Three-dimensional model phases proteins

In Fig. 30, a three-dimensional model is presented in which only the organic phases are shown. Hexagonal plates of MM alternate with pleated sheets of CP. The hydrophobic sides of MM are facing each other and encase the mineral phase. The relationship between hydrophobic bonding and accessible surface area in proteins, and the effect of polar and non-polar side groups on free energy values has recently been discussed246. For informations on hydrophobicity in protein systems see Refs.247-252. ... 

The steepness of the unfolding transition of a protein as compared with that of a helical polypeptide, is, therefore, seen to be a consequence of the fact that the structure of the forma- extends in three dimensions (25). The two and three dimensional Isiiig model can show true phase transitions when the lattice is infinitely large, while the one dimensional model cannot (cf. Ref. (58)). Apparently, the finite three dimensional model approaches maximum cooperativity (not of course a true phase transition) rather easily. 

For molecules of molecular weight above 20,000 g/mol, X-ray diffraction remains the only experimental approach available to obtain detailed and reliable three-dimensional atomic models. The major steps of the method include the obtention of large and well-ordered crystals, their exposure to X-rays and collection of diffraction data and the phasing of these data to obtain by Fourier analysis a three-dimensional view (or map) of the electron density of the molecule. Finally a three-dimensional atomic model of the protein is fitted like a hand in a glove within this map, using a kit containing all the available biochemical and spectroscopic information (Table 6.2). The reliability of the final atomic model is of course dependent on the qnality of the electron density map. This qnality depends on the number of X-ray data per atom and on the resolution and accnracy of these data, which in turn are highly dependent on the size and quality of the crystals. 

An x-ray analysis will measure the diffraction pattern (positions and intensities) and the phases of the waves that formed each spot in the pattern. These parameters combined result in a three-dimensional image of the electron clouds of the molecule, known as an electron density map. A molecular model of the sequence of amino acids, which must be previously identified, is fitted to the electron density map and a series of refinements are performed. A complication arises if disorder or thermal motion exist in areas of the protein crystal this makes it difficult or impossible to discern the three-dimensional structure (Perczel et al. 2003). 

When protein solutions are shaken, insoluble protein is often seen to separate out (Bull and Neurath, 1937). The coagulation occurs at the interface and may be observed when protein is allowed to adsorb from solution at a quiescent interface (Cumper and Alexander, 1950) or when spread protein monolayers are compressed (Kaplan and Frazer, 1953). This is an interesting type of phase separation in which a three-dimensional coagulum is formed from the two-dimensional monolayer, once a certain critical value of the interfacial pressure is exceeded. The concentration of protein in the monolayer when the critical pressure is reached may be thought of as the solubility in the interface under those conditions. When this concentration is exceeded, precipitation occurs. A simple model may help to illustrate how free energy considerations govern the coagulation. 

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