Deconvolution method, structural

Both methods are also limited in accuracy of secondary structure determinations because spectral peaks must be deconvolved estimates are made of the overlapping contributions of different structural regions. These estimates may introduce error based on the reference spectra used and because deconvolution methods equate crystallographic secondary structure with the secondary structure of the protein in solution (Pelton and McLean, 2000). As amyloid fibrils are neither crystalline nor soluble, there may be even greater error in estimates of secondary structure. To compound the problem, estimates of /f-sheet content are less reliable than those of a-helix, because of the flexibility and variable twist of / -structure (Pelton and McLean, 2000). In addition, / -sheet and turn bands overlap in FTIR spectroscopy (Jackson and Mantsch, 1995 Pelton and McLean, 2000). Side chains also contribute to spectral peaks in both methods, and they can skew estimates of secondary structure if not properly accounted for. In FTIR spectra, up to 10-15% of the amide I band may arise from side chain contributions (Jackson and Mantsch, 1995). 

The preferred mode of preparation for both mixture and split synthesis libraries is the solid phase. Both polymer matrices or pins and resin beads have been used. The solid-phase approach is preferred because of its simplicity and ease of purification and isolation of the reaction products. Unlike the spatially addressable library when structure is defined by position in a set of reaction vessels, the structure of interesting library members prepared by mixture or split synthesis must be defined by highly sensitive analytical methods or indirectly by encoding or by biological results combined with resynthesis, the so-called deconvolution method. 

There has been some discussion as to whether CD can distinguish parallel from antiparallel p sheets. As stable, well-defined model compounds are lacking, the spectra available have been derived from secondary structure deconvolutions (see below). Overall, the ability of CD to provide adequate estimates of both parallel and antiparallel p sheet contents is still an ongoing question. Johnson and co-workers were the first to derive basis spectra which corresponded to both parallel and antiparallel p sheet structures in globular proteins using the singular value deconvolution method [11, 12, 51-53], However, the basis spectra were significantly different from spectra reported for model sleet structures. Recently, Perczel et al. [54] employed another approach, convex curve analysis, to obtain improved p sheet baas spectra. The major improvement was to include more p sheet proteins into the data base. 

The first section will be devoted to the synthesis of these libraries using the so-called mix-and-split or divide-and-recombine approach (2, 3) and to their analytical characterization. The following sections will focus on different methods to determine the structure of an active component from an SP pool library direct structure determination (Section 7.2) and indirect structure determination, via deconvolutive methods (Section 7.3) or encoding methods (Section 7.4), will be covered. Finally, a section will be devoted to new trends in SP pool libraries, paying particular attention to innovative methods for the fast and reliable discovery of new active structures through miniaturization (bead-based techniques). 

Direct structure determination methods, where positives are characterized directly via off-bead or on-bead identification of their chemical structure, will be described in detail in this section. Indirect methods that determine the structure of positives from the library architecture will be covered later they use either deconvolutive methods (Section 7.3), where the iterative synthesis of library pools with decreasing complexity via sequential determination of the best monomers leads to the identification of a positive structure, or encoding methods (Section 7.4), where, during the library synthesis, the structure of each component is coupled to a tag that can be read from a single bead after the library screening. 

Encoding methods provide generally a larger set of more detailed data but also require additional complexity to be added to the library structure. Direct deconvolution methods also have appealing features such as being often independent from analytical techniques, easy to perform, and often reliable. An absolute choice among the two main structure determination method classes, and among different methods in the same class, does not exist. The skilled chemist,... 

DeRose and coworkers have explored conformational changes of TAR RNA upon binding of divalent metal ions (Ca " ) by measuring the dipolar coupling between two attached spin labels 20 using CW EPR (Fig. 2). The U25-U40 distances obtained from Fourier deconvolution methods are 11.9 0.3 A for TAR RNA in the absence of divalent metal cations and 14.2 0.3 A when 50 mM Ca " was added [45]. These results are in accordance with the proposed coaxial stacking of the two TAR helices upon addition of metal ions based on the X-ray crystal structure [80]. 

The deconvolution method proposed earlier by our group, translated the 3D cross peak intensities into 2D NOE intensities, which can be used to derive accurate distance constraints that can be used in structure refinement by an iterative relaxation matrix approach (11). This approach avoids systematic errors while retaining computational efficiency. 

JJ Baldwin, RE Dolle. Deconvolution methods in solid-phase synthesis. In WH Moos, MR Pavia, BK Kay, AD Ellington, eds. Annual Reports in Combinatorial Chemistry and Molecular Diversity. Leiden ESCOM, 1997, pp. 287-297 X-Y Xiao, MP Nova. Radiofrequency encoding and additional techniques for the structure elucidation of synthetic combinatorial libraries. In SR Wilson, AW Czarnik, eds. Combinatorial Chemistry Synthesis and Application. New York Wiley, 1997, pp. 135-152. 

For liquid sprays, the droplet size varies at different radial and axial directions from the nozzle. The time-averaged measurement and data analysis procedures described above cannot provide information about the local structure of the droplet size distribution. Several techniques have been developed to transform ordinary laser diffraction measurements into spatially resolved local measurements along the radial directions of the spray. The data from the measurements at different radial directions are then processed using either a deconvolution method with optical extinction and scattering coefficients [45] or a tomographical transformation method [46,47], yielding pointwise droplet size and liquid concentration distribution as well as all mean diameters of practical interest. 

Table I illustrates the utility of DRUV-visible data in determining the surface structures involving Ti. Samples of TS-1 were prepared by three different methods or treatments. Samples 1 and 2 were prepared by conventional hydrothermal synthesis and sample 3 by synthesis in a fluoride medium. TS-2 was synthesized as reported (7). At least five bands could be discerned by deconvolution (Fig. 3), at 205, 228, 258, 290, and 330 nm. Band 1 at 205 nm is assigned to tetrahedral, tetrapodal Ti present in TS-1, TS-2, and Ti-beta. Band 5 at 330 nm is assigned to an...

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