B-form

Metals A and B form an alloy or solid solution. To take a hypothetical case, suppose that the structure is simple cubic, so that each interior atom has six nearest neighbors and each surface atom has five. A particular alloy has a bulk mole fraction XA = 0.50, the side of the unit cell is 4.0 A, and the energies of vaporization Ea and Eb are 30 and 35 kcal/mol for the respective pure metals. The A—A bond energy is aa and the B—B bond energy is bb assume that ab = j( aa + bb)- Calculate the surface energy as a function of surface composition. What should the surface composition be at 0 K In what direction should it change on heaf)pg, and why ... 

The hydration shell is formed with the increasing of the water content of the sample and the NA transforms from the unordered to A- and then to B form, in the case of DNA and DNA-like polynucleotides and salt concentrations similar to in vivo conditions. The reverse process, dehydration of NA, results in the reverse conformational transitions but they take place at the values of relative humidity (r.h.) less than the forward direction [12]. Thus, there is a conformational hysteresis over the hydration-dehydration loop. The adsorption isotherms of the NAs, i.e. the plots of the number of the adsorbed water molecules versus the r.h. of the sample at constant temperature, also demonstrate the hysteresis phenomena [13]. The hysteresis is i( producible and its value does not decrease for at least a week. 

Let us introduce the variables which are the probabilities of finding an arbitrary nnit in a certain conformational state U for unordered state, A for A- and B for B-form of the NA. There is the natural relationship between the variables ... 

Fig. 1. The dependence of the stable stationary values of the adsorption and conformational variables on the control parameter, Xe. a-total adsorption per the mole of the nucleotides, b-the probability of finding of an arbitrary NA unit in the A form, c-the probability of finding of an arbitrary NA unit in the B-form. Param-(ders values used to obtain numerical results Vmi = 3,nL = 15.4, = 3.24,6° =...

Fig. 9. Holographic pattern recognition system, (a) Recording an angularly multiplexed hologram (b) forming correlation outputs using arbitrary input...

Some oligonucleotides adopt an A-form helical stmcture (Fig. 2a) (5). The average stmctural parameters have been found consistent with the fiber diffraction model, but, as for B-form DNA, considerable variation is apparent among iadividual base pairs. 

The numerical results for the case of two counterions of equal valence where a resin bead, initially partially saturated with A, is completely converted to the B form, is expressed by ... 

W-Metbylpbenotbiazine [1207-72-3] M 213.2, a-form m 99.3" and b 360-365", 0-form m 78-79". Recrystn (three times) from EtOH gave a-form (prisms). Recrystn from EtOH/ benzene gave the B-form (needles). Also purified by vacuum sublimation and carefully dried in a vacuum line. Also crystd from toluene and stored in the dark [Guarr et al. J Am Chem Soc 107 5104 1985 Olmsted et al. J Am Chem Soc 109 3297 1987.]... 

Figure 5 Time dependence of RMSD of atomic coordinates from canonical A- and B-DNA forms m two trajectories of a partially hydrated dodecamer duplex. The A and B (A and B coiTespond to A and B forms) trajectories started from the same state and were computed with internal and Cartesian coordinates as independent variables, respectively. (From Ref. 54.)...

Figure 5.9 The six four-stranded motifs in a single subunit of neuraminidase form the six blades of a propeller-like structure. A schematic diagram of the subunit structure shows the propeller viewed from its side (a). An idealized propeller structure viewed from the side to highlight the position of the active site is shown in (b). The loop regions that connect the motifs (red in b) in combination with the loops that connect strands 2 and 3 within the motifs (green in b) form a wide funnel-shaped active site pocket, [(a) Adapted from P. Colman et ah, Nature 326 358-363, 1987.]...

The specific protein-DNA interactions described in this book are all with DNA in its regular B-form, or, in some cases with distorted B-DNA. In biological systems DNA appears not to adopt the A conformation, although double-stranded RNA does preferentially adopt this conformation in vivo. Whether or not Z-DNA occurs in nature is a matter of controversy. However, the formation of A-DNA and Z-DNA in vitro does illustrate the large structural changes that DNA can be forced to undergo. 

Figure 8.20 Schematic diagrams of docking the trp repressor to DNA in its inactive (a) and active (b) forms. When L-tryptophan, which is a corepressor, hinds to the repressor, the "heads" change their positions relative to the core to produce the active form of the repressor, which hinds to DNA. The structures of DNA and the trp repressor are outlined.

Figure 16.13 The known subunit structures of plant. Insect, and animal viruses are of the jelly roll antiparallel p barrel type, described in Chapter 5. This fold, which is schematically illustrated in two different ways, (a) and (b), forms the core of the S domain of the subunit of tomato bushy stunt virus (c). [(b), (c) Adapted from A.J. Olson et al., /. Mol. Biol. 171 61-93, 1983.1...

Knowing the helix pitch, it is possible to determine an approximate value for the radius of the helix in the B form from the inclination of the... 

Fig. 4.59. Raman spectrum of methyl mercaptan (a) and SERS spectrum of methyl mercaptide (b) formed by adsorption ofthe mercaptan on a silver surface. The surface reaction is proven by the disappearance ofthe S-H stretching and bending bands at 2575 cm" and 806 cm", respectively. The Raman shift ofthe C-S stretching band at approximately 700 cm" is reduced during adsorption by withdrawal of electron density from the C-S, because of bonding to the silver. The symmetric methyl stretching appears above 2900cm" [4.303].

Now to separate solute (B) form (C) the following conditions must be met,... 

The subject was then fully investigated by Pyman, who found that the products obtained depended partly on the material started with and partly on the conditions of the experiment. Thus under his conditions, Z-canadine methohydroxide when dried in vacuo gave rise to three anhydro-bases, a and b optically inactive, and c optically active whilst the methohydroxide of the dZ-base formed only two, a and Z , but the proportion of b formed in this instance was equal to the amount of b and c together in the case of the Z-base (canadine). For this and other reasons b was regarded as the racemic form of c and, like it, is represented by F (R = Me),... 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

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