Prediction of Folding Preference of 10 kDa Silk-like Proteins Using a Lego Approach and ab Initio Calculations

Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol⁻¹ per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol⁻¹ per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol⁻¹ per residue excess stabilization.

Role of water in protein folding, oligomerization, amyloidosis and miniprotein

The essential involvement of water in most fundamental extra-cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide-chain by hydration or helps the globular chain-folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies--with a few exceptions--have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis.

A theoretical comparison of self-assembling alpha- and beta-peptide nanostructures: toward design of beta-barrel frameworks

Self-assembling peptide-based nanotubes are among the most investigated bioactive compounds as a result of their numerous potential applications as novel biomaterials. To support rational bottom-up design of such artificial nanosystems, here we investigate structural and energetic properties of various sheet-derived nanotubes. We carried out high level quantum chemical calculations on large models, composed of up to 32 amino acids, and characterized structures from extended beta-sheets to the molecular framework of beta-barrel proteins. Surprisingly, enzyme-resistant nonnatural beta-peptides have an affinity to form nanotubes that is remarkably higher than that of natural alpha-peptides. We analyzed the stability of both systems depending on (i) parallel or antiparallel orientation, (ii) the number of peptide strands, and (iii) the formed hydrogen bond pattern. Applicability is outlined by investigating guest molecules in the tubes. It is hoped that the structural and energetic data presented here will be effectively used in the design of novel peptide nanosystems.