Element structures

In sections, where exists high probability of presence of defects, on the base formed in the binary type of projections acoustical tomographic images of only defective structure elements of sections is restored. IT of restoring stipulates such operations ... 

It also requires two- sided aceess to the structural element in question. The degree of contrast between homogenius concrete and concrete with voids will not decrease linearly with increasing thickness, and the maximum practical thickness of concrete elements which can be studied for small voids using film radiography is of course limited, but sufficient for most civil engineering applications. 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Protein dynamics occurs on very different time scales ([McCammon and Harvey 1987, Jardetzky 1996]). Here, we are most interested in long time scale motions such as relative motion between secondary structure elements, and inter-domain motion. 

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. 

A completely new method of determining siufaces arises from the enormous developments in electron microscopy. In contrast to the above-mentioned methods where the surfaces were calculated, molecular surfaces can be determined experimentally through new technologies such as electron cryomicroscopy [188]. Here, the molecular surface is limited by the resolution of the experimental instruments. Current methods can reach resolutions down to about 10 A, which allows the visualization of protein structures and secondary structure elements [189]. The advantage of this method is that it can be apphed to derive molecular structures of maaomolecules in the native state. 

In order to develop a quantitative interpretation of the effects contributing to heats of atomization, we will introduce other schemes that have been advocated for estimating heats of formation and heats of atomization. We will discuss two schemes and illustrate them with the example of alkanes. Laidler [11] modified a bond additivity scheme by using different bond contributions for C-H bonds, depending on whether hydrogen is bonded to a primary (F(C-H)p), secondary ( (C-H)g), or tertiary ( (C-H)t) carbon atom. Thus, in effect, Laidler also used four different kinds of structure elements to estimate heats of formation of alkanes, in agreement with the four different groups used by Benson. 

Inspection of the values for the structure elements and their contribution to the heats of formation again allows interpretation The B-terms correspond to the energies to break these bonds, and a sequence of three carbon atoms introduces stabihty into an alkane whereas the arrangement of three carbon atoms around a central carbon atom leads to the destabilization of an alkane. 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

The comparison of both data sources qualitatively shows a similar picture. Regions of high mobflity are located especially between the secondary structure elements, which are marked on the abscissa of the plot in Figure 7-17. Please remember that the fluctuations plotted in this example also include the amino acid side chains, not only the protein backbone. This is the reason why the side chains of large and flexible amino acids like lysine or arginine can increase the fluctuations dramatically, although the corresponding backbone remains almost immobile. In these cases, it is useful to analyze the fluctuations of the protein backbone and side chains individually. 

Structural keys describe the chemical composition and structural motifs of molecules represented as a Boolean array. If a certain structural feature is present in a molecule or a substructure, a particular bit is set to 1 (true), otherwise to 0 (false). A bit in this array may encode a particular functional group (such as a carboxylic acid or an amidelinkage), a structural element (e.g., a substituted cyclohexane), or at least n occurrences of a particular element (e.g., a carbon atom). Alternatively, the structural key can be defined as an array of integers where the elements of this array contain the frequency of a specific feature in the molecule. 

The common structural element in the crystal lattice of fluoroaluminates is the hexafluoroaluminate octahedron, AIF. The differing stmctural features of the fluoroaluminates confer distinct physical properties to the species as compared to aluminum trifluoride. For example, in A1F. all corners are shared and the crystal becomes a giant molecule of very high melting point (13). In KAIF, all four equatorial atoms of each octahedron are shared and a layer lattice results. When the ratio of fluorine to aluminum is 6, as in cryoHte, Na AlF, the AIFp ions are separate and bound in position by the balancing metal ions. Fluorine atoms may be shared between octahedrons. When opposite corners of each octahedron are shared with a corner of each neighboring octahedron, an infinite chain is formed as, for example, in TI AIF [33897-68-6]. More complex relations exist in chioUte, wherein one-third of the hexafluoroaluminate octahedra share four corners each and two-thirds share only two corners (14). 

Fig. 1. Structures of two types of opioid agonists where dotted circles surround structural elements common to both compounds (a) Leu-enkephalin and...

Table 1 lists some of the common binucleophiles utilized in heterocyclic synthesis, the numerical prefixes referring to the relative positions of the nucleophilic centers to each other. Higher order binucleophiles, e.g. 1,5-systems, come readily to mind and the above illustrative examples rapidly increase in scope when the incorporation of these structural elements into heterocyclic systems is considered. This last group offers many opportunities for ring annulations. 

Bahar et al. [46] have used this kind of approach to predict the B-factors of 12 X-ray structures. Elements in the Hessian corresponding to atom pairs separated by a distance of less than 7 A are set to zero, and the remainder have the same value dependent on a single adjustable parameter. Generally B-factor predictions for the a-carbons compare very well with the B-factors measured by X-ray crystallography. Figure 1 shows the result for the subunit A of endodeoxyribonuclease I complexed with actin. 

BVB Reddy TL Blundell. Packing of secondary structural elements m proteins. Analysis and prediction of mter-helix distances. J Mol Biol 233 464-479, 1993. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

The secondary structure elements, formed in this way and held together by the hydrophobic core, provide a rigid and stable framework. They exhibit relatively little flexibility with respect to each other, and they are the best-defined parts of protein structures determined by both x-ray and NMR techniques. Functional groups of the protein are attached to this framework, either directly by their side chains or, more frequently, in loop regions that connect sequentially adjacent secondary structure elements. We will now have a closer look at these structural elements. 

Secondary structure elements are connected to form simple motifs... 

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

---