Protein structure random coil conformation

Proteins fold on a time scale from [is to s. Starting from a random coil conformation, proteins can find their stable fold quickly although the number of possible conformations is astronomically high. The protein folding problem is to predict the folding and the final structure of a protein solely from its sequence. 

Independently, Ruan etal. (1990) demonstrated that unnatural metal-ligating residues may likewise be utilized toward the stabilization of short a helices by transition metal ions (including Zn " ")—these investigators reported that an 11-mer is converted from the random coil conformation to about 80% a helix by the addition of Cd at 4°C. These results suggest that the engineering of zinc-binding sites in small peptides or large proteins may be a powerful approach toward the stabilization of protein secondary structure. 

As a prelude to discussing the mechanism of folding of intact proteins in the next chapter, we end this one with a discussion of the kinetics and mechanism of folding of isolated secondary structural elements of proteins from the random coil conformation. 

Calsequestrin is a calcium-storage protein found in the sacroplasmic reticulum, which binds about 50 calcium ions per monomer (molecular weight 40 000) with binding constants in the range 103-105 dm3 mol. Release and uptake of Ca2+ during muscle contradion and relaxation involve this store. Calsequestrin from rabbit skeletal muscle has a random coil conformation in the absence of calcium. Binding of Ca2+ is associated with a change to a more compact structure.267... 

Polypeptides and poly(a-amino acid)s have a quite unique position amongst synthetic polymers. The reason for this is that most common synthetic polymers have very little long range order in solution and their properties are the products of statistical random coil conformations. Polypeptides, in contrast, can adopt well defined, ordered structures typical of those existing in proteins, such as a-helix and P-struc-tures. Moreover, the ordered structures can undergo conformational changes to the random coil state as cooperative transitions, analogous to the denaturation of proteins. 

The major casein monomer subunits have random coil conformation that facilitates strong protein-protein interaction via hydrophobic and ionic bonding. The unique amphiphilic structure, which arises from separately clustered hydrophobic and negatively charged (acidic and ester phosphate) amino acid residues along the polypeptide chain, makes them susceptible to pH and Ca ion concentration effects. This amphiphilic nature is probably responsible for the excellent surfactant properties of commercial caseinate in a variety of food applications. 

Previous works have shown that a basic PRP (IB8c) binds to condensed tannins much more effectively than a-amylase (de Freitas and Mateus 2002). This can be explained by the 3D structure of proteins a-amylase is a globular protein, and IB8c is likely to adopt an extended random coil conformation, which would allow the protein to offer more contact sites to interact with tannins. However, a-amylase seems to be more specific and selective than PRPs in the aggregation with samples containing different amounts of procyanidins (Mateus et al. 2004c). 

Studies by Anfinsen of the reversible denaturation of the pancreatic enzyme ribonuclease prompted the hypothesis that secondary and tertiary structures are derived inclusively from the primary structure of a protein (Figures 4-11 and 4-12). RNase A, which consists of a single polypeptide chain of 124 amino acid residues, has four disulfide bonds. Treatment of the enzyme with 8 M urea, which disrupts noncovalent bonds, and j8-mercaptoethanol, which reduces disulfide linkages to cysteinyl residues, yields a random coil conformation. 

Light-absorption and CD data of this blue copper(II)-protein from horse-radish roots were measured and resolved in the range 200 to over 700 nm at various pH values. The relatively largest rotatory strength of the several bands observed appeared to be above 740 nm, which was the limit of the measurements. The spectra were similar to those of the Pseudomonas blue protein. The origin of the bands was not identified. Far ultraviolet data indicated very little a-helix content, about 40% /3-structure and the remainder to be in random-coil conformations (111). 

The random coil conformation of a protein structure is the most difficult to evaluate. Usually the recognizable a-heUx and P-sheet contributions to the optical activity are estimated and the random coil is estimated by subtraction. 

The CD Spectra of P-sheet and random-coil conformations are isodichroic (identical elUp-ticity values) at 208 nm with an average effipticity of OOOdegcm dmor. The observed ellipticity at 208 nm for a-helix is -32600 4000deg cm dmoC. Thus the a-helical content (fraction of a-helical structure, of proteins can be estimated according to... 

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