Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent

Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play

The interaction between a protein and external electric field (EF) can alter its structure and dynamical behavior, which has a potential impact on the biological function of proteins and cause uncertain health consequences. Conversely, the application of EFs of judiciously selected intensity and frequency can help to treat disease, and optimization of this requires a greater understanding of EF-induced effects underpinning basic protein biophysics. In the present study, chignolin─an artificial protein sufficiently small to undergo fast-folding events and transitions─was selected as an ideal prototype to investigate how, and to what extent, externally applied electric fields may manipulate or influence protein-folding phenomena. Nonequilibrium molecular dynamics (NEMD) simulations have been performed of solvated chignolin to determine the distribution of folding states and their underlying transition dynamics, in the absence and presence of externally applied electric fields (both static and alternating); a key focus has been to ascertain how folding pathways are altered in an athermal sense by external fields. Compared to zero-field conditions, a dramatically different─indeed, bifurcated─behavior of chignolin-folding processes emerges between static- and alternating-field scenarios, especially vis-à-vis incipient stages of hydrophobic-core formation: in alternating fields, fold-state populations diversified, with an attendant acceleration of state-hopping folding kinetics, featuring the concomitant emergence of a new, quasi-stable structure compared to the native structure, in field-shifted energy landscapes.

Unsupervised Learning Methods for Molecular Simulation Data

Unsupervised learning is becoming an essential tool to analyze the increasingly large amounts of data produced by atomistic and molecular simulations, in material science, solid state physics, biophysics, and biochemistry. In this Review, we provide a comprehensive overview of the methods of unsupervised learning that have been most commonly used to investigate simulation data and indicate likely directions for further developments in the field. In particular, we discuss feature representation of molecular systems and present state-of-the-art algorithms of dimensionality reduction, density estimation, and clustering, and kinetic models. We divide our discussion into self-contained sections, each discussing a specific method. In each section, we briefly touch upon the mathematical and algorithmic foundations of the method, highlight its strengths and limitations, and describe the specific ways in which it has been used-or can be used-to analyze molecular simulation data.

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20-50% of the ordered structures with three force fields, but not with a fourth. A defining feature of the misfold is that Gly-7 adopts a β(PR) conformation rather than α(L). By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for β(PR) is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to the wild-type and does not populate the misfolded state in simulation. Our results highlight the complexity of interpreting NMR data for small, weakly structured, peptides in solution, as well as the importance of accurate glycine parameters in force fields, for a correct description of turn structures.

The CLN025 decapeptide retains a β-hairpin conformation in urea and guanidinium chloride

The conformational stability of the β-hairpin miniprotein, CLN025, a variant of chignolin in which the N- and C-terminal glycines are replaced by tyrosines, in various concentrations of guanidinium chloride (GdmCl) and urea was examined by molecular dynamics simulations and electronic circular dichroism (ECD) spectropolarimetry. The peptide maintains its β-hairpin conformation in GdmCl and urea solutions. In GdmCl, Gly7 influences the turn to reduce the number of Asp3-Gly7 H-bonds and the Tyr1-Trp9 H-bond is lost. The structure of the peptide is less stable in 3 M GdmCl than in water or 6 M GdmCl, because the number of Asp3-Thr8 and Tyr1-Tyr10 H-bonds are reduced and the Tyr2 side chain moves away from the Pro4 and Trp9 side chains and toward the Tyr10 side chain. This reduces the number of Tyr2-Pro4 CH-π interactions and Tyr2-Trp9 and Tyr1-Tyr10 aromatic-aromatic (Ar-Ar) interactions and increases the number of Tyr2-Tyr10 Ar-Ar interactions. In 6 M GdmCl at 300 and 333 K, the number of Tyr1-Tyr10 and Asp3-Thr8 H-bonds increases, but fewer structures have Tyr2-Pro4 CH-π and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In urea, Gly7 is in a mixture of β-turn and random meander structures and the number of Asp3-Thr6 and Tyr1-Tyr10 H-bonds are reduced as are the number of Tyr2-Pro4 CH-π interactions and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In 4 M urea, a shorter turn places Gly7 into the β-sheet region and Tyr10 is pushed out into the solvent. In 8 M urea, the number of Asp3-Glu5 H-bonds is increased and the β-sheet is lost, but the electrostatic interaction between the charged termini is restored and a cation-π interaction between the indolyl ring of Trp9 and the positively charged N-terminus is formed. In 8 M urea at 333 K, the β-hairpin conformation is almost lost. The structure of CLN025 is stable, because the weakly polar interactions and H-bonds maintain the β-hairpin conformation in the various environments. CLN025 should not be considered a miniprotein, because it lacks a well-defined tertiary structure, it is resistant to denaturation, it does not have an increased heat capacity near its melting temperature, and the structures near and above the melting temperature retain a β-hairpin conformation.