Molecule, kinked

The extended chain is another conformation which has been discussed often and proved to exist—e.g., in linear polyethylene crystallized at high pressures. It has also been assumed for amorphous polymers in the form of strands of parallel molecules [kink model (57)]. The maximum length L (x-ray) of a sequence of vinyl monomers of basic molecular weight M0 is 2.52 A. Straight strands of molecules can be... 

The central 10 base pairs of the palindromic DNA molecule have a regular B-DNA structure. Between base pairs 5 and 6 in each half of the fragment (base pairs are counted from the center) there is a 40° kink which causes these base pairs to be unstacked (Figure 8.24a). After this localized kink the two end regions have an essentially B-DNA structure. The kink occurs at a TG step in the sequence GTG. These TG steps at positions 5 and 6 are highly conserved in both halves of different CAP-binding sites, presumably in part because they facilitate kinking. 

The C-terminal transmembrane helix, the inner helix, faces the central pore while the N-terminal helix, the outer helix, faces the lipid membrane. The four inner helices of the molecule are tilted and kinked so that the subunits open like petals of a flower towards the outside of the cell (Figure 12.10). The open petals house the region of the polypeptide chain between the two transmembrane helices. This segment of about 30 residues contains an additional helix, the pore helix, and loop regions which form the outer part of the ion channel. One of these loop regions with its counterparts from the three other subunits forms the narrow selectivity filter that is responsible for ion selectivity. The central and inner parts of the ion channel are lined by residues from the four inner helices. 

Quite large elastic strains are possible with minimal stress in TPEs these are the synthetic rubbers. TPEs have two specific characteristics their glass transition temperature (7 ) is below that at which they are commonly used, and their molecules are highly kinked as in natural TS rubber (isoprene). When a stress is applied, the molecular chain uncoils and the end-to-end length can be extended several hundred percent, with minimum stresses. Some TPEs have an initial modulus of elasticity of less than 10 MPa (1,500 psi) once the molecules are extended, the modulus increases. 

Considering a fiber or thread of nylon-66, which is an unoriented glassy polymer, its modulus of elasticity is about 2,000 MPa (300,000 psi). Above the Tg its elastic modulus drops even lower, because small stresses will readily straighten the kinked molecular chains. However, once it is extended and has its molecules oriented in the direction of the stress, larger stresses are required to produce added strain. The elastic modulus increases. 

Figure 41-5. Diagram of a section of a bilayer membrane formed from phospholipid molecules. The unsaturated fatty acid tails are kinked and lead to more spacing between the polar head groups, hence to more room for movement. This in turn results in increased membrane fluidity. (Slightly modified and reproduced, with permission, from Stryer L Biochemistry, 2nd ed. Freeman, 1981.)...

In addition, Winnewisser et al. [36] have demonstrated quantum monodromy for the NCNCS molecule, not only in the (vb, Ka) eigenvalues but also in the Bes = B + C)/2 rotational constant, which varies smoothly with Ka, at fixed Vb for Vb = 0-2, but shows a kink for Vb = 3-5. This observation is a key to the assignment of the extremely congested rotational spectrum of this interesting quasilinear molecule. 

Although most of an RNA molecule is single-stranded, there often are some double-stranded regions. Intramolecular base pairing between guanine and cytosine and between adenine and uracil creates loops and kinks in the RNA molecule. The structure of one kind of RNA molecule is shown in Figure 13-30. 

The lattice gas model of Bell et al. [33] neither gave any detailed mechanism of the orientational ordering nor separated the contributions of the headgroup and the acyl chain. Lavis et al. [34] discussed Ref. 33 critically and concluded that the sharp kink point in the isotherm at transition was an artifact of the mean field approximation used. An improved correspondence to experimental data was claimed by the use of the real-space renormalization group method [35]. The same authors returned to the problem [35] and concluded that in addition to the orientation of the molecules, chain melting had to be included in a model which could interpret the phase transitions. 

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