General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics-fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.

/pdf/principles-of-protein-folding-a-perspective-from-simple-3k57kibqjs.pdf

Principles of protein folding--a perspective from simple exact models.

Helix propensities of the amino acids have been measured in alanine-based peptides in the absence of helix-stabilizing side-chain interactions. Fifty-eight peptides have been studied. A modified form of the Lifson-Roig theory for the helix-coil transition, which includes helix capping (Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL, 1994, Biochemistry 33:3396-3403), was used to analyze the results. Substitutions were made at various positions of homologous helical peptides. Helix-capping interactions were found to contribute to helix stability, even when the substitution site was not at the end of the peptide. Analysis of our data with the original Lifson-Roig theory, which neglects capping effects, does not produce as good a fit to the experimental data as does analysis with the modified Lifson-Roig theory. At 0 “C, Ala is a strong helix former, Leu and Arg are helix-indifferent, and all other amino acids are helix breakers of varying severity. Because Ala has a small side chain that cannot interact significantly with other side chains, helix formation by Ala is stabilized predominantly by the backbone (“peptide H-bonds”). The implication for protein folding is that formation of peptide H-bonds can largely offset the unfavorable entropy change caused by fixing the peptide backbone. The helix propensities of most amino acids oppose folding; consequently, the majority of isolated helices derived from proteins are unstable, unless specific side-chain interactions stabilize them.

/pdf/helix-propensities-of-the-amino-acids-measured-in-alanine-47pghskm9j.pdf

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

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.

Cooperative conformational transitions in linear macromolecules undergoing chiral perturbations

/pdf/protein-structure-and-function-from-a-colloidal-to-a-1t1d4qfdqn.pdf

Protein structure and function, from a colloidal to a molecular view

Helix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine]

Helix-coil stability constants for the naturally occurring amino acids in water. 20. Reinvestigation of valine parameters from random poly[(hydroxypropyl)glutamine-co-L-valine]

Helix-coil transition in multicomponent random copolypeptides in water. 1. Theory and application to random copolymers of (hydroxypropyl)-L-glutamine, L-alanine, and glycine

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Helix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine]

Helix-coil stability constants for the naturally occurring amino acids in water. 20. Reinvestigation of valine parameters from random poly[(hydroxypropyl)glutamine-co-L-valine]

Helix-coil transition in multicomponent random copolypeptides in water. 1. Theory and application to random copolymers of (hydroxypropyl)-L-glutamine, L-alanine, and glycine