Aggregated protein structures

Another mechanism preventing aggregation is the immunization against aggregated protein structures. A dramatic success had been archived using this method by Schenk et al. 1999 in the case of amyloid p [81]. He was able to prevent further amyloid deposition, in older mice that already had neuritic senile plaques due to a overexpression of a mutant form of the Alzheimer precursor protein (APP) that generates high level of amyloid p. 

Quaternary structure (Section 26.9) The highest level of protein structure, involving a specific aggregation of individual proteins into a larger cluster. 

There are three potential methods by which a protein s three-dimensional structure can be visualized X-ray diffraction, NMR and electron microscopy. The latter method reveals structural information at low resolution, giving little or no atomic detail. It is used mainly to obtain the gross three-dimensional shape of very large (multi-polypeptide) proteins, or of protein aggregates such as the outer viral caspid. X-ray diffraction and NMR are the techniques most widely used to obtain high-resolution protein structural information, and details of both the principles and practice of these techniques may be sourced from selected references provided at the end of this chapter. The experimentally determined three-dimensional structures of some polypeptides are presented in Figure 2.8. 

The first problem encountered once the peptide has been successfully synthesized is that standard purification protocols fail. Although very hydrophobic peptides are soluble in acids such as TFA, these harsh conditions are not suitable for purification, because they can reduce column life times and denature native protein structures. Hence residual acid has to be removed, and many peptides can then be redissolved in mixtures of water and tert-butanol. Peptides with a strong tendency to aggregate may be dissolved either in trifluoroethanol (TFE), hexafluoroisopropanol (HFIP), mixtures of 1-propanol and 1-butanol, 20% acetic acid or 70-90% formic acid. 

The cascade consists of a number of steps which involve protein structure modification by proteolysis or through conformational change and aggregation. 

The ELISA is an appropriate method to detect some, but not all, of these product variants. The reactivity of antibodies is not affected much by glycosylation of the antigen. An ELISA would not be the most appropriate method to analyze product variants due to differences in glycosylation. ELISA would be appropriate for analysis of variants, such as aggregates, that contain a different protein structure that can be specifically recognized by an antibody. 

Quaternary structure refers to the specific aggregation or association of separate protein chains to form a well-defined structure. Part D of Figure 2.4 compares the quaternary structure of a dimeric protein (two polypeptide chains) to the lower levels of protein structure. The separate protein chains are often referred to as subunits or monomers these subunits may be identical or may be of quite different sequence... 

It has been our approach to protein structure determination by x-ray crystallography that it is imperative to begin with well-characterized and well-behaved protein. In particular, it is important that the protein be reasonably soluble and monodisperse in solution. Unfortunately, as discussed above, recombinant HIV-1 integrase satisfies neither of these conditions. One approach we and others have taken to circumvent these problems has been to examine truncated versions of HIV-1 integrase to determine if removal of amino acids from either terminus or both affects solubility and aggregation properties. 

---