Folding thermodynamics of protein-like oligomers with heterogeneous backbones

Abstract

The thermodynamics of protein folding are dictated by a complex interplay of interatomic interactions and physical forces. A variety of unnatural protein-like oligomers have the capacity to manifest defined folding patterns. While the energetics of folding in natural proteins is well studied, little is known about the forces that govern folding in modified backbones. Here, we explore the thermodynamic consequences of backbone alteration on protein folding, focusing on two types of chemical changes made in different structural contexts of a compact tertiary fold. Our results reveal a surprising favorable impact on folding entropy that accompanies modifications that increase disorder in the ensemble of unfolded states, due to differences in the solvation of natural and unnatural backbones.

Effects of Single α-to-β Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization

“…show that the α-helix-like local conformation of the ACPC residue is manifested also in backbone-modified variants of the GB1 tertiary structure. 19,20 …”

Helix Propensities of Amino Acid Residues via Thioester Exchange

“…Restriction of rotation upon folding might increase the entropic cost of helix formation for a β 3 hAla residue relative to an Ala residue; however, experiments by Reinert and Horne have shown that α→β 3 substitution in a different tertiary context causes a helix stability penalty that is enthalpic. 19 It is possible that the backbone modification in our system causes subtle changes in the arrangement of side chains projected from the other side of the helix 20 (positions a and d ), which could affect the energetics of knobs-into-holes packing at the coiled-coil interface. Such changes in helix-helix packing energy would contribute to Δ G fold .…”

Comparison of design strategies for α-helix backbone modification in a protein tertiary fold

“…Though the exact origin of the entropy enthalpy compensation is not clear, changes in the sensitivity of the folded state to chemical denaturant and the heat capacity difference between the folded and unfolded states (Table S3) suggest a more compact denatured ensemble in β 2 -residue containing variants vs. β 3 counterparts. 12 …”

“…21 Protein 6 is a previously reported variant of 2 in which rigidified β cyc residues replace two β 3 -residues. 12 In the GB1 tertiary fold, β 3 →β cyc substitution was structurally well accommodated but led to only a modest increase in folded stability. β cyc -Residues limit energetically accessible backbone conformational space by incorporating an otherwise freely rotatable bond into a ring.…”