Amino protein stability, composition

With a knowledge of the methodology in hand, let s review the results of amino acid composition and sequence studies on proteins. Table 5.8 lists the relative frequencies of the amino acids in various proteins. It is very unusual for a globular protein to have an amino acid composition that deviates substantially from these values. Apparently, these abundances reflect a distribution of amino acid polarities that is optimal for protein stability in an aqueous milieu. Membrane proteins have relatively more hydrophobic and fewer ionic amino acids, a condition consistent with their location. Fibrous proteins may show compositions that are atypical with respect to these norms, indicating an underlying relationship between the composition and the structure of these proteins. 

Peptide and protein stability is highly dependent on amino acid composition and sequence and, for proteins, on the formation of higher-order structures, which means that every protein has to be considered as a special case. Given a certain sequence, external factors such as pH, ionic strength, temperature, pressure, and the existence of interfaces can also have a tremendous impact on peptide and protein integrity [24], There are two main degradation pathways ... 

With so many specificities, it is clear that a simplified model of a uniformly charged protein surface is not appropriate to describe the relevant interaction effects. On the other hand, some general features indeed exist. For example, knowing the amino acid residues that are accessible to bulk water and ions, it should be possible to predict the influence of each salt on protein stability at a given salt concentration. The term salt includes also the buffer composition, in which the protein is immersed. Indeed, Kim et showed in an elegant work that the enzymatic activity depends on the chosen buffer, even when the pH is the same for different buffers used. 

Fig. 6. Structural stability of major ampullate silk protein in constrained Nephila edulis. The graph shows a time series of circular dichroism spectra of major ampullate (MA) protein at 1% w/v in distilled water. The spiders prior to dissection were prevented from spinning, but fed and watered for at least 2 weeks. With time, the secondary structure of silk protein is becoming more and more disordered. The arrow indicates increasing time (days). Note that the amino acid composition of the silk protein was similar to that of a native N. edulis spider. Interestingly, silk protein extracted from the constrained spider did not respond to denaturing conditions (detergents, alcohols, pH, and salts Dicko et al, 2004a, 2005).

In proteins, specific combinations of the dihedral angles c ) and / (see p. 66) are much more common than others. When several successive residues adopt one of these conformations, defined secondary structures arise, which are stabilized by hydrogen bonds either within the peptide chain or between neighboring chains. When a large part of a protein takes on a defined secondary structure, the protein often forms mechanically stable filaments or fibers. Structural proteins of this type (see p. 70) usually have characteristic amino acid compositions. 

The structural proteins give extracellular structures mechanical stability, and are involved in the structure of the cytoskeleton (see p. 204). Most of these proteins contain a high percentage of specific secondary structures (see p. 68). For this reason, the amino acid composition of many structural proteins is also characteristic (see below). 

This section deals with the standard repertoire of techniques needed for working with proteins, that can be used to get information about concentration and purity, molar mass, amino add composition and sequence, and tertiary conformation and stability. 

Ponnuswamy P Muthusamy, R Manavalan, P. Amino acid composition and thermal stability of proteins. Internal. J. Biol. Macro-moL 1982 4 186-190. 

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