Superhelix

Collagen is a superhelix formed by three parallel, very extended left-handed helices... 

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

The difference between the linking number of a DNA and the linking number of its relaxed form is AL AL = (L — To) - In our example with four negative supercoils, AL = 4. The superhelix density or specific linking difference... 

Richmond and collaborators (Figure 12.30). The octamer (Figure 12.29) has surface landmarks that guide the course of the DNA around the octamer 146 bp of B-DNA in a flat, left-handed superhelical conformation make 1.65 turns around the histone core (Figure 12.30), which itself is a protein superhelix consisting of a spiral array of the four histone dimers. Histone 1, a three-domain protein, serves to seal the ends of the DNA turns to the nucleosome core and to organize the additional 40 to 60 bp of DNA that link consecutive nucleo-... 

Fig. 8. Space Ailing model of a poly-L-lysine a-helix with CIO4 anions inserted between the NH3 -side groups forming a left-handed superhelix 911...

Fig. 3.18 Nucleosome core particle (NCP)-polyamide co-crystal structures (PDB codes 1M18 and 1M19). (Top) Partial structure, viewed down the superhelical axis. Base pairs 58-145 (shown in white) and associated proteins (H3, blue H4, green H2A, yellow H2B, red) are shown for each complex. Superhelix locations (SHLs) are labeled as each major...

The four histone groups that are composed of ho-mogeneous proteins, H2A, H2B, H3, and H4, make up the nucleosome core. Each core consists of two copies of the four histones. The double-stranded DNA is wrapped twice around each core in a left-handed superhelix. A superhelix is the name given to the additional helix made by the double-stranded, helical DNA as it is wrapped around the nucleosome core. A familiar superhelix in everyday life is a twisted spiral telephone cord. The nucleosome core of histones do not recognize specific DNA structures rather, they can bind to any stretch of DNA as long as it is not too close to a neighboring nucleosome. The order of contact of histones to the DNA is as follows ... 

Figure 4.24 Superhelix with helix angle < > governing handedness of packing between preferential helical main chains of contiguous polysilane chains for origin of Cotton effect of polysilane aggregates.

Figure 7.9 Different handedness of packing of right-handed helices with different pitch-to-diameter ratios. Right-handed helices with p/d < n interact to give right-handed superhelix, while when p/d > it, superhelix is left-handed. (Reprinted with permission of Wiley-VCH from Chemistry—A European Journal, Vol. 6, p. 3249 ad ff., copyright 2000.)...

Fig. 3. Three-dimensional structures of three examples of superstructures formed by sequence repeats a linear rod (the spectrin a-chain dimer [PDB 2spc]), a superhelix of repeats (armadillo repeats of importin a-subunit [PDB lbk5]), and a closed /3-propeller (WD40 repeats from a fragment of the /3-subunit of the guanine nucleotide binding protein 1 [PDB lgg2 chain B]).

The effective potential governing torsional deformations could conceivably be quite anharmonic, so that overwinding is much more strongly resisted than underwinding for finite deformations. This question is addressed by examining the dependence of the torsion constant on temperature(40) and on superhelix density. 

Figure 4.10. Best-fit torsion constant a versus experimental time span for two different samples of supercoiled pUC8 dimer. The two samples are in 10 mAf Nad, 10 mAf Tris, 1 mAf EDTA, at pH 8 and T = 20°C, and differ only in their mean superhelix density (it) ,

A. S. Benight, J. Langowski, B. S. Fujimoto, and J. M. Schurr, unpublished results). It appears that the transition is not induced in samples with higher than normal superhelix densities. This suggests that the equilibrium between the secondary structure states a and b might be rather sensitive to superhelical stress. This question is addressed immediately below. 

Samples of pUC8 dimer (5434 bp) with different median superhelix densities were prepared by relaxing the native plasmid with topoisomerase I... 

Figure 4.20. Variation of the molar ellipticity [0] and torsion constant a of pUC8 dimer with superhelix density. All samples were prepared from the same stock solution as described in the text. Solution conditions were 10 mM NaCl, 10 mM Tris, 1 mM EDTA, and pH 8, and the DNA concentrations were between 40 and 50 g/ml. , Five days after preparation +, 15 days after preparation , 2 months after preparation , samples prepared from the same initial stock solution 4 months after the other samples and measured within 5 days. Top [0] versus superhelix density a. Only the a = -0.015 sample changed significantly over the first few weeks. Bottom a versus superhelix density. Torsion constants are averages for 70- and 120-ns time spans. For the FPA measurements only, ethidium was added to a concentration of 1 dye per 300 base pairs. With the exception of a - - 0.025, the samples denoted by did not change significantly over a period of 2 months, and it is the final values that are plotted. The final measurement for the a= -0.025 sample is denoted by . The error bars are less than or equal to the size of the symbols in the figure. Complete data for o= —0.048 and o= —0.031 are given in Figure 4.10, which demonstrates the ability of FPA measurements to distinguish between samples whose torsion constants differ by only 10%.

Figure 4.21. D0 and Z)pU, for pUC8 dimer versus superhelix density. Conditions are the same as in Figure 4.20. All samples were measured at 5-7 days after preparation, again at 2-3 weeks, and finally at l -2 months. , Five days after preparation +,...

Top Dplu versus superhelix density. >plat is the apparent DLS diffusion coefficient at A2 = 20 x 10 ° cm 2. The lower values at a = —0.015, —0.020, and -0.025 suggest that, in this intermediate range, DNA exhibits a different secondary structure with decreased torsional and/or bending rigidity. 

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