A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function

The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins

Proteins transporting ions or other molecules across the membrane, whose proper concentration is required to maintain homeostasis, perform very sophisticated biological functions. The symport and antiport active transport can be performed only by the structures specially prepared for this purpose. In the present work, such structures in both In and Out conformations have been analyzed with respect to the hydrophobicity distribution using the FOD-M model. This allowed for identifying the role of individual protein chain fragments in the stabilization of the specific cell membrane environment as well as the contribution of hydrophobic interactions to the conformational changes between In/Out conformations.

Learning the relationship between nanoscale chemical patterning and hydrophobicity

The hydrophobicity of proteins and similar surfaces, which display chemical heterogeneity at the nanoscale, drives countless aqueous interactions and assemblies. However, predicting how surface chemical patterning influences hydrophobicity remains a challenge. Here, we address this challenge by using molecular simulations and machine learning to characterize and model the hydrophobicity of a diverse library of patterned surfaces, spanning a wide range of sizes, shapes, and chemical compositions. We find that simple models, based only on polar content, are inaccurate, whereas complex neural network models are accurate but challenging to interpret. However, by systematically incorporating chemical correlations between surface groups into our models, we are able to construct a series of minimal models of hydrophobicity, which are both accurate and interpretable. Our models highlight that the number of proximal polar groups is a key determinant of hydrophobicity and that polar neighbors enhance hydrophobicity. Although our minimal models are trained on particular patch size and shape, their interpretability enables us to generalize them to rectangular patches of all shapes and sizes. We also demonstrate how our models can be used to predict hot-spot locations with the largest marginal contributions to hydrophobicity and to design chemical patterns that have a fixed polar content but vary widely in their hydrophobicity. Our data-driven models and the principles they furnish for modulating hydrophobicity could facilitate the design of novel materials and engineered proteins with stronger interactions or enhanced solubilities.

Perturbation effect of single polar group substitution on the Self-Association of amphiphilic peptide helices

As an important attempt towards creating hierarchical structures more like nature, the peptide is employed as a building block to build supramolecular architectures. An emerging question is whether the molecular mechanism of self-assembly obtained from the small molecule system, e.g., the driving forces of assembly are conventionally regarded as pairwise-additive, can be manifested in the self-association of biologically relevant amphiphilic peptides. A peptide, KRT-R, was derived from the 120-144 segment of keratin 14. The single cation-to-cation substitution with KRT-R at the site of 125 from arginine (R) to either lysine (K) or histidine (H) results in the peptide helices, KRT-K and KRT-H, sharing 96% sequence identity. These KRT-derived peptides possess similarities in the folding structures but exhibit divergent self-assembled structures. KRT-R and KRT-K self-assemble into sheets and fibrils, respectively. Whereas KRT-H associates into heterogeneous structures, including sheets, particles, and branched networks. The intrinsic tyrosine fluorescence spectroscopy measurements with the KRT-derived peptides within a temperature range of 25 °C to 95 °C reveal that the heating-triggered structural transitions of KRT-derived peptides are divergent. The alternation of single cationic residue changes the thermodynamic signature of peptide assemblies upon heating. A chemical denaturation experiment with KRT-derived peptides indicates that the intermolecular interactions that govern the supramolecular architectures formed by peptides are distinct. Overall, our work demonstrates the contribution of the interplay among various noncovalent interactions to supramolecular assembly.

A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly

Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures. Accumulating evidence leads to a hypothesis that the hydrophobicity of a nonpolar patch of a molecule is non-additive and susceptible to the chemical context of a judicious polar patch. However, the quantification of the hydrophobic interaction at the nanoscale remains a central challenge to validate the hypothesis. In this review, we aim to outline the recent efforts made to determine the hydrophobic interaction at a nanoscopic length scale. The advances achieved in the understanding of proximal polar groups perturbing the magnitude of hydrophobic interaction generated by the nonpolar patch are introduced. We will also discuss the influence of chemical heterogeneity on the modulation of amphiphilic peptide/protein assembly and molecular recognition.

Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures.

Rapid fabrication of precise high-throughput filters from membrane protein nanosheets

Biological membranes are ideal for separations as they provide high permeability while maintaining high solute selectivity due to the presence of specialized membrane protein (MP) channels. However, successful integration of MPs into manufactured membranes has remained a significant challenge. Here, we demonstrate a two-hour organic solvent method to develop 2D crystals and nanosheets of highly packed pore-forming MPs in block copolymers (BCPs). We then integrate these hybrid materials into scalable MP-BCP biomimetic membranes. These MP-BCP nanosheet membranes maintain the molecular selectivity of the three types of β-barrel MP channels used, with pore sizes of 0.8 nm, 1.3 nm, and 1.5 nm. These biomimetic membranes demonstrate water permeability that is 20-1,000 times greater than that of commercial membranes and 1.5-45 times greater than that of the latest research membranes with comparable molecular exclusion ratings. This approach could provide high performance alternatives in the challenging sub-nanometre to few-nanometre size range.

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute-water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.

Molecular dynamics simulations on the conformational transitions from the GA 98 (GA 88) to GB 98 (GB 88) proteins

We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the G_A 98 protein with only 1 mutation of Leu45Tyr to G_B 98 and from the G_A 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to G_B 88. The results show that the conformational transition mechanism from the mutated 3α G_A 98 (G_A 88) state to the α+4β G_B 98 (G_B 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of G_A 98 to G_B 98 are markedly different from those in G_A 88 to G_B 88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd.

Scaling and self-organized criticality in proteins: Lysozyme c

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is often dominated by long-range hydro(phobic/philic) interactions, which both drive protein compaction and mediate protein-protein interactions. In contrast to previous reductionist short-range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity scale [Phys. Rev. E 75, 011920 (2007)] represents a hydroanalytic tool that bioinformatically quantifies SOC in a way fully compatible with evolution. Hydroprofiling identifies chemical trends in the activities and substrate binding abilities of model enzymes and antibiotic animal lysozymes c , as well as defensins, which have been the subject of tens of thousands of experimental studies. The analysis is simple and easily performed and immediately yields insights not obtainable by traditional methods based on short-range real-space interactions, as described either by classical force fields used in molecular-dynamics simulations, or hydrophobicity scales based on transference energies from water to organic solvents or solvent-accessible areas.

Self-similarity and protein compactness

The hydrophobic effect is the major factor that drives a protein toward collapse and folding. As a consequence of the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We analyze the solvent-accessible surface area of 1825 nonhomolog protein chains deposited in the Brookhaven Protein Data Bank. This solvent-accessible surface area presents an intrinsic self-similarity behavior. The comparison between the accessible surface area as function of the number of amino acids and the accessible surface area as function of gyration radius supplies a measure of the scaling exponent close to the one observed by volume as function of radius of gyration or by mass-size exponent. The present finding indicates that the fractal analysis describes the protein compactness as an object packing between random spheres in percolation threshold and crumpled wires.

Scaling and self-organized criticality in proteins II

The complexity of proteins is substantially simplified by regarding them as archetypical examples of self-organized criticality (SOC). To test this idea and to elaborate it, this article applies the Moret-Zebende (MZ) SOC hydrophobicity scale to transport repeat proteins of the HEAT superfamily, importin beta, and transportin, as well as the export protein Cse1p, and their ubiquitous cargo manager Ran. The difference between the MZ scale and conventional hydrophobicity scales reflects long-range conformational forces that are central to protein functionality. These compete with long-range Coulomb forces associated with cationic and anionic side chains in a revealing way.