Stabilization, compact protein

Hydrophobic effects are thus of practical interest. If we accept the goal of a simple, physical, molecularly valid explanation, then hydrophobic effects have also proved conceptually subtle. The reason is that hydrophobic phenomena are not tied directly to a simple dominating interaction as is the case for hydrophilic hydration of Na+, as an example. Instead hydrophobic effects are built up more collectively. In concert with this indirectness, hydrophobic effects are viewed as entropic interactions and exhibit counterintuitive temperature dependencies. An example is the cold denaturation of globular proteins. Though it is believed that hydrophobic effects stabilize compact protein structures and proteins denature when heated sufficiently, it now appears common for protein structures to unfold upon appropriate cooling. This entropic character of hydrophobic effects makes them more fascinating and more difficult. 

Groves, M.J. and Teng, C.D. (1992). The effect of compaction and moisture on some physical and biological properties of proteins. In Stability of Protein Pharmaceuticals, Part A Chemical and Physical Pathways of Protein Degradation, T.J. Ahem and M.C. Manning, eds. Plenum Press, New York, 311-359. 

The stability of proteins toward covalent degradation pathways can often depend on the protein s folded state. In each pathway, solvent accessibility and varying degrees of structural freedom of the peptide backbone and/or side chains around the labile residue are required for reactions to take place. Accordingly, stabilization of the protein s folded state (i.e., its compact structure) that minimizes solvent accessibility can lower the reaction rate of some covalent protein modifications, extending the shelf life of the protein product. Therefore, the selection of formulation excipients depends on their direct and indirect influence on the rates of covalent protein degradation. 

As discussed earlier in this chapter and also in chapter 6, thermal stabilities of proteins in vivo are influenced by many constituents of the intracellular milieu, including low-molecular-mass protein stabilizers. The process of protein folding, whether during initial synthesis or following heat-induced unfolding, thus will be influenced not only by activities of protein chaperones, but also by the activities of low-mole-cular-mass organic solutes. In principle, heat stress could be ameliorated in part by accumulation of low-molecular-mass protein-stabilizing solutes that favor formation of the compact, folded state of proteins. Such chemical chaperones could complement the activities of protein chaperones. 

In the pioneering work on the occurrence and stability of proteins and amino acids in fossils, Abelson determined that thermally unstable amino acids such as threonine and serine were either much reduced or absent in fossils, whereas more stable amino acids, such as glycine and alanine, were still present (see ref. 5). The total concentration of amino acids decreases dramatically with time, von Endt and Erhardt reported their results concerning the differential chemical disintegration of amino acids in compact... 

The following example may serve as an indication of the contribution from hydro-phobic interaction to the stabilization of a compact protein structure. 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

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