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The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D projection). It is shown that the letter code of the protein makes it possible to reconstruct its overall shape without ambiguity (1D-3D translation). Accordingly, the letter code is used for the development of classification rules that distinguish supersecondary structures by the properties of their turns and the orientation of the flanking helix or strand structures. The orientations of turn and flanking structures are collected in an octant system that helps to specify 196 supersecondary groups for (alpha,alpha)-, (alpha,beta)-, (beta,alpha)-, (beta,beta)-class. 391 protein chains leading to 2499 super secondary structures were analyzed. Frequently occurring super secondary structures are identified with the help of the octant classification system and explained on the basis of their letter and classification codes., Comment: 40 pages, 5 figures

A new method for the Automated Protein Structure Analysis (APSA) is derived, which simplifies the protein backbone to a smooth curve in 3-dimensional space. For the purpose of obtaining this smooth line each amino acid is represented by its C$_{\alpha}$ atom, which serves as suitable anchor point for a cubic spline fit. The backbone line is characterized by arc length $s$, curvature $\kappa(s)$, and torsion $\tau(s)$. The $\kappa(s)$ and $\tau(s)$ diagrams of the protein backbone suppress, because of the level of coarse graining applied, details of the bond framework of the backbone, however reveal accurately all secondary structure features of a protein. Advantages of APSA are its quantitative representation and analysis of 3-dimensional structure in form of 2-dimensional curvature and torsion patterns, its easy visualization of complicated conformational features, and its general applicability. Typical differences between 3$_{10}$-,$\alpha$-, $\pi$-helices, and $\beta$-strands are quantified with the help of the $\kappa(s)$ and $\tau(s)$ diagrams. For a test set of 20 proteins, 63 % of all helical residues and 48.5 % of all extended residues are identified to be in ideal conformational environments with the help of APSA. APSA is compared with other methods for protein structure analysis and its applicability to higher levels of protein structure is discussed., Comment: 27 pages, 7 figures

RHF calcns. have been carried out for 1,3,5-cycloheptatriene, norcaradiene, 1H-azepine, benzenimine (azanorcaradiene), oxepin and benzene oxide (oxanorcaradiene) employing the STO-3G, 4-31G and 6-31G* basis sets. Theor. geometries, conformation and barriers to ring inversion have been obtained and compared with the available exptl. structural data. The cyclotrienes possess a boat conformation with a const. admix. of 22% chair character leading to a flattening of the triene part and p-electron delocalization typical for a planar polyene. The structural data suggest that cyclic delocalization of either 6p (homoaromaticity) or 8p electrons (antiaromaticity) is not present in the 3 cyclotrienes. The former possibility, however, cannot be excluded in the case of 3 norcaradienes., CAN 102:94944 22-2 Physical Organic Chemistry 291-70-3; 544-25-2; 1488-25-1; 12764-48-6; 14515-09-4; 57784-62-0 Role: PRP (Properties) (geometry and conformation of)

The energy profiles for the valence-tautomeric equil. I.dblharw.II and III.dblharw.IV were detd. by ab initio calcns. The energy barrier for the forward and back reaction for I.dblharw.II was 7.3 and 2.3 kcal/mol; these values are .apprx.3 kcal/mol smaller than those for the III.dblharw.IV equil., CAN 98:16035 22-2 Physical Organic Chemistry 61997-35-1; 61997-37-3 Role: RCT (Reactant), RACT (Reactant or reagent) (valence isomerization of); 174-23-2; 544-25-2; 2443-46-1; 14515-09-4 Role: RCT (Reactant), RACT (Reactant or reagent) (valence isomerization of, MO calcns. in relation to)