Three-dimensional spectroscopy protein structure determination

Oschkinat H, Muller T and Dieckmann T 1994 Protein structure determination with three- and four-dimensional spectroscopy Angew. Chem. Int. Ed. Engl. 33 277-93... 

G. M. Clore and A. M. Gronenborn, Prog. NMR Spectrosc., 23, 43 (1991). Applications of Three- and Four-Dimensional Heteronudear NMR Spectroscopy to Protein Structure Determination. 

A crucial question is. What does the three-dimensional structure of a specific protein look like Protein structure determines function, given that the specificity of active sites and binding sites depends on the precise threedimensional conformation. Nuclear magnetic resonance spectroscopy and x-ray crystallography are two of the most important techniques for elucidating the conformation of proteins. 

Clore GM and Gronenborn AM (1991) Application of three- and four-dimensional heteronuclear NMR spectroscopy to protein structure determination. Progress in NMR Spectroscopy 26 43. 

Clore, G.M., Gronenborn, A.M. Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magetic resonance spectroscopy. CRC Crit. Rev. Biochem. 24 479-564, 1989. 

NOESY NMR spectroscopy is a homonuclear two-dimensional experiment that identifies proton nuclei that are close to each other in space. If one has already identified proton resonances in one-dimensional NMR spectroscopy or by other methods, it is then possible to determine three dimensional structure through NOESY. For instance, it is possible to determine how large molecules such as proteins fold themselves in three-dimensional space using the NOESY technique. The solution structures thus determined can be compared with solid-state information on the same protein obtained from X-ray crystallographic studies. The pulse sequence for a simple NOESY experiment is shown in Figure 3.23 as adapted from Figure 8.12 of reference 19. 

In de novo three-dimensional structure determinations of proteins in solution by NMR spectroscopy, the key conformational data are upper distance limits derived from nuclear Overhauser effects (NOEs) [11, 14]. In order to extract distance constraints from a NOESY spectrum, its cross peaks have to be assigned, i.e. the pairs of hydrogen atoms that give rise to cross peaks have to be identified. The basis for the NOESY assignment... 

Aside from the direct techniques of X-ray or electron diffraction, the major possible routes to knowledge of three-dimensional protein structure are prediction from the amino acid sequence and analysis of spectroscopic measurements such as circular dichroism, laser Raman spectroscopy, and nuclear magnetic resonance. With the large data base now available of known three-dimensional protein structures, all of these approaches are making considerable progress, and it seems possible that within a few years some combination of noncrystallo-graphic techniques may be capable of correctly determining new protein structures. Because the problem is inherently quite difficult, it will undoubtedly be essential to make the best possible use of all hints available from the known structures. 

Even though these approaches are powerful methods for determining functional sites on proteins, they are limited if not coupled with some form of structural determination. As Figure 2 illustrates, molecular biology and synthetic peptide/antibody approaches are not only interdependent, they are tied in with structural determination. Structural determination methods can take many forms, from the classic x-ray crystallography and NMR for three-dimensional determination, to two-dimensional methods such as circular dichroism and Fourier Transformed Infrared Spectroscopy, to predictive methods and modeling. A structural analysis is crucial to the interpretation of experimental results obtained from mutational and synthetic peptide/antibody techniques. 

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