3D characterization

The surprising discovery that small oligo-P-peptides exhibit extraordinary tendencies to form stable secondary structures has led to rapid developments in the chemistry of these peptides. The earliest work in the field revolved around the synthesis of P-peptide polymers (the so-called nylon-3 derivatives). 2 Polymerization of P-amino acids led to polymers of undefined length. It was noted they could form stable structures but it proved impossible to gain any concrete information about the nature of those structures at that time. The developments in the synthesis of P-peptide oligomers of predefined length and advances in methods (i.e., NMR spectroscopy and X-ray crystallography) for the 3D characterization of such compounds has led to the discovery of new helical structures found to be adopted by a variety of P-peptides. I1,3-7 ... 

Lin CL, Miller JD. 3D characterization and analysis of particle shape using x-ray micro-tomography (xmt). Powder Technol 2(X)5 154(I) 6l-9. 

Table 2. List of ISO standards related to the 3D characterization of surface finishing.

Related Methods Approaches relying on specific sample pretreatments are hardly compatible with depth profile analysis, and therefore, appear restricted to molecular imaging. For 3D characterization, other signal-enhancement procedures relying on a constant feeding or flooding of the sample must be devised. 

NMR spectra are basically characterized by the chemical shift and coupling constants of signals. The chemical shift for a particular atom is influenced by the 3D arrangement and bond types of the chemical environment of the atom and by its hybridization. The multiplicity of a signal depends on the coupling partners and on the bond types between atom and couphng partner. 

A combination of physicochemical, topological, and geometric information is used to encode the environment of a proton, The geometric information is based on (local) proton radial distribution function (RDF) descriptors and characterizes the 3D environment of the proton. Counterpropagation neural networks established the relationship between protons and their h NMR chemical shifts (for details of neural networks, see Section 9,5). Four different types of protons were... 

Many different approaches to QSAR have been developed since Hansch s seminal work. These include both two-dimensional (2D) and 3D QSAR methods. The major differences among these methods can be analyzed from two viewpoints (1) the strucmral parameters that are used to characterize molecular identities and (2) the mathematical procedure that is employed to obtain the quantitative relationship between a biological activity and the structural parameters. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

In 1996, the 3D-structure of D. vulgaris Rr was published by de-Mare and collaborators 48), and all the studies earlier published were proved to be correct. The protein is described as a tetramer of two-domain subunits (Fig. 4). Each subunit contains a domain characterized by a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like Fe(RS)4 domain (see Fig. 2). In this last do-... 

D. gigas AOR was the first Mo-pterin-containing protein whose 3D structure was solved. From D. desulfuricans, a homologous AOR (MOD) was purified, characterized, and crystallized. Both proteins are homodimers with-100 kDa subunits and contain one Mo-pterin site (MCD-cofactor) and two [2Fe-2S] clusters. Flavin moieties are not found. The visible absorption spectrum of the proteins (absorption wavelengths, extinction coefficients, and optical ratios at characteristic wavelengths) are similar to those observed for the deflavo-forms of... 

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