A-helical

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.

Figure Bl.17.11. Reconstructed density of an a,p-tiibulin protein dimer as obtained from electron crystallography (Nogales etal 1997). Note the appearance of the p-sheets ((a), marked B) and the a-helices ((b), marked H) in the density. In particular the right-handed a-helix H6 is very clear. Pictures by courtesy of E Nogales and Academic Press.

Figure C 1.4.7. Spatial variation of the polarization from tire field resulting from two counteriDropagating, circularly polarized fields witli equal amplitude but polarized in opposite senses. Note tliat tire polarization remains linear but tliat tire axis rotates in tire x-y plane witli a helical pitch along tire z axis of lengtli X.

Figure C2.2.2. Isotropic, nematic and chiral nematic phases. Here n denotes tire director. In tire chiral nematic phase, tire director undergoes a helical rotation, as schematically indicated by its reorientation around a cone.

Circular dicliroism has been a useful servant to tire biophysical chemist since it allows tire non-invasive detennination of secondary stmcture (a-helices and P-sheets) in dissolved biopolymers. Due to tire dissymmetry of tliese stmctures (containing chiral centres) tliey are biaxial and show circular birefringence. Circular dicliroism is tlie Kramers-Kronig transfonnation of tlie resulting optical rotatory dispersion. The spectral window useful for distinguishing between a-helices and so on lies in tlie region 200-250 nm and hence is masked by certain salts. The metliod as usually applied is only semi-quantitative, since tlie measured optical rotations also depend on tlie exact amino acid sequence. 

Figure C3.2.6. Zones associated witlr the distinctive decay of electronic coupling tlrrough a-helical against p-sheet stmctures in proteins. Points shown refer to specific rates in mtlrenium-modified proteins aird in tire photosyntlretic reaction centre. From Gray H B aird Wiirkler J R 1996 Electron trairsfer in proteins A . Rev. Biochem. 65 537.

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. 

Fig. 5.17 Histogram of the normal modes calculated for a polyalanine polypeptide in an a-helical conformation. The height of each bar indicates the number of normal modes in each 50cm section.

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,... 

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

Dou ble hel ix (Section 28 8) The form in which DNA normally occurs in living systems Two complementary strands of DNA are associated with each other by hydrogen bonds be tween their base pairs and each DNA strand adopts a helical shape... 

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 ... 

FIG. 18-21 Effect of impeller speed on circulation time for a helical impeller in the Reynolds niimher arranged less than 10. 

The unit consists essentially of tvv o rotating elements, the outer being a solid-shell conical-shaped bowl and the inner comprising a helical-screw conveyor revolving at a speed slightly lovv er than that of the bowl. Raw feed sliiri v is delivered through a stationai"v feed pipe... 

Chloroacetonitrile [107-14-2] M 75.5, b 125 . Refluxed with P2O5 for one day, then distd through a helices-packed column. Also purified by gas chromatography. LACHRYMATOR, HIGHLY TOXIC. 

V-Methylmorpholine [109-02-4] M 101.2, h 116-117 /764mm, d 0.919, n 1.436, pK 7.38. Dried by refluxing with BaO or sodium, then fractionally distd through a helices-packed column. 

Trimethylsilyl trifluoromethane (trifluoromethyl trimethylsilane) [81290-20-2] M 142.2, b 54-55°, 55-55.5°, d 0.962, n 1.332. Purified by distilling from trap to trap in a vacuum of 20mm using a bath at 45° and Dry ice-Me2CO bath for the trap. The liquid in the trap is then washed with ice cold H2O (3x), the top layer is collected, dried (Na2S04), the liquid was decanted and fractionated through a helices packed column at atmospheric pressure. H, C, F, and Si NMR can be used for assessing the purity of fractions. [Tetrahedron Lett 25 2195 1984 J Org Chem 56 984 1991.]... 

In making the edge dislocation of Fig. 9.3 we could, after making the cut, have displaced the lower part of the crystal under the upper part in a direction parallel to the bottom of the cut, instead of normal to it. Figure 9.7 shows the result it, too, is a dislocation, called a screw dislocation (because it converts the planes of atoms into a helical surface, or screw). Like an edge dislocation, it produces plastic strain when it... 

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