Globular proteins compact

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

Globular protein (Section 26.9) A protein that is coiled into a compact, nearly spherical shape. These proteins, which are generally water-soluble and mobile within the cell, are the structural class to which enzymes belong. 

Globular proteins are compact, are roughly spherical or ovoid in shape, and have axial ratios (the ratio of their shortest to longest dimensions) of not over 3. Most enzymes are globular proteins, whose large internal volume provides ample space in which to construct cavities of the specific shape, charge, and hy-drophobicity or hydrophilicity required to bind substrates and promote catalysis. By contrast, many structural proteins adopt highly extended conformations. These fibrous proteins possess axial ratios of 10 or more. 

The association of secondary structures to give super-secondary structures, which frequently constitute compactly folded domains in globular proteins, is completed by the a-a motifs in which two a-helices are packed in an anti-parallel fashion, with a short connecting loop (Figure 4.8c). Examples of these three structural domains, often referred to as folds, are illustrated in Figures 4.9—4.11. The schematic representation of the main chains of proteins, introduced by Jane Richardson, is used with the polypeptide backbone... 

The peptide chain in globular proteins is folded into fairly compact conformations. Water-soluble enzymes are typical globular proteins which have most of the hydrophobic amino acid residues located in the interior and the hydrophilic residues located mainly at the surface in contact with solvent water. The average radii are 20-40 A (Boyer, 1970). It is clear that there are common morphological features between surfactant micelles and enzyme molecules. This fact has prompted many chemists to use micelles as enzyme models. However, it must be emphasized that micelles exist in dynamic equilibria with monomeric surfactant and their hydrophobic core is quite fluid, whereas enzyme molecules have precisely fixed three-dimensional structures. 

Any crystal of a globular protein can be regarded as an ordered and open array of compact molecules that make nearly minimal contact with... 

Before we examine some specific solvation effects on cooperativity we must first consider various aspects of the solvation Gibbs energy of a macromolecule a. We present here one possible decomposition of AG which will be useful for our purposes. Consider a globular protein a which, for simplicity, is assumed to be compactly packed so that there are no solvent molecules within some spherical region to which we refer as the hard core of the protein. The interaction energy between a and the fth solvent molecule (the solvent is presmned to be water, w) is written as... 

The essence of this model for the second virial coefficient is that an excluded volume is defined by surface contact between solute molecules. As such, the model is more appropriate for molecules with a rigid structure than for those with more diffuse structures. For example, protein molecules are held in compact forms by disulfide bridges and intramolecular hydrogen bonds by contrast, a randomly coiled molecule has a constantly changing outline and imbibes solvent into the domain of the coil to give it a very soft surface. The present model, therefore, is much more appropriate for the globular protein than for the latter. Example 3.3 applies the excluded-volume interpretation of B to an aqueous protein solution. 

Table 4-2 shows the proportions of a helix and J8 conformation (expressed as percentage of residues in each secondary structure) in several small, single-chain, globular proteins. Each of these proteins has a distinct structure, adapted for its particular biological function, but together they share several important properties. Each is folded compactly, and in each case the hydro-... 

The unique three-dimensional structure of each polypeptide is determined by its amino acid sequence. Interactions between the amino acid side chains guide the folding of the polypeptide to form a compact structure. Four types of interactions cooperate in stabilizing the tertiary structures of globular proteins. 

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