Folding fragments

Fig. 9.2. Schematic illustration of the (Pa)g-barrel structure. The highly symmetrical structure presumably arose by multiple gene duplication events from a Pa-fragment. This hypothesis was tested using reverse engineering. Bisection of the barrel into two halves yielded correctly folded fragments which, upon heterodimerization, regained parental function. However, further fragmentation awaits experimental exploration.

Figure C2.14.1. Diagram of a fragment of a folded RNA polymer, the QP replicase MDV-1 [176]. Note the various stmctural features stems closed with a loop ( hairjDins ), bows, and single strands.

Figure 8.11 The DNA-binding domain of 434 repressor. It is a dimer in its complexes with DNA fragments. Each subunit (green and brown) folds into a bundle of four a helices (1-4) that have a structure similar to the corresponding region of the lambda repressor (see Figure 8.7) including the helix-turn-helix motif (blue and red). A fifth a helix (5) is involved in the subunit interactions, details of which are different from those of the lambda repressor fragment. The structure of the 434 Cro dimer is very similar to the 434 repressor shown here.

Residues 50-64 of the GAL4 fragment fold into an amphipathic a helix and the dimer interface is formed by the packing of these helices into a coiled coil, like those found in fibrous proteins (Chapters 3 and 14) and also in the leucine zipper families of transcription factors to be described later. The fragment of GAL4 comprising only residues 1-65 does not dimerize in the absence of DNA, but the intact GAL4 molecule does, because in the complete molecule residues between 65 and iOO also contribute to dimer interactions. 

Because of the double helical nature of DNA molecules, their size can be represented in terms of the numbers of nucleotide base pairs they contain. For example, the E. coli chromosome consists of 4.64 X 10 base pairs (abbreviated bp) or 4.64 X 10 kilobase pairs (kbp). DNA is a threadlike molecule. The diameter of the DNA double helix is only 2 nm, but the length of the DNA molecule forming the E. coli chromosome is over 1.6 X 10 nm (1.6 mm). Because the long dimension of an E. coli cell is only 2000 nm (0.002 mm), its chromosome must be highly folded. Because of their long, threadlike nature, DNA molecules are easily sheared into shorter fragments during isolation procedures, and it is difficult to obtain intact chromosomes even from the simple cells of prokaryotes. 

This closeness of 0 to zero explains the existence of a gas-oversaturated solution area in the polymer melt, when P < Pg, but the entire volume of gas remains in the solution. The degree of oversaturation, particularly upon free foaming (not in flow) can be 2- to 3-fold. In real polymer compositions, there are always solid admixtures, which have poor wetting areas. This reduces the degree of oversaturation at the interface melt-molding tool. Moreover, bubble nuclei can result from fragmentation of gas bubbles in the polymer [16]. Another factor that promotes the formation of bubble nuclei is the presence of localized hot points in the polymer melt they act as nuc-leation centres. Hot points appear either after a chemical reaction in the melt polymer [17], or in overheated areas on the surface of metal equipment [18]. Density of nucleation can be improved via introduction of various agents that reduce tension of the polymer [19]. 

Fig. 7. Comparison of the cluster binding fold of the water-soluble Rieske fragment from bovine heart 6ci complex (ISF, left PDB file IRIE) with the structure of ru-bredoxin (middle PDB file 7RXN) and with the zinc-ribbon motif (right PDB file ITFl). The metal binding loops are shown as ball-and-stick models of the backbone atoms.

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