Publisher Summary In the proper environment, a polypeptide chain can fold spontaneously to the three-dimensional structure of a native protein, and despite the possible presence of barriers in conformational space, the chain can find its way around these barriers to reach the structure of lowest free energy. This chapter describes the spontaneous folding of proteins; in vitro complementation of protein fragments; flexibility of proteins in solution: effect of cross-links and ligands, synthetic analogs of proteins; experimental approaches to the study of conformation; and energetic factors determining protein folding. The interatomic interactions within the chain and between the chain and the solvent dictate the folding and the range of the forces involved, is such that near-neighbor interactions are dominant. Folding is envisaged as taking place by the formation of nucleation sites in various parts of the chain, in response to near-neighbor interactions; the various nucleation sites become stabilized, when they are brought into proximity, so that long-range interactions can become operative. However, the development of conformational energy calculation procedures will enable the three-dimensional structure of a native protein to be predicted from the knowledge of its amino acid sequence and its interactions with the solvent in which it is dissolved.

Experimental and theoretical aspects of protein folding.

Using an empirical analysis of experimental data we have estimated a set of energy contributions which accounts for the stability of isolated α-helices. With this database and an algorithm based on statistical mechanics, we describe the average helical behaviour in solution of 323 peptides and the helicity per residue of those peptides analyzed by nuclear magnetic resonance. Moreover the algorithm successfully detects the α-helical tendency, in solution, of a peptide corresponding to a β-strand of ubiquitin.

Elucidating the folding problem of helical peptides using empirical parameters

Circular dichroism spectra have been obtained for albumin, alpha-chymotrypsinogen, collagen, concanavalin A, elastase, hemoglobin, histone f2b, alpha-lactalbumin, lactate dehydrogenase, beta-lactoglobulin, lysozyme, myoglobin, papain, ribonuclease A, and thermolysin in the presence of sodium dodecyl sulfate and dithiothreitol. While all spectra have the shape anticipated for a mixture of random coil and alpha helix, the intensities differ markedly ([theta]222 ranges from --1400 to --15 000 deg cm2/dmol). The variation in the circular dichroism can be quantitatively explained by a model which assumes that the arginyl, histidyl, and lysyl residues have an enhanced probability of propagating a helical segment in the presence of the detergent. The model also permits the computation of dimensional properties (unperturbed end-to-end distance and radius of gyration) for polypeptides of known amino acid sequence. Such computations have been performed for 67 proteins. The computed dimensions are compatible with experimental values and with the molecular weight dependence of the transport properties of the complexes. Furthermore, the model can account for the abnormal transport properties of the sodium dodecyl sulfate complexes formed by ribonuclease A, collagen fragments, and histones f2a1, f2a2, f2b, and f3. Even though some of the protein--sodium dodecyl sulfate complexes have helical contents as high as 50%, their overall conformation more closely approximates that of a random coil than a rod.

Conformational properties of the complexes formed by proteins and sodium dodecyl sulfate

A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long-range interactions between different regions, incorporating all these interactions in a single Ising-like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α- and β-structures for different residues in synthetic polypeptides, while long-range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x-ray structural data became available.

Theory of protein secondary structure and algorithm of its prediction.

Conformational studies of poly(oxyethylene)-bound peptides and protein sequences

Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. II. Characterization of the Host Polymers and Application of the Host-Guest Technique to Random Poly(hydroxypropylglutamine-co-hydroxybutylglutamine)

Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. I. Properties of Copolymers and Approximate Theories

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Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. II. Characterization of the Host Polymers and Application of the Host-Guest Technique to Random Poly(hydroxypropylglutamine-co-hydroxybutylglutamine)

Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. I. Properties of Copolymers and Approximate Theories