Neutron protein crystallography

The Determination of Structural Water by Neutron Protein Crystallography... 

Myles, D.A.A. (2006) Neutron protein crystallography current status and a brighter future. Current Opinion in Structured Biology, 16, 630-637. 

Niimura. N. Minezaki. Y. Nonaka. T. Castagna. J.C. Cipriani, E. Hoghoj, P. Eehmann. M.S. Wilkinson. C. Neutron Eaue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat. Struct. Biol. 1997. 4. 909-914. 

The mechanism by which serine peptidases, particularly serine endopep-tidases (EC 3.4.21), hydrolyze peptide bonds in peptides and proteins has been extensively investigated by X-ray crystallography, site-directed mutagenesis, detection of intermediates, chemical modification, H-NMR spectroscopy, and neutron diffraction [2-14], These studies revealed that all serine peptidases possess a catalytic triad, composed of a serine, a histidine, and an aspartate residue, and a so-called oxyanion hole formed by backbone NH groups. 

Kossiakoff AA (1985) The application of neutron crystallography to the study of dynamic and hydration properties of proteins. Annu Rev Biochem 54 1195-1227... 

Small-angle neutron scattering (SANS) yields much weaker data than SAXS, but the ease with which, at low resolution, the contrast of a particular chemical species within the virus such as lipid, nucleic acid, or protein can be suppressed by adjusting the ratio of H2O H2O to match the mean scattering of that component means it can, for example, be useful in determining their radial distributions. However, it should be noted that methods have now been developed that yield this kind of information with improved resolution from cryo-EM maps (Spahn et at, 2000, 2001) (and indeed X-ray crystallography maps J. M. Diprose, J. M. Grimes, and D. I. Stuart, unpublished data). 

As with any protein simulation, the nature and limitations of the structural solutions for proteins provided by X-ray crystallography should always be borne in mind [125]. One obvious point is that hydrogen atoms are generally not observed because of their low electron density (neutron diffraction experiments can be useful to overcome this problem), and so it can be difficult to assign protonation states unambiguously, and to decide between possible rotamers or tautomers. This, and other factors such as model bias (for example in a molecular replacement solution), or simple error in construction of a model, may lead to the structural model being incomplete or incorrect in some places. 

This model was established by Chen and Schoenbom when identifying water molecules and ions in a crystal of CO myoglobin protein by combining neutrons and x-ray crystallography. The surface structure exhibits 85 water molecules and 5 ions while the access path of the CO to the heme is devoid of bound water. Thus there is a subtle interplay between the hydrophilic and hydrophobic phenomena that control the stability of the folded state. 

The 3D structure of proteins is also determined by neutron diffraction. A protein crystal is exposed to the neutron beam, and the position of atoms in a protein is determined by the scattered neutron. Unlike X-ray diffraction, the neutron is scattered by the nucleus of the atom and not by electron therefore, this method yields a different kind of picture at the atomic level than X-ray crystallography. Only a small number of proteins have been analyzed by neutron scattering. One major problem of this method is that only a handful of neutron scattering devices are available in the world. Thus, fewer than a dozen proteins have been analyzed at the atomic level by this method. 

The advent of white neutron sources, before SR facilities, stimulated the use of multiple wavelength techniques and several structures were solved in this way (table 9.3 from Ramaseshan and Narayan (1981)). The technique is limited to only a few nuclei (unlike the ubiquity of X-ray absorption edges) such as 113Cd, H9Sm, 151Eu and 157Gd. The low flux of neutron sources has restricted their use in protein crystallography. 

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