Substructures Three Dimensional

Chemscape Sen/er integrates directly into Netscape Sen/er and provides full ISIS/Host structure and data searching and retrieval capabilities (including substructure, three-dimensional, reaction, and ORACLE searches) from within a web browser. 

Sheridan RP, Nilakantan R, Rusinko A, Bauman N, Haraki KS, Venkataraghavan R. 3DSEARCH a system for three-dimensional substructure searching. / Chem Inf Comput Sci 1989 29 255-60. 

The main advantage of NMR spectroscopy is its use with proteins in solution. In consequence, rather than obtaining a single three-dimensional structure of the protein, the final result for an NMR structure is a set of more or less overlying structures which fulfill the criteria and constraints given particularly by the NOEs. Typically, flexibly oriented protein loops appear as largely diverging structures in this part of the protein. Likewise, two distinct local conformations of the protein are represented by two differentiated populations of NMR structures. Conformational dynamics are observable on different time scales. The rates of equilibration of two (or more) substructures can be calculated from analysis of the line shape of the resonances and from spin relaxation times Tj and T2, respectively. 

Composite crystals, in which the structure can be described as resulting from two or more substructures (related to two or more sets of three dimensional lattices) having different periodicity along at least one direction (chimney-ladder structures, vernier structures, misfit-layer structures, etc.). See the scheme presented in Fig. 3.42. 

Van drie, J.H., Weininger, D., and Martin, Y.C. ALADDIN an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures./. Comput.-Aided Mol. Des. 1998, 3, 225-251. 

The zeolites are generally thought of as having three-dimensional rather than sheet or chain structures. The existence of tetrahedral ring linkages that produce chainlike substructures characteristic of the natural zeolitic species found as needles or fibers reinforces the earlier statement fibers can be constructed from any number of basic units that grow in a preferential direction. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

Our discussion of globular protein structure begins with the principles gleaned from the earliest protein structures to be elucidated. This is followed by a detailed description of protein substructure and comparative categorization. Such discussions are possible only because of the vast amount of information available over the Internet from resources such as the Protein Data Bank (PDB www.rcsb.org/pdb), an archive of experimentally determined three-dimensional structures of biological macromolecules. 

Fig. 8. Generation of the form of the helical diffraction pattern. (A) shows that a continuous helical wire can be considered as a convolution of one turn of the helix and a set of points (actually three-dimensional delta-functions) aligned along the helix axis and separated axially by the pitch P. (B) shows that a discontinuous helix (i.e., a helical array of subunits) can be thought of as a product of the continuous helix in (A) and a set of horizontal density planes spaced h apart, where h is the subunit axial translation as in Fig. 7. This discontinuous set of points can then be convoluted with an atom (or a more complicated motif) to give a helical polymer. (C)-(F) represent helical objects and their computed diffraction patterns. (C) is half a turn of a helical wire. Its transform is a cross of intensity (high intensity is shown as white). (D) A full turn gives a similar cross with some substructure. A continuous helical wire has the transform of a complete helical turn, multiplied by the transform of the array of points in the middle of (A), namely, a set of planes of intensity a distance n/P apart (see Fig. 7). This means that in the transform in (E) the helix cross in (D) is only seen on the intensity planes, which are n/P apart. (F) shows the effect of making the helix in (E) discontinuous. The broken helix cross in (E) is now convoluted with the transform of the set of planes in (B), which are h apart. This transform is a set of points along the meridian of the diffraction pattern and separated by m/h. The resulting transform in (F) is therefore a series of helix crosses as in (E) but placed with their centers at the positions m/h from the pattern center. (Transforms calculated using MusLabel or FIELIX.)...

The database search process starts with a rapid screening process within which molecules possessing properties required from potential hits are sorted out from those that can be excluded a priori. The screen involves substructure match followed by screens matching three-dimensional pharmacophore features, molecular shapes or exclusion volumes and text constraints (ID properties) if present in the query (through Oracle). All this greatly reduces the number of potential hit compounds in the database. The next step of the search pro-... 

It is interesting that in the 3-dimensional structures of them, obtained from X-ray diffraction data [24-26], they can be superimposed on one another at the point of the largest common substructure [31]. Figure 7 shows a three dimensional stereoscopic view of the common part of them, which were superimposed by the least squares method. 

Fig. 7. A stereoscopic view of the three-dimensional superimposition of the largest common substructure, (ii) in Fig. 6, among three narcotic analgesics...

In addition to investigations by mere structure overlapping methods and retrieval of three-dimensional substructures, there have been studies focused on developing an automated operation for recognizing common substructures, which takes into account the three-dimensional geometry of the molecules [49-54]. These approaches are greatly different from conventional one in that the designation of a query structure is not required. 

Figure 2. (a) The amino acid sequence of the enzyme lysozyme (from egg white). Blocks enclosing two cysteines (Cys) denote intramolecular covalent cross-links (disulfide bonds). This molecule in crystalline form has the three-dimensional structure sketched in part (b). Note the helical subdomains and sheet substructures formed by nearby extended segments. Reprinted by permission from C. C. F. Blake, Structure of Hen Egg-White Lysozyme, Nature vol. 206 p. 757. Copyright (c) 1967 Macmillan Magazines Ltd. 

Figure 7 (a) The three-dimensional structure of [ Cu2(tppz)(H20)2 (Mo50i5)(03POH)2]-3H20(3 3H20). (b) The one-dimensional Cu2Mo5Oi5(03POH)2 substructure of 3. 

Incommensurate structures have been known for a long time in minerals, whereas TTF-TCNQ is one of the very first organic material in which a incommensurate phase has been observed. There are two main types of incommensurate crystal structures. The first class is that of intergrowth or composite structures, where two (or more) mutually incommensurate substructures coexist, each with a different three-dimensional translational periodicity. As a result, the composite crystal consists of several modulated substructures, which penetrate each other and we cannot say which is the host substructure. The second class is that of a basic triperiodic structure which exhibits a periodic distortion either of the atomic positions (displa-cive modulation) and/or of the occupation probability of atoms (density modulation). When the distortion is commensurate with the translation period of the underlying lattice, the result is a superstructure otherwise, it is an incommensurately modulated structure (IMS) that has no three-dimensional lattice periodicity. 

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