Packing families/types

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

The styrene-divinylbenzene matrix of the Styragel packings is chemically very inert, which makes this family of packings useful for a broad range of applications. The chromatographic conditions for the analysis of many polymers have been worked out in detail. A more specific discussion of the solvents recommended for the different polymer types is included in Section III,A,4. 

Thin-layer chromatography (TLC) is a type of liquid chromatography in which the stationary pease is in the form of a thin layer on a flat surface rather than packed into a tube (column). It is a member of a family cf techniques that include some types of electrophoresis and paper chromatography, more generally referred to as planar chromatccraphy. Since we will not discuss electrophoresis in this section, and since TLC has virtually superseded paper chromategr pby in most analytical... 

Several cubic structures, therefore, in which (besides 0, 0, 0 0, K, M M, 0, M M, M, 0) one or more of the reported coordinate groups are occupied could be considered as filled-up derivatives of the cubic close-packed structures. The NaCl, CaF2, ZnS (sphalerite), AgMgAs and Li3Bi-type structures could, therefore, be included in this family of derivative structures. For this purpose, however, it may be useful to note that the radii of small spheres which fit exactly into tetrahedral and octahedral holes are, respectively, 0.225. and 0.414... if the radius of the close-packed spheres is 1.0. For a given phase pertaining to one of the aforementioned types (NaCl, ZnS, etc.) if the stated dimensional conditions are not fulfilled, alternative descriptions of the structure may be more convenient than the reported derivation schemes. 

More recently, the Pam amino acid chimera has also been incorporated into a small j0j0a-motif peptide scaffold [28]. The family of BBA peptides was developed in our laboratory as structured platforms for the design of functional motifs. These motifs are attractive because they are small enough (23 residues) to be easily synthesized by standard solid phase synthesis methods. Additionally, the motifs appear to possess sufficient structural complexity to influence coenzyme properties while still being amenable to structural characterization by standard spectroscopic techniques [3, 29, 30]. The BBA peptides include a -hairpin domain with a type IT turn connected by a loop region to an a-heli-cal domain (Fig. 10). Packing of the sheet and helix against one another is accomplished by hydrophobic contacts created by a hydrophobic core of residues. 

Over 100 stationary phases of various types have been described in the literature for packed columns, which are slowly being abandoned. However, for bonded phase capillary columns the choice of stationary phase is limited because the generation of the film at the surface of the column requires a different principle than impregnation. Generally, two families of compounds are used to modify the polarity polysiloxanes and polyethylene (silicones) glycols. Very special phases such as cyclodextrins can be used for enantiomeric separations. Stationary phases can be used between a minimum temperature under which equilibrium is too slow to occur and a maximum temperature above which degradation of the polymer occurs. The maximum temperature depends on the film thickness and the nature of the polymer. 

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