Refinement of protein crystal structure

Yu N, Yennawar H, Merz KM Jr (2005) Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. Acta Crystallogr D Biol Crystallogr 61 322-332... 

Pellegrini, M., Gronbech-Jensen, N., Kelly J. A., Pfluegl, G., and Yeates, T. O. (1997) Highly constrained multiple-copy refinement of protein crystal structures. Proteins 29, 426-432. 

The electron density distribution for solvent molecules can be improved if the contribution from bulk water to the X-ray scattering is included in the model. This affects the low-angle j X-ray intensity data which are omitted in early stages of the least-squares refinement of protein crystal structures. If they are included in refinement and properly accounted for, the signal-to-noise ratio in the electron density maps is significantly improved and the interpretation of solvent sites is less ambiguous. 

Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr (2007) Ensemble refinement of protein crystal structures validation and application. Structure 15 1040-1052... 

Rice, P.A., Sosnick, T.R., and Freed, K.F. (2011) Automated real-space refinement of protein crystal structures... 

The information obtained from X-ray measurements on the arrangement of the water molecules naturally depends very much on the resolution and state of refinement of the crystal structure investigated. For detailed information on the organization of water molecules in the protein hydration shell at the surface and on the bulk water in the crystals a 1,2 to 1,8 A resolution range is necessary 153>. 

The trouble with this method of least squares is that the result of the refinement may be a local rather than global minimum. Therefore it is common to refine a protein crystal structure by use of molecular dynamics. This means that each atom is assigned a velocity, and equations of motion are solved under the restraints of X-ray information. The assigned velocities, while initially corres-... 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

Yu N et al (2006) Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Protein Sci 15(12) 2773-2784... 

Steinbacher, S., Miller, S., Baxa, U., Budisa, N., Weintraub, A., Seckler, R., and Huber, R. (1997). Phage P22 tailspike protein Crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage. J. Mol. Biol. 267, 865-880. 

Of great interest to the molecular biologist is the relationship of protein form to function. Recent years have shown that although structural information is necessary, some appreciation of the molecular flexibility and dynamics is essential. Classically this information has been derived from the crystallographic atomic thermal parameters and more recently from molecular dynamics simulations (see for example McCammon 1984) which yield independent atomic trajectories. A diaracteristic feature of protein crystals, however, is that their diffraction patterns extend to quite limited resolution even employing SR. This lack of resolution is especially apparent in medium to large proteins where diffraction data may extend to only 2 A or worse, thus limiting any analysis of the protein conformational flexibility from refined atomic thermal parameters. It is precisely these crystals where flexibility is likely to be important in the protein function. 

In the X-ray analysis of a protein crystal structure, solvent molecules appear as spheres of electron density in difference Fourier maps calculated at the end of a refinement. In a strict sense, the electron density map exhibits preferred.s/tes of hydration which are occupied by freely interchanging solvent molecules. This electron density is well defined for the tightly bound solvent molecules and can be as spurious as just above background for ill-defined molecules which exhibit large temperature factors and/or only partly occupied atomic positions. Since these two parameters are correlated in least-squares refinement, this gives rise to methodological problems. 

R.B. Von Dreele, Combined Rietveld and stereochemical restraint refinement of a protein crystal structure, J. Appl. Cryst. 32, 1084 (1999). 

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