Elongated molecules

Fig. 2. Schematic representation of the orientational distribution function f 6) for three classes of condensed media that are composed of elongated molecules A, soHd phase, where /(0) is highly peaked about an angle (here, 0 = 0°) which is restricted by the lattice B, isotropic fluid, where aU. orientations are equally probable and C, Hquid crystal, where orientational order of the soHd has not melted completely.

Discotic Phases. Molecules which are disk-shaped rather than elongated also form thermotropic Hquid crystal phases. Usually these molecules have aromatic cores and six lateral substituents, although the predominance of six lateral substituents is solely historical molecules with four lateral substituents also can form Hquid crystal phases. Although the flatness of these molecules creates a steric effect promoting alignment of the normal to the disks, the fact that disordered side chains are also necessary for the formation of these phases (as is often the case for Hquid crystallinity in elongated molecules) should not be ignored. 

If the molecules are chiral or if a chiral dopant is added to a discotic Hquid crystal, a chiral nematic discotic phase can form. The director configuration ia this phase is just like the director configuration ia the chiral nematic phase formed by elongated molecules (12). Recendy, discotic blue phases have been observed. 

Detailed protein structures have been reported for BPI and CETP. Given the aforementioned similarities within this gene family, these protein structures serve as a likely model for the protein structure of PLTP. CETP and BPI are elongated molecules, shaped like a boomerang. There are two domains with similar folds, and a central beta-sheet domain between these two domains. The molecules contain two lipid-binding sites, one in each domain near the interface of the barrels and the central beta-sheet. 

Mature human albumin consists of one polypeptide chain of 585 amino acids and contains 17 disulfide bonds. By the use of proteases, albumin can be subdivided into three domains, which have different functions. Albumin has an ellipsoidal shape, which means that it does not increase the viscosity of the plasma as much as an elongated molecule such as fibrinogen does. Because of its relatively low molecular mass (about 69 kDa) and high concentration, albumin is thought to be responsible for 75-80% of the osmotic pressure of human plasma. Electrophoretic smdies have shown that the plasma of certain humans lacks albumin. These subjects are said to exhibit analbuminemia. One cause of this condition is a mutation that affects spUcing. Subjects with analbuminemia show only moderate edema, despite the fact that albumin is the major determinant of plasma osmotic pressure. It is thought that the amounts of the other plasma proteins increase and compensate for the lack of albumin. 

The overall process can be divided into several stages activation (or initiation), binding to a macromolecule, elongation, movement of the elongating molecule, termination and post-synthetic modification. Analogous processes occur in the synthesis of polysaccharides and peptides (Chapters 6 and 20. See Table 6.2). 

Figure 5-21 Nucleosomes. (A) Electron micrographs of individual nucleosomes reconstituted from 256-bp DNA fragments and separated proteins. From Hamiche et al.213 Courtesy of Ariel Prunell. (B) Model of a nucleosome core. The 1.75-tum (145-bp) DNA superhelix winds around the histone octomer which consists of two subunits apiece of histones H2A, H2B, H3, and H4. In addition, two elongated molecules of proteins HMG-14 or HMG-17 are indicated (see also Chapter 27). (C) Schematic radial projection of the doublehelical DNA showing areas protected from cleavage by hydroxyl radicals (see Fig. 5-50) by the bound proteins. The shaded areas are those protected by HMGs. The zigzag lines near the dyad axis indicate the most prominent regions of protection. (B) and (C) are from Alfonso et al.2U...

Isolated microtubules always contain small amounts of larger 300-kDa microtubule-associated proteins (MAPS).330 These elongated molecules may in part lie in the grooves between the tubulin subunits and in part be extended outward to form a low-density layer around the tubule.283 309 Nerve cells that contain stable microtubules have associated stabilizing proteins.331 A family of proteins formed by differential splicing of mRNA are known as tau. The tau proteins are prominent components of the cytoskeleton of neurons. They not only interact with microtubules but also undergo reversible phosphorylation. Hyperphosphorylated tau is the primary component of the paired helical filaments found in the brains of persons with Alzheimer disease.330... 

Fibrinogen is an elongated molecule with an (apy)2 structure.524,541,5413 Thrombin cleaves specific Arg-Gly bonds in the a and P chains releasing short (14- tol6-residue) "fibrinopeptides" from the N termini of the peptide chains. This leaves Gly-Pro-Arg "knobs" at... 

However, the RDF(CM) is not appropriate when the solute is an elongated molecule, as it was discussed before, for the case of (3-carotene in several solvents [47] and benzophenone in water [50], In these cases of elongated solutes, an appropriate function is the minimum-distance distribution function (MDDF), where the histogram used to calculate the distribution function is not the distance between the CMs of solute-solvent, but the minimum distance between them. The MDDF is defined as... 

The double helix is a relatively stiff and elongated molecule. Consequently, a solution of DNA has a high viscosity. If such a solution is heated to 95°C, the viscosity drops markedly, reflecting a collapse of the double-helical structure. This is known as denaturation and is accompanied by separation of the duplex into its single strands, which are fairly flexible. Denaturation and renaturation provide valuable information on important properties of the DNA obtained from various sources. Denaturation also provides the basis for very precise and sensitive approaches to the identification of specific sequences in both DNA and RNA. This has been central to the rapid developments in molecular genetics. 

This form of Vsr is particularly efficient for rod-shaped, elongated molecules. For such molecules a direct expansion of Vsr in terms of Pl(cos0) would have a prohibitively slow convergence because of the strong radial-angular coupling of the PES. However, the as a... 

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