. The compounds were isolated and their structures determined by nmr and mass spectrometry35. ... 

The present suitability and versatility of NMR to study macromolecules has been made available, among others, by the pioneering work of Nobel laureates Richard R. Ernst and Kurt Wiithrich (Nobel Prize in Chemistry, 1991 and 2002). The established protocol of structure determination by NMR consists of the... 

Although in the past years, significant progress has been made in generating dynamically relevant ensembles, these methods are still not used widely used. Such calculations require efforts beyond the current routine of protein structure determination by NMR both from the experimental side, as heteronuclear relaxation and /or... 

The same computational methodology is also applicable to the refinement of structures determined by NMR spectroscopy.241... 

---