Principles of Protein Structural Organization - H. Schultz 1982

Protein Evolution
Protein Specialization
Effect of Amino Acid Substitutions on Folding Dynamics

Mutations affecting the folding process are investigated using protein models. Previous sections discussed The impact of Amino Acid Substitutions on the function or stability of folded Proteins. However, it is evident that mutations have their most detrimental effect on the folding kinetics of the polypeptide chain. Investigating this issue using natural mutants is challenging for two reasons. First, if the folding pathway of a mutant protein is completely blocked, the polypeptide chain cannot be identified and isolated using standard Biochemical Methods (although immunological [94, 418] or complementation techniques [446] can be employed). Furthermore, Polypeptides that fail to fold at all or fold too slowly following Biosynthesis are often rapidly degraded in vivo [154]. These difficulties have prompted researchers to search for models to study the effects of mutations on protein folding among semi-synthetic protein analogues [497–499] or proteins with modified side chains [445] (Section 8.2).

Helix-initiating amino acid residues were identified through sequence comparisons. Structure/19.html">The Importance of incorporating specific groups for folding kinetics was established in a comparative study of globin molecules [500]. In this case, all α-helices carry either Pro or residues with short polar side chains (Asn, Asp, His, Ser, Thr) at their N-terminal regions, which are capable of forming Hydrogen Bonds with the backbone. These hydrogen bonds appear essential for helix initiation, much like the presence of Proline in certain cases, which fixes the dihedral angle required for the α-Helix. These factors lead to a favorable balance between binding energy and chain Entropy: hydrogen bonds increase the binding energy, while Pro reduces the number of accessible Conformations and, consequently, the chain entropy. In accordance with equation (3.2), the value of ∆G_общ for this local region of the chain has a large negative magnitude, causing such a region to exhibit a strong tendency toward forming a small folding nucleation site.

The high conservation of chain folding is driven by constraints imposed by folding kinetics. The evolutionary tendency observed in proteins to preserve their chain-folding topology apparently cannot be explained solely by the preservation of the delicate energy (or functional) balance of a given protein. Both of these conditions apply far more significantly to amino acid side chains than to the main chain. Therefore, it must be inferred that chain topology strongly correlates with folding kinetics, which ultimately imposes the primary constraints on the protein.