Helical structure helicate

Figure Bl.17.10. Principles of 3D reconstruction methods, (a) Principle of single axis tomography a particle is projected from different angles to record correspondmg images (left panel) this is most easily realized in the case of a helical complex (right panel), (b) Principle of data processing and data merging to obtain a complete 3D structure from a set of projections.

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. 

Qualitatively similar results were obtained in preliminary calculations of several (Ala)io and (Aib)io helical structures in water. 

Table 2. Geometric description of MD average helical structures...

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

Where helical secondaiy structures are represented by the cylinder model, the /i-strand. structures are visualized by the ribbon model (see the ribbons in Figure 2-124c). The broader side of these ribbons is oriented parallel to the peptide bond. Other representations replace the flat ribbons with flat arrows to visualize the sequence of the primary structure. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

Amorphous or "plastic" sulfur is obtained by fast cooling of the crystalline form. X-ray studies indicate that amorphous sulfur may have a helical structure with eight atoms per spiral. Crystalline sulfur seems to be made of rings, each containing eight sulfur atoms, which fit together to give a normal X-ray pattern. 

Rule-based systems try to identify certain subsequences of amino acids that tend to have a particular secondary structure, such as sheets, a-helices, (I-strands,... 

In biological systems molecular assemblies connected by non-covalent interactions are as common as biopolymers. Examples arc protein and DNA helices, enzyme-substrate and multienzyme complexes, bilayer lipid membranes (BLMs), and aggregates of biopolymers forming various aqueous gels, e.g, the eye lens. About 50% of the organic substances in humans are accounted for by the membrane structures of cells, which constitute the medium for the vast majority of biochemical reactions. Evidently organic synthesis should also develop tools to mimic the Structure and propertiesof biopolymer, biomembrane, and gel structures in aqueous media. 

A helical structure for DNA strands had been suggested in 1949 by Sven Furberg in his Ph D dissertation at the University of London... 

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

Section 28 9 Within the cell nucleus double helical DNA adopts a supercoiled terti ary structure m which short sections are wound around proteins called histones This reduces the effective length of the DNA and maintains it m an ordered arrangement... 

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

R = -CH2CH(CH3)2, there occurs a modest deviation from a strict 0°-120° alternation which characterizes the trans-gauche sequence. This produces a helical structure with seven repeat units occurring in two turns. Even bulkier substituents, for example, o-methyl phenyl, produce still more open helices... 

Poly(7-benzyl-L-glutamate) is known to possess a helical structure in certain solvents. As part of an investigationf of this molecule, a fractionated sample was examined in chloroform (CHCI3) and chloroform saturated ( 0.5%) with dimethyl formamide (DMF). The following results were obtained ... 

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