Temperature factor studies

Three factors influence the rate of corrosion of metals—moisture, type of pollutant, and temperature. A study by Hudson (1) confirms these three factors. Steel samples were exposed for 1 year at 20 locations throughout the world. Samples at dry or cold locations had the lowest rate of corrosion, samples in the tropics and marine environments were intermediate, and samples in polluted industrial locations had the highest rate of corrosion. Corrosion values at an industrial site in England were 100 times higher than those found in an arid African location. 

In summary, there are three important generalizations about error estimation in protein crystallography. The first is that the level of information varies enormously as a function primarily of resolution, but also of sequence knowledge and extent of refinement. The second generalization is that no single item of information is completely immune from possible error. If the electron density map is available or indicators such as temperature factors are known from refinement, then it is possible to tell which parameters are most at risk. The third important generalization is that errors occur at a very low absolute rate 95% of the reported information is completely accurate, and it represents a detailed and objective storehouse of knowledge with which all other studies of proteins must be reconciled. 

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). 

Kagawa and Toyama in Tokyo followed 20 normal 11-yr-old school children once a week from June to December 1972 with a battery of pulmonary-function tests. Environmental factors studied included oxidant, ozone, hydrocarbon, nitric oxide, nitrogen dioxide, sulfur dioxide, particles, temperature, and relative humidity. Temperature was found to be the most important environmental factor affecting respiratory tests. The observers noted that pulmonary-function tests of the upper airway were more susceptible to increased temperature than those of the lower airway. Although the effect of temperature was the most marked, ozone concentration was significantly associated with airway resistance and specific airway conductance. Increased ozone concentrations usually occur at the same time as increased temperature, so their relative contributions could not be determined. 

Finally, yet another issue enters into the interpretation of nonlinear Arrhenius plots of enzyme-catalyzed reactions. As is seen in the examples above, one typically plots In y ax (or. In kcat) versus the reciprocal absolute temperature. This protocol is certainly valid for rapid equilibrium enzymes whose rate-determining step does not change throughout the temperature range studied (and, in addition, remains rapid equilibrium throughout this range). However, for steady-state enzymes, other factors can influence the interpretation of the nonlinear data. For example, for an ordered two-substrate, two-product reaction, kcat is equal to kskjl ks + k ) in which ks and k are the off-rate constants for the two products. If these two rate constants have a different temperature dependency (e.g., ks > ky at one temperature but not at another temperature), then a nonlinear Arrhenius plot may result. See Arrhenius Equation Owl Transition-State Theory van t Hoff Relationship... 

Early studies, which did not include many high-order reflections, revealed systematic differences between spherical-atom X-ray- and neutron-temperature factors (Coppens 1968). Though the spherical-atom approximation of the X-ray treatment is an important contributor to such discrepancies, differences in data-collection temperature (for studies at nonambient temperatures) and systematic errors due to other effects cannot be ignored. For instance, thermal diffuse scattering (TDS) is different for neutrons and X-rays. As the effect of TDS on the Bragg intensities can be mimicked by adjustment of the thermal parameters, systematic differences may occur. Furthermore, since neutron samples must be... 

The electron diffraction study was complemented by an all-electron theoretical calculation of Lu, Wei, and Zunger (LWZ) (1992), using the local density approximation for the exchange and correlation terms in the Hamiltonian. They find agreement within x0.6% between the calculated and dynamic structure factor values for the lowest three reflections, (100), (110), and (111). But for (200), with sin 0/A = 0.3464 A-1, the discrepancy is as large as 1.7%. The discrepancy is attributed to insufficiently accurate knowledge of the temperature factors in this diatomic crystal, which affect the derivation of the X-ray structure factor from the electron diffraction measurement, as well as the calculation of the dynamic theoretical structure factors needed for the comparison with experiment. For the monoatomic Si crystal for which the B values are well known, the agreement is... 

A further result of this analysis, as shown in Fig. 4, is that while the relative spectral intensities are determined by the individual site f-factors, the temperature dependence of all the sub-spectra together in the temperature range studied is determined by the motion of the center of mass of the whole Auj, cluster. This can be seen by the uniform decrease of the total intensity with increasing temperature, without any visible change in the general shape of the spectrum. In effect, this means that the f-factors for the individual sites must be multiplied by an f-factor due to the motion of the whole particle [24]. See also Refs. [95,96,97], where this concept was originally developed. The use of such an inter-cluster f-factor, in addition to the usual intra-cluster f-factor, also resolved the problem of the apparent deficiency in the total f-factor at 1.25 K when compared to bulk gold. 

The effect of reaction temperature was studied in some detail, and its role in the formation of the primary reactions as opposed to the side reactions was determined. At reaction temperatures lower than 80°C. the reaction is slower by a considerable factor, especially when compared with the reaction carried out at, say, 50°C. At higher temperatures, the side reactions are favored and the most prevalent side reactions which occur are those illustrated in Figure 1 as numbers 3 and 6. 

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