Helix model

One of the most thoroughly investigated examples of polymeric biomolecules in regard to the stabilization of ordered structures by hydration are the DNAs. Only shortly after establishing the double-helix model by Watson and Crick 1953 it became clear, that the hydration shell of DNA plays an important role in stabilizing the native conformation. The data obtained by the authors working in this field up until 1977 are reviewed by Hopfinger155>. 

The secondary structure of DNA is shown in Figure B. This "double helix" model was first proposed in 1953 by James Watson and Francis Crick, who used the x-ray crystallographic data of Rosalind Franklin and Maurice Wilkins. Beyond that, they were intrigued by the results of analyses that showed that in DNA the ratio of adenine to thymine molecules is almost exactly 1 1, as is the ratio of cytosine to guanine ... 

The double helix model provides a simple explanation for cell division and reproduction. In the reproduction process, the two DNA chains unwind from each other. As this happens, a new matching chain of DNA is synthesized on each of the original ones, creating two double helices. Since the base pairs in each new double helix must match in the same way as in the original, the two new double helices must be identical to the original. Exact replication of genetic data is thereby accomplished, however complex that data may be. 

Kajava, A. V., Cheng, N., Cleaver, R., Kessel, M., Simon, M. N., Willery, E., Jacob-Dubuisson, F., Locht, C., and Steven, A. C. (2001). Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Mol. Microbiol. 42, 279-292. 

Govaerts et al. (2004) proposed a parallel /1-helix model for prion rods that is consistent in overall dimensions with their low-resolution EM studies of two-dimensional PrP 27-30 crystals (Wille et al, 2002). In this model, residues 89-174 form 4 coils, or complete helical turns (Jenkins and Pickersgill, 2001), of a left-handed, parallel /Hielix (Fig. 5B). The coils of one monomer are proposed to stack on the coils of another to form an extended triangular -structure. Three of these triangular units pack together to form the fibril (Fig. 5G and D). The G-terminal a-helices (a2 and a3) of monomeric PrP are proposed to retain their native structure in the fibril and pack around the outside of the trimer (Fig. 5G and D). The presence of these helices in the prion rods is consistent with antibody binding studies (Peretz et al, 1997), the presence of a disulfide bond (Turk et al, 1988), and FTIR measurements (Wille et al, 1996). 

The parallel /f-helix model does not provide an 8.8-A sheet-to-sheet spacing, suggested by the 8.8-A reflection of the prion rod diffraction pattern (Nguyen et al., 1995). However, the authors (Govaerts et al, 2004) note that a number of jS-sandwich folds are consistent with the general structural requirements for a model of fibrillar PrP, although they do not attempt to model it as such. 

Fig. 14. Cylindrical /1-helix model of polyglutamine fibrils, from Perutz et at. (2002a).

Bertoft, E. (2004). On the nature of categories of chains in amylopectin and their connection to the super helix model. Carbohydr. Polym., 57, 211-224. 

In a refined staircase model the exact orientation of the planar groups is described using three angles. The authors 145) conclude that the triple helix model can be used to account for the optical rotation of helicenes, but that more sophisticated quantum mechanical calculations can better be based on the refined staircase model. 

The nucleic acids are among the most complex molecules that you will encounter in your biochemical studies. When the dynamic role that is played by DNA in the life of a cell is realized, the complexity is understandable. It is difficult to comprehend all the structural characteristics that are inherent in the DNA molecules, but most biochemistry students are familiar with the double-helix model of Watson and Crick. The discovery of the double-helical structure of DNA is one of the most significant breakthroughs in our understanding of the chemistry of life. This experiment will introduce you to the basic structural characteristics of the DNA molecule and to the forces that help establish the complementary interactions between the two polynucleotide strands. 

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