Three-dimensional spectroscopy proteins

The use of three-dimensional spectroscopy involving chemical shift/ H- N dipolar coupling/ N chemical shift correlation has been shown to improve spectral resolution in studies of membrane proteins with helices aligned parallel to the membrane surface. Such a measurement on the antibiotic peptide magainin enabled the three-dimensional orientation of this helical peptide to be determined in the lipid bilayer. The orientation of the insect antiobiotic peptide cecropin A in the phospholipid bilayer membrane has been determined using solid-state NMR spectroscopy and the result discussed in relation to the mechanism of action of the peptide. ... 

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... 

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. 

Ikura M, Kay LE, Tsudin R, Bax A. Three-dimensional NOESY-HMQC spectroscopy of a 13C-labelled protein. J Magn Reson 1990 86 204-209. 

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. 

The main advantage of NMR spectroscopy is its use with proteins in solution. In consequence, rather than obtaining a single three-dimensional structure of the protein, the final result for an NMR structure is a set of more or less overlying structures which fulfill the criteria and constraints given particularly by the NOEs. Typically, flexibly oriented protein loops appear as largely diverging structures in this part of the protein. Likewise, two distinct local conformations of the protein are represented by two differentiated populations of NMR structures. Conformational dynamics are observable on different time scales. The rates of equilibration of two (or more) substructures can be calculated from analysis of the line shape of the resonances and from spin relaxation times Tj and T2, respectively. 

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. 

Native monellin consists of two polypeptide chains, a 45-residue A-chain and a 50-residue B-chain, linked by non-covalent interactions. At neutral pH, it is fairly resistant to heat denaturation with a higher than 80 °C. The crystal structure of native monellin shows a tertiary structure comprising an anti-parallel /1-sheet with five strands and an a-helix. H NMR spectroscopy and hydrogen exchange methods have been used to characterize the alcohol-denaturated state of monellin in order to understand how its secondary structure depends on environmental conditions. " Structural and dynamic studies by NMR have been carried out in order to compare native monellin and a non-sweet analogue in which Asp was replaced by Abu . The three-dimensional structures of the two proteins are found to be very... 

Although small in size, the conotoxins contain many of the structural elements present in larger proteins, including a-helices, -sheets and fl-turns, hence, they are often referred to as mini-proteins. Their relative ease of synthesis allows accurate three-dimensional structures to be obtained using techniques such as X-ray crystallography and NMR spectroscopy. 

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