Biophysical data

Resonance Raman studies on the putative prismane protein would provide other important information. In the frequency region of 200-430 cm the putative prismane protein showed bands that at first sight seemed to be typical for Fe-S clusters, but at a closer look appeared to be broader than those observed in basic Fe-S proteins. Also, the resonance frequencies were slightly different from known Fe-S clusters, and it was contended that A prismane-type [6Fe-6S] core is clearly an excellent candidate in light of the available analytical and biophysical data [28]. 

Beechem, J. M. (1992). Global analysis of biochemical and biophysical data. Methods Enzymol. 210, 37-54. 

The primary choice in this assessment is whether to utilize a biochemical or biophysical screen as the primary filter. Although it seems like an either/or choice, this is a false dichotomy. The most successful fragment screens obtain orthogonal data, i.e. both biochemical and biophysical data in parallel or in quick succession. With orthogonal data, the probability of false positives (or negatives) is reduced. Most commonly biochemical and biophysical data are obtained. However, all the different biochemical and biophysical screens can be considered orthogonal. We would recommend that if two biophysical methods are to be used at least one should be a direct method (discussed below). As is noted many times in this book, rapid iterations among the various data sources are the key to a successful process. 

A pitfall of screening fragments by all biophysical methods, such as those already described, is that they do not reveal whether a fragment that is found to bind to a target protein has an effect on the normal function of the protein (see below). This is why biochemical data should be collected in parallel with biophysical data whenever possible. 

External Data to Back Up a Pharmacophore Model 15.2.4.1 Biophysical Data... 

Albeit very prudent, Ghose and Wendoloski suggested the use of a biophysical data source to determine the conformation of the free ligand as another means to validate a pharmacophore model [45]. After all, when one has no other data to start with, why would one discard it ... 

How do the models comply with external biophysical data ... 

Although the mechanisms of electroporation, electrofusion, and electroinsertion are not known, biophysical data suggest that the primary field pulse effect is interfacial polarization by ion accumulation at the membrane surfaces. The resulting transmembrane electric field causes rearrangements of the lipids such that pores are formed1718. Electropores anneal slowly (over a period of minutes) when the pulse is switched off. 

In both systems, membrane-bound ubiquinone plays crucial roles in the respiratory chain. Indeed, various quinones, including ubiquinone and menaquinone, are used to connect the redox reactions of various membrane proteins. In spite of the large amount of biochemical and biophysical data on quinone and quinone binding proteins, little structural... 

The structural data, together with a large number of biochemical, genetic and biophysical data, provide a detailed mechanistic and structural picture of how the various partners talk to each other and how the switch function of the heterotrimeric G proteins is to be explained. Only some of these points will be discussed in the following. 

Lapresle J, Duckett S, Galle P, et al [Clinical, anatomical and biophysical data on a case of encephalopathy with aluminum deposits]. C R Seances Soc Biol Fil 169 282-285, 1975... 

Strategies for the implementation of global analysis of biophysical data are described in detail elsewhere (159). However, it should be kept in mind that global analysis of an entire RSSF data set consisting of 100 or more spectra collected over a 250-nm wavelength region may become cumbersome due to the large number of data points, which must be processed. In some cases, it may be necessary to choose a subset of the data for simultaneous analysis. Secondly, relaxations that correspond to relatively fast processes may not be adequately determined due to limitations imposed by the time resolution (typically, 1-5 ms/ scan) of a RSSF experiment (162). 

---