Folded proteins, conformational stability

Upon biosynthesis, a polypeptide folds into its native conformation, which is structurally stable and functionally active. The conformation adopted ultimately depends upon the polypeptide s amino acid sequence, explaining why different polypeptide types have different characteristic conformations. We have previously noted that stretches of secondary structure are stabilized by short-range interactions between adjacent amino acid residues. Tertiary structure, on the other hand, is stabilized by interactions between amino acid residues that may be far apart from each other in terms of amino acid sequence, but which are brought into close proximity by protein folding. The major stabilizing forces of a polypeptide s overall conformation are ... 

The characteristics that discourage the use of RPLC for preparative isolation of bioactive proteins favor its use as an analytical tool for studying protein conformation. Chromatographic profiles can provide information on conformational stability of a protein and the kinetics of folding and unfolding processes. Information about solvent exposure of certain amino acid residues (e.g., tryptophan) as a function of the folding state can be obtained by on-line spectral analysis using diode array UV-vis detection or fluorescence detection. 

Another example of a quantal repeat—but with considerable variation in sequence—is seen in the keratin-associated proteins (KAPs). In sheep, these display pentapeptide and decapeptide consensus repeats of the form G—G—Q—P—S/T and C-C-Q/R—P—S/T—C/S/T—C—Q—P/T—S, respectively (Parry et al., 1979). Some of the positions, as indicated by the presence of a consensus sequence, contain residues that occur much more frequently than others, but the absolute conservation of a residue in any position is not observed. The decapeptide consists of a pair of five-residue repeats closely related, but different to that displayed by the pentapeptide. Although the repeats have an undetermined structure, the similarity of the repeat to a sequence in snake neurotoxin suggests that the pentapeptides will adopt a closed loop conformation stabilized by a disulphide bond between cysteine residues four apart (Fig. 5 Fraser et al., 1988 Parry et al, 1979). Relative freedom of rotation about the single bond connecting disulphide-bonded knots would give rise to the concept of a linear array of knots that can fold up to form a variety of tertiary structures. The KAPS display imperfect disulphide stabilization of knots and have interacting... 

Primary, secondary, tertiary, and quaternary structure are familiar concepts for proteins and refer to the amino acid sequence, local folding arrangement, three-dimensional organization, and subunit interactions of polypeptide chains, respectively. Here, tertiary and quaternary structure shall be considered in the most general way, to include also the small molecules or ions that are essential for the conformational stability of the polypeptide chains. This is especially relevant for halophilic proteins, which have extensive interactions with solvent components (water molecules and salt ions). The known structure of a protein (at any level) always results from experiment, and as such is known only within appropriate error limits. 

The disulfide bond differs from other types of interactions in folded proteins, such as hydrogen bonds and hydrophobic, electrostatic and van der Waals interactions. The disulfide bond is a covalent bond that is able to significantly stabilize folded conformations by 2-5 kcal/ mol for each disulfide.11 The effect is presumed to be due mainly to a decrease in the configurational chain entropy of the unfolded polypeptide.21 On the other hand, another view is that the disulfide bond destabilizes folded structures entropically, but stabilizes them enthalpically to a greater extent.31... 

More work needs to be done to develop increasingly accurate representations of the electronic states of peptides and various side chain chromophores. Once this is completed, the models are in place to examine interactions between these states for a given protein conformation. An accurate and flexible model which can calculate CD spectra of a variety of protein structures would be invaluable in the study of protein folding, stability, and structure. 

Not necessarily It is possible that replacement of one amino acid with another may abolish specific interactions critical for local folding or even overall protein stability. It is essential in these types of study to monitor protein conformation after mutagenesis. It is even more helpful if detailed structures, either from x-ray crystallography or NMR (Chap. 4), are available for the wild-type and mutant forms of the enzymes. 

Casadio, R., Compiani, M Fariselli, P. Vivarelli, F. (1995). Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks. Intelligent Systems for Molecular Biology 3,81-8. 

The interactions between various segments of a protein which are separated by several amino acids along the polypeptide chain but which fall within a short geometrical distance from one another due to the actual folding pattern, are expected to contribute to the stability of the protein conformation to a significant degree. 

In native proteins of known three-dimensional structure about 7% of all prolyl peptide bonds are cis (Stewart et al., 1990 MacArthur and Thornton, 1991). Usually, the conformational state of each peptide bond is clearly defined. It is either cis or trans in every molecule, depending on the structural framework imposed by the folded protein chain. There are a few exceptions to this rule. In the native states of staphylococcal nuclease (Evans et al., 1987), insulin (Higgins et al., 1988), and calbindin (Chazin et al., 1989) cis-trans equilibria at particular Xaa-Pro bonds have been detected in solution by NMR. In staphylococcal nuclease, the cis conformer of the Lys 116-Pro 117 bond can be selectively stabilized by bind-... 

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