Local order and mobility of water molecules around ambivalent helices

Convergence behaviour of solvation shells in simulated liquids

A convenient way to analyse solvent structure around a solute is to use solvation shells, whereby solvent position around the solute is discretised by the size of a solvent molecule, leading to multiple shells around the solute. The two main ways to define multiple shells around a solute are either directly with respect to the solute, called solute-centric, or locally for both solute and solvent molecules alike. It might be assumed that both methods lead to solvation shells with similar properties. However, our analysis suggests otherwise. Solvation shells are analysed in a series of simulations of five pure liquids of differing polarity. Shells are defined locally working outwards from each molecule treated as a reference molecule using two methods: the cutoff at the first minimum in the radial distribution function and the parameter-free Relative Angular Distance method (RAD). The molecular properties studied are potential energy, coordination number and coordination radius. Rather than converging to bulk values, as might be expected for pure solvents, properties are found to deviate as a function of shell index. This behaviour occurs because molecules with larger coordination numbers and radius have more neighbours, which make them more likely to be connected to the reference molecule via fewer shells. The effect is amplified for RAD because of its more variable coordination radii and for water with its more open structure and stronger interactions. These findings indicate that locally defined shells should not be thought of as directly comparable to solute-centric shells or to distance. As well as showing how box size and cutoff affect the non-convergence, to restore convergence we propose a hybrid method by defining a new set of shells with boundaries at the uppermost distance of each locally derived shell.

Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load

Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.

Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin

Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.

Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model

Secondary structural preferences of the beta-hairpin of the 2GB1 protein in the folded and unfolded ensembles are shown to be sensitive to the choice of water model.

Helical ambivalency induced by point mutations

Background

Mutation of amino acid sequences in a protein may have diverse effects on its structure and function. Point mutations of even a single amino acid residue in the helices of the non-redundant database may lead to sequentially identical peptides which adopt different secondary structures in different proteins. However, various physico-chemical factors which govern the formation of these ambivalent helices generated by point mutations of a sequence are not clearly known.

Results

Sequences generated by point mutations of helices are mapped on to their non-helical counterparts in the SCOP database. The results show that short helices are prone to transform into non-helical conformations upon point mutations. Mutation of amino acid residues by helix breakers preferentially yield non-helical conformations, while mutation with residues of intermediate helix propensity display least preferences for non-helical conformations. Differences in the solvent accessibility of the mutating/mutated residues are found to be a major criteria for these sequences to conform to non-helical conformations. Even with minimal differences in the amino acid distributions of the sequences flanking the helical and non-helical conformations, helix-flanking sequences are found be more solvent accessible.

Conclusions

All types of mutations from helical to non-helical conformations are investigated. The primary factors attributing such changes in conformation can be: i) type/propensity of the mutating and mutant residues ii) solvent accessibility of the residue at the mutation site iii) context/environment dependence of the flanking sequences. The results from the present study may be used to design de novo proteins via point mutations.

Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.