Structure, three-dimensional 3-sheet

The physical properties of the silicates correlate closely with their structures. Talc, Mg3(Si40io)(OH)2, is an example of an infinite layered structure (see Fig. 22.If). In talc, all of the bonding interactions among the atoms occur in a single layer. Layers of talc sheets are attracted to one another only by van der Waals interactions, which (being weak) permit one layer to slip easily across another. This accounts for the slippery feel of talc (called talcum powder). When all four vertices of each tetrahedron are linked to other tetrahedra, three-dimensional network structures such as cristobalite (see Fig. 22.Ig) or quartz (Fig. 22.2) result. Note that the quartz network carries no charge consequently, there are no cations in its structure. Three-dimensional network silicates such as quartz are much stiffer and harder than the linear and layered silicates, and they resist deformation well. 

Figure 1. Antiparallel and parallel P-sheet structures. (Three-dimensional structures of this as well as of structures occurring e.g. in Figures 2, 22, 26, and Scheme 4 can be seen as animated views with the help of CHIME etc. from our website httpy/www.uni-sb.de/matfak/fbll/schneidei).

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

Figure 11.13 Schematic diagram of the three-dimensional structure of subtilisin viewed down the central parallel p sheet. The N-terminal region that contains the a/p stmcture is blue.

The three-dimensional structure of Ras was determined by the groups of Sung-Hou Kim at the University of California, Berkeley, and Ken Holmes at the Max-Planck Institute, Heidelberg. Ras has an a/p-type structure in which the central p sheet comprises six p strands, five of which are parallel (Figure... 

Proteins are usually separated into two distinct functional classes passive structural materials, which are built up from long fibers, and active components of cellular machinery in which the protein chains are arranged in small compact domains, as we have discussed in earlier chapters. In spite of their differences in structure and function, both these classes of proteins contain a helices and/or p sheets separated by regions of irregular structure. In most cases the fibrous proteins contain specific repetitive amino acid sequences that are necessary for their specific three-dimensional structure. 

The optimised interlayer distance of a concentric bilayered CNT by density-functional theory treatment was calculated to be 3.39 A [23] compared with the experimental value of 3.4 A [24]. Modification of the electronic structure (especially metallic state) due to the inner tube has been examined for two kinds of models of concentric bilayered CNT, (5, 5)-(10, 10) and (9, 0)-(18, 0), in the framework of the Huckel-type treatment [25]. The stacked layer patterns considered are illustrated in Fig. 8. It has been predicted that metallic property would not change within this stacking mode due to symmetry reason, which is almost similar to the case in the interlayer interaction of two graphene sheets [26]. Moreover, in the three-dimensional graphite, the interlayer distance of which is 3.35 A [27], there is only a slight overlapping (0.03-0.04 eV) of the HO and the LU bands at the Fermi level of a sheet of graphite plane [28,29],... 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

In diamond, carbon is sp hybridized and forms a tetrahedral, three-dimensional network structure, which is extremely rigid. Graphite carbon is sp2 hybridized and planar. Its application as a lubricant results from the fact that the two-dimensional sheets can slide across one another, thereby reducing friction. In graphite, the unhybridized p-electrons are free to move from one carbon atom to another, which results in its high electrical conductivity. In diamond, all electrons are localized in sp3 hybridized C—C cr-bonds, so diamond is a poor conductor of electricity. 

A variety of other structures are possible with silicate minerals, including sheets and three-dimensional frameworks. In all cases, the structure includes bonds that are predominantly covalent and directional. They can therefore be viewed as being based on increasingly crosslinked inorganic polymers. 

Figure 3 shows the three-dimensional structure of the MoFe protein from Klebsiella pneumoniae, Kpl, obtained at 1.65-A resolution (7). The overall structure of the polypeptides is frilly consistent with that reported earlier for Avl (3). The a and /8 subunits exhibit similar polypeptide folds with three domains of parallel /3 sheet/a helical type. At the interface between the three domains in the a subunit is a wide shallow cleft with the FeMoco at the bottom of the cleft about 10 A from the solvent. FeMoco is enclosed within the a subunit. The P cluster, however, is buried within the protein at the interface between the a and /8 subunits, being bound by cysteine residues from each subunit. A pseudo-twofold rotation axis passes between the two halves of the P cluster and relates the a and (3 subunits. Each af3 pair of subunits contains one FeMoco and one P cluster and thus appears... 

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

Figure 1. The three-dimensional structure of PelC. A. A schematic diagram illustrating the major secondary structural features of the PelC polypeptide backbone. The three parallel p sheets are represented by arrows in light, medium and dark gray.

It is helpful in the discussion to describe silicate structures using the Q nomenclature, where Q represents [SiOJ tetrahedra and the superscript n the number of Q units in the second coordination sphere. Thus, isolated [SiO ] " are represented as Q and those fully connected to other Q units as Q. In general, minerals based on Q , Q and units are decomposed by acids. Such minerals are those containing isolated silicate ions, the orthosilicates, SiO (Q ) the pyrosilicates, Si O " (Q ) ring and chain silicates, (SiOg) (Q ). Certain sheet and three-dimensional silicates can also yield gels with acids if they contain sites vulnerable to acid attack. This occurs with aluminosilicates provided the Al/Si ratio is at least 2 3 when attack occurs at A1 sites, with scission of the network (Murata, 1943). 

Fig. 3.4.12 Three-dimensional rendered spin-echo image of water filled cracks in a cement paste specimen [13]. Three cracks are visible in the image a large triangular crack in the forefront, a smaller crack in the bottom left corner and a sheet-like structure at the top of the image. Water droplets can also be observed condensing on the cement paste surfaces. The measurement parameters were FOV 20 x 20 x 20 mm, acquisition points 128 x 128 x 64, nominal resolution 156 x 156 x 312 pm, echo time 2.7 ms, repetition time 500 ms and acquisition time 270 min.

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