Helix parameters

The parameters indexed with a are connected with the nucleation step or other effects occurring only once per triple helix. Parameters denoted by s are related with the equilibrium constants of the propagation steps and are ordered to be independent of the position of the reacting chain segment. This implies that end effects are neglected. Since the same dependences are valid for AH° and AS, with the help of their chain length dependence we can determine AG by extrapolation up to 3 n - 2 = 0, and thus, a can be estimated it depends neither on temperature nor on the chain length. 

Most DNA, natural and synthetic, can adopt the B-form as defined by its characteristic X-ray pattern [3]. There are few a species of synthetic DNA, namely poly(dA) poly(dT), poly(dI) poly(dC), poly(dA-dI) poly(dC-dT) and poly(dI-dC)-poly(dI-dC), which have a B-form that significantly differs from that of the other complementary deoxy polymers due to their different intramolecular packing arrangements and slightly changed value for the rise per residue. The helix parameters are presented in Table 1. The linear sequen-... 

Table 25. Helix Parameters (in nm) According to the Triple Helical Model... 

It is well known that PLL can assume an a-helical conformation above pH 10. The complex formation between PLL and heme was carried out at pH 12, where the e-amino groups of the side chain of PLL were not protonated and PLL formed a complete a-helix14. The helix parameter (molar dlipticity at 222 nm) was the same before and after complex formation with heme. The helix content, Le. the overall conformation of PLL, was not affected. The viscosity of the PLL solution also remained constant on the addition of ferriheme14. These results mean that complex formation occurs with a structure complementary to the a-helical conformation and that bending of the PLL helix does not occur. The inter-polymer sandwich structure proposed by Blauer [Fig. 4(c)]9 is thus ruled out. The structure... 

The conformational energies and helix parameters are calculated for the various states of polymethylphenylsilylene chain. The calculations are performed for the three different relative dispositions of the phenyls attached to three successive silicon atoms. The minima are invariably shifted from perfectly staggered positions. 

N 143 "Conformational Energy Calculations on Alginic Acid I. Helix Parameters and Flexibility of the Homopolymers"... 

H-DNA, proposed structure 226 helical twist 216 helix parameters 216 Holliday junction 228 - 230 hydration of 216 hydrolysis of 249, 251 hypersensitive sites 266 interaction with spermidine and... 

A dramatically different form of the double helix has been observed in DNA containing alternating purine-pyrimidine sequences, especially d(CG)n but also d(TG)n. It is a left-handed, rather than a right-handed helix and is known as the Z form of DNA. Helix parameters are contrasted in Table 7.2 and space-filling models of the Z form and B form of DNA are compared below (Fig. 7-4.). 

Table 1. Backbone Dihedral Angles and Helix Parameters for Some Exolipophilic-Endopolarophilic Conformations of PHBab...

Sundararajan has studied silane polymers including polymethylphenyl-silylene)243 and polysilapropylene. " " Different tacticities and conformations of polymethylphenylsilylene were examined and the relative stabilities of each were reported. The most stable configuration was for the syndiotactic polymer with an all-trans conformation. Helix parameters, a priori bond probability, and characteristic ratios were calculated for this polymer. Polysilapropylene was studied in a similar manner. MM2 energies of the minimum for each of the different rotational isomers were included. As with the first study, contour plots of both energy and helix parameters versus (j) and < ) + 1 angles were given. 

The crystal structure of an unmodified hanmierhead RNA in the absence of divalent metal ions has been solved. The X-ray crystal structure of the oligonucleotide d(GGCGAATTGG) has been described. It was designed to contain the d(G.GC)2 fragment and thus provide the basic repeat unit of a DNA triple helix. Parameters derived from this crystal structure enabled construction of models of both parallel and antiparallel triple helices. A variety of physical techniques has been used to investigate the structure of DNA containing the deoxyribosyl derivative 5-nitroindole. ... 

Helical symmetry The polymeric proteins of filamentous viruses and the cytoskel-ton possess helical symmetry, in which subunits are related by a translation, as well as a rotational component. Actin, myosin, tubulin and various other fibrous proteins all interact with helical symmetry, which is often called screw symmetry. Screw symmetry, which relates the positions of adjacent subunits, combines a translation along the helix axis with the rotation. Actin forms a two-stranded helix of globular actin subunits. However, important variations in the helix parameters occur (Egehnan et al, 1982). The rise per subunit is relatively constant, but the twist or relative rotation around the helix axis is highly variable. This polymorphic tendency is probably important for the smooth functioning of muscle contraction, which involves considerable force generation. 

NMR structures of d(CGCGAATTCGCG) have been reported by Nerdal et al. (39) and Lane et al. (40) based on 2D-NOESY data. Nerdal et al, proposed a highly underwound structure with kinks at the primary and secondary roll points and at the ApT step. Lane et al. propose an NMR structure much closer to that of conventional B DNA. The limit of the nuclear Overhauser effect to interproton distances -4.5 A makes unequivocal determination of the helix parameters in an... 

The mean helix parameters of the three forms of DNA are given in the Table. 

The considerations of the preceding section are illustrated in more detail here by describing a procedure that has been implemented for studying polymer crystal packing [2]. It allows the simultaneous optimization of the internal atom coordinates of the chain unit and the helix parameters along with the cell packing parameters. 

There are several coordinate systems that have to be dealt with. Ultimately, in order to carry out the minimization process, the total energy is best expressed in terms of Cartesian coordinates. However, a general unit cell or lattice is characterized by non-orthogonal basis vectors. A cylindrical coordinate system is used to represent the molecular helix. The intramolecular energy is expressed in terms of valence coordinates. Thus transformations must be set up that relate the Cartesian coordinates to the helix parameters, the unit cell parameters and the valence coordinates. The helix operations and the unit cell parameters are considered first. 

Since the crystal energy is expressed as a iimction of the position vectors Xg, j(i)it follows that the independent basis param ers to be optimized in energy minimization are the unrotated CRU coordinates, v, the helix parameters, a and d, a chain setting angle, chain c axis offset, Zo and the lattice parameters, a, b, (X, P, y. The basis parameters are collected into a vector, P,... 

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