Crystallographic B-factors

The relative molecular dynamics fluctuations shown in Figure 7-17 can be compared with the crystallographic B-factors, which are also called temperature factors. The latter name, especially, indicates the information content of these factors they show how well defined within the X-ray structure the position of an atom is. Atoms with high temperature have an increased mobility. In principle, this is the same information as is provided by the molecular dynamics fluctuations. Using Eq. (48), the RMS fluctuation of an atom j can be converted into a B-factor... 

The crystal structures of four chlorinated derivatives of di-benzo-p-dioxin have been determined by x-ray diffraction from diffractometer data (MoKa radiation). The compounds, their formulae, cell dimensions, space groups, the number of molecules per unit cell, the crystallographic B.-factors, and the number of observed reflections are given. The dioxin crystal structures were performed to provide absolute standards for assignment of isomeric structures and have been of considerable practical use in combination with x-ray powder diffraction analysis. 

Figure 4. The dynamics of. EcaL-ASNase. A plot of the crystallographic B-factors along the polypeptide chain obtained from the crystal structure of E. carotovora L-asparaginase, (PDB code 1ZCF). The plot was produced by WF1AT IF software package (Barrow, 1973 Vriend, 1990). The height at each residue position indicates the average B-factor of all atoms in the residue.

Powers, R., Clore, G. M., Garrett, D. S., and Gronenbom, A. M. (1993). Relationships between the precision of high-resolution protein NMR structures, solution-order parameters, and crystallographic B factors, J. Mag. Res., BlOl, 325-327. 

We used principal component analysis to identify correlated motions in different forms of hPNP, namely, its apo and complexed forms, and assess whether they facilitate the 241-265 loop rearrangement prior to the subsequent phosphorolysis reaction. We compared the principal components for the apo and complexed hPNP simulations, and examined the different correlated motions for each form of the enzyme, comparing directly to the crystallographic B-factors. Finally, via experimental site-directed mutagenesis, several residues implicated in the correlated motion were mutated, and the kinetic constants kcat and KM (fingerprints of catalytic efficiency), were measured to weigh the impact of these residues in the phosphorolytic efficiency. 

Clore GM, Schwieters CD (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein a unified picture of high probability, fast atomic motions in proteins. J Mol Biol 355(5) 879-886... 

Figure 10. Distribution of crystallographic B factors averaged over the residues of the RNA dodecamer with UUCG internal loop. Larger B factors indicate regions of greater average mobility or flexibility.

Finally, we note that low-temperature crystallographic studies have been carried out on one nucleic acid, the 5-DNA dodecamer whose room-temperature structure was solved in Dickerson s laboratory (Dickerson, 1981). Refinement at 16 K revealed a large overall drop in B, but some of the atoms in the molecule still had very large B-factors even at this very low temperature. These large residual mean-square displacements were interpreted as demonstrating the presence of static disorder however, by analogy with the results on myoglobin, a disorder which is dynamic at room temperature but becomes frozen into a static distribution at low temperature is also consistent with the observations. It is also possible that the disorder in these atoms is dynamic even at 16 K this point has been considered by Hartmann et al. (1982). 

It has been found out that the structure of proteins is flexible and there are many differences between the static spatial image of a protein and a dynamic view of its structure. This divergence is caused by the fact that the repetitive part of a-helices and [3-strands of protein folds, often described as a succession of secondary structures, can assume different local spatial orientation. Two experimental methods can be used to measure the flexibility in precise regions of protein structures (the anatomic mean square displacement, B-factor, measured during crystallographic experiments, and indirectly by NMR experiments which show different local conformation that could correspond directly to different stages of protein structures) (Bornot et al., 2007). 

Table 24.3. Mean crystallographic temperature factors B (A2) for base, sugar and phosphate atoms in the DNA dodecamer d(CGCGAATTCGCG) investigated under different conditions [867]. The mean vibrational amplitudes fi are obtained according to B = 8 n2fi2 ...

Unfortunately, fantasy atoms are often found in crystallographic structures with frill occupancy values, low or medium B-factors, or unmarked as multiple alternatives. Combined with the ambiguities... 

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