Hydrophobicity of amino acid residues: differential scanning calorimetry and synthesis of the aromatic analogues of the polypentapeptide of elastin

Mutations in the WG and GW motifs of the three RNA silencing suppressors of grapevine fanleaf virus alter their systemic suppression ability and affect virus infectivity

Viral suppressors of RNA silencing (VSRs) encoded by grapevine fanleaf virus (GFLV), one of the most economically consequential viruses of grapevine (Vitis spp.), were recently identified. GFLV VSRs include the RNA1-encoded protein 1A and the putative helicase protein 1BHel, as well as their fused form (1ABHel). Key characteristics underlying the suppression function of the GFLV VSRs are unknown. In this study, we explored the role of the conserved tryptophan-glycine (WG) motif in protein 1A and glycine-tryptophan (GW) motif in protein 1BHel in their systemic RNA silencing suppression ability by co-infiltrating Nicotiana benthamiana 16c line plants with a GFP silencing construct and a wildtype or a mutant GFLV VSR. We analyzed and compared wildtype and mutant GFLV VSRs for their (i) efficiency at suppressing RNA silencing, (ii) ability to limit siRNA accumulation, (iii) modulation of the expression of six host genes involved in RNA silencing, (iv) impact on virus infectivity in planta, and (v) variations in predicted protein structures using molecular and biochemical assays, as well as bioinformatics tools such as AlphaFold2. Mutating W to alanine (A) in WG of proteins 1A and 1ABHel abolished their ability to induce systemic RNA silencing suppression, limit siRNA accumulation, and downregulate NbAGO2 expression by 1ABHel. This mutation in the GFLV genome resulted in a non-infectious virus. Mutating W to A in GW of proteins 1BHel and 1ABHel reduced their ability to suppress systemic RNA silencing and abolished the downregulation of NbDCL2, NbDCL4,, and NbRDR6 expression by 1BHel. This mutation in the GFLV genome delayed infection at the local level and inhibited systemic infection in planta. Double mutations of W to A in WG and GW of protein 1ABHel abolished its ability to induce RNA silencing suppression, limit siRNA accumulation, and downregulate NbDCL2 and NbRDR6 expression. Finally, in silico protein structure prediction indicated that a W to A substitution potentially modifies the structure and physicochemical properties of the three GFLV VSRs. Together, this study provided insights into the specific roles of WG/GW not only in GFLV VSR functions but also in GFLV biology.

Structural and physical basis for the elasticity of elastin

Elastin function is to endow vertebrate tissues with elasticity so that they can adapt to local mechanical constraints. The hydrophobicity and insolubility of the mature elastin polymer have hampered studies of its molecular organisation and structure-elasticity relationships. Nevertheless, a growing number of studies from a broad range of disciplines have provided invaluable insights, and several structural models of elastin have been proposed. However, many questions remain regarding how the primary sequence of elastin (and the soluble precursor tropoelastin) governs the molecular structure, its organisation into a polymeric network, and the mechanical properties of the resulting material. The elasticity of elastin is known to be largely entropic in origin, a property that is understood to arise from both its disordered molecular structure and its hydrophobic character. Despite a high degree of hydrophobicity, elastin does not form compact, water-excluding domains and remains highly disordered. However, elastin contains both stable and labile secondary structure elements. Current models of elastin structure and function are drawn from data collected on tropoelastin and on elastin-like peptides (ELPs) but at the tissue level, elasticity is only achieved after polymerisation of the mature elastin. In tissues, the reticulation of tropoelastin chains in water defines the polymer elastin that bears elasticity. Similarly, ELPs require polymerisation to become elastic. There is considerable interest in elastin especially in the biomaterials and cosmetic fields where ELPs are widely used. This review aims to provide an up-to-date survey of/perspective on current knowledge about the interplay between elastin structure, solvation, and entropic elasticity.

Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding

Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.

Smart tools for antimicrobial peptides expression and application: The elastic perspective

In recent years, antimicrobial peptides (AMPs) have become a promising alternative to the use of conventional and chemically synthesized antibiotics, especially after the emergence of multidrug-resistant organisms. Thus, this review aims to provide an updated overview of the state-of-the-art for producing antimicrobial peptides fused or conjugated with the elastin-like (ELP) peculiar carriers, and that are mostly intended for biomedical application. The elastin-like biopolymers are thermosensitive proteins with unique properties. Due to the flexibility of their modular structure, their features can be tuned and customized to improve the production of the antimicrobial domain while reducing their toxic effects on the host cells. Both fields of research faced a huge rise in interest in the last decade, as witnessed by the increasing number of publications on these topics, and several recombinant fusion proteins made of these two domains have been already described but they still present a limited variability. Herein, the approaches described to recombinantly fuse and chemically conjugate diverse AMPs with ELPs are reviewed, and the nature of the AMPs and the ELPs used, as well as the main features of the expression and production systems are summarized.

Non-specificity as the sticky problem in therapeutic antibody development

Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.

Affinity-Recognition-Based Gravimetric Nanosensor for Equilin Detection

The estrogenic hormones that are widely used in postmenopausal hormone supplements for women contaminate natural water resources. Equilin (Equ) is one of the estrogenic hormones that have a maximum contaminant level of 0.35 µg/L in the chemical pollutants list. In this study, estrogenic hormones were precisely detected in a short time by affinity-recognition-based interactions in Quartz Crystal Microbalance (QCM) sensors. The QCM sensors were modified with 11-mercaptoundecanoic acid forming a self-assembled monolayer and with amino acids, namely tyrosine, tryptophan and phenylalanine. The affinity interactions between Equ and amino acids were studied using docking tools and confirmed by QCM experiments. The LODs of Equ were obtained as 4.59, 5.05 and 6.30 ng/L for tyrosine-, tryptophan- and phenylalanine-modified QCM nanosensors, respectively, with linear dynamic detection in the range of 25–500 nM. In terms of the LOD, selectivity and sensitivity calculations, the tyrosine-modified QCM nanosensor was found to have the highest performance for Equ detection compared to the tryptophan- and phenylalanine-modified ones.

Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions

Multivalent proteins and nucleic acids can self-assemble into biomolecular condensates that contribute to compartmentalize the cell interior. Computer simulations offer a unique view to elucidate the mechanisms and key intermolecular interactions behind the dynamic formation and dissolution of these condensates. In this work, we present a novel approach to include explicit water and salt in sequence-dependent coarse-grained (CG) models for proteins and RNA, enabling the study of biomolecular condensate formation in a salt-dependent manner. Our framework combines a reparameterized version of the HPS protein force field with the monoatomic mW water model and the mW-ion potential for NaCl. We show how our CG model qualitatively captures the experimental radius of the gyration trend of a subset of intrinsically disordered proteins and reproduces the experimental protein concentration and water percentage of the human fused in sarcoma (FUS) low-complexity-domain droplets at physiological salt concentration. Moreover, we perform seeding simulations as a function of salt concentration for two antagonist systems: the engineered peptide PR₂₅ and poly-uridine/poly-arginine mixtures, finding good agreement with their reported in vitro phase behavior with salt concentration in both cases. Taken together, our work represents a step forward towards extending sequence-dependent CG models to include water and salt, and to consider their key role in biomolecular condensate self-assembly.

β-Cyclodextrin/Fe3O4 nanocomposites for an electrochemical non-enzymatic cholesterol sensor

A sensitive, specific, and miniaturized non-enzymatic cholesterol sensor was prepared based on the competition of inclusion complex formation between β-cyclodextrin (BCD) and cholesterol, and between BCD and methylene blue (MB). BCD was immobilized on the surface of Fe3O4 magnetic nanoparticles instead of the electrode surface to increase the kinetic rate and enhance the sensitivity of the sensor. Furthermore, the use of magnetic nanocomposites and a screen-printed carbon electrode reduces the overall analysis time and simplifies the sample measurement procedures, making the sensor suitable for point-of-care analysis. The electrochemical measurement results of MB, released from the reactions between BCD and solutions containing various concentrations of cholesterol were used as the input signal to calculate the cholesterol concentrations. A good linearity as well as an excellent accuracy and repeatability in the concentration range of 0-150 μM with an estimated limit of detection of 2.88 μM could be achieved by using the amperometric technique at a constant potential of -0.43 V. The sensor showed a good selectivity in the presence of 1 mM concentrations of interfering agents, including NaCl, CaCl2, glycine, glucose, and ascorbic acid. Furthermore, a validation performed for cholesterol determination in milk samples was in agreement with the measurements performed by using the HPLC method, suggesting that the developed sensor is reliable.

Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7

The human voltage-gated sodium channel sub-type 1.7 (hNa_V1.7) is emerging as an attractive target for the development of potent and sub-type selective novel analgesics with increased potency and fewer side effects than existing therapeutics. HwTx-IV, a spider derived peptide toxin, inhibits hNa_V1.7 with high potency and is therefore of great interest as an analgesic lead. In the current study we examined whether engineering a HwTx-IV analogue with increased ability to bind to lipid membranes would improve its inhibitory potency at hNa_V1.7. This hypothesis was explored by comparing HwTx-IV and two analogues [E1PyrE]HwTx-IV (mHwTx-IV) and [E1G,E4G,F6W,Y30W]HwTx-IV (gHwTx-IV) on their membrane-binding affinity and hNa_V1.7 inhibitory potency using a range of biophysical techniques including computational analysis, NMR spectroscopy, surface plasmon resonance, and fluorescence spectroscopy. HwTx-IV and mHwTx-IV exhibited weak affinity for lipid membranes, whereas gHwTx-IV showed improved affinity for the model membranes studied. In addition, activity assays using SH-SY5Y neuroblastoma cells expressing hNa_V1.7 showed that gHwTx-IV has increased activity at hNa_V1.7 compared to HwTx-IV. Based on these results we hypothesize that an increase in the affinity of HwTx-IV for lipid membranes is accompanied by improved inhibitory potency at hNa_V1.7 and that increasing the affinity of gating modifier toxins to lipid bilayers is a strategy that may be useful for improving their potency at hNa_V1.7.

Designing protein-based biomaterials for medical applications

Biomaterials produced by nature have been honed through billions of years, evolving exquisitely precise structure-function relationships that scientists strive to emulate. Advances in genetic engineering have facilitated extensive investigations to determine how changes in even a single peptide within a protein sequence can produce biomaterials with unique thermal, mechanical and biological properties. Elastin, a naturally occurring protein polymer, serves as a model protein to determine the relationship between specific structural elements and desirable material characteristics. The modular, repetitive nature of the protein facilitates the formation of well-defined secondary structures with the ability to self-assemble into complex three-dimensional architectures on a variety of length scales. Furthermore, many opportunities exist to incorporate other protein-based motifs and inorganic materials into recombinant protein-based materials, extending the range and usefulness of these materials in potential biomedical applications. Elastin-like polypeptides (ELPs) can be assembled into 3-D architectures with precise control over payload encapsulation, mechanical and thermal properties, as well as unique functionalization opportunities through both genetic and enzymatic means. An overview of current protein-based materials, their properties and uses in biomedicine will be provided, with a focus on the advantages of ELPs. Applications of these biomaterials as imaging and therapeutic delivery agents will be discussed. Finally, broader implications and future directions of these materials as diagnostic and therapeutic systems will be explored.

Tunable self-assembly of genetically engineered silk--elastin-like protein polymers

Silk--elastin-like protein polymers (SELPs), consisting of the repeating units of silk and elastin blocks, combine a set of outstanding physical and biological properties of silk and elastin. Because of the unique properties, SELPs have been widely fabricated into various materials for the applications in drug delivery and tissue engineering. However, little is known about the fundamental self-assembly characteristics of these remarkable polymers. Here we propose a two-step self-assembly process of SELPs in aqueous solution for the first time and report the importance of the ratio of silk-to-elastin blocks in a SELP's repeating unit on the assembly of the SELP. Through precise tuning of the ratio of silk to elastin, various structures including nanoparticles, hydrogels, and nanofibers could be generated either reversibly or irreversibly. This assembly process might provide opportunities to generate innovative smart materials for biosensors, tissue engineering, and drug delivery. Furthermore, the newly developed SELPs in this study may be potentially useful as biomaterials for controlled drug delivery and biomedical engineering.

Recombinant elastin-mimetic biomaterials: Emerging applications in medicine

Biomaterials derived from protein-based block copolymers are increasingly investigated for potential application in medicine. In particular, recombinant elastin block copolymers provide significant opportunities to modulate material microstructure and can be processed in various forms, including particles, films, gels, and fiber networks. As a consequence, biological and mechanical responses of elastin-based biomaterials are tunable through precise control of block size and amino acid sequence. In this review, the synthesis of a set of elastin-mimetic triblock copolymers and their diverse processing methods for generating material platforms currently applied in medicine will be discussed.

Recombinant protein purification by self-cleaving elastin-like polypeptide fusion tag

This unit presents a rapid and simple method for the nonchromatographic purification of recombinant proteins expressed in E. coli. This method relies on a thermally responsive elastin-like polypeptide (ELP) tag, where the tagged protein is precipitated using a mild temperature shift. The tag is then induced to self-cleave by a mild pH shift and is subsequently removed by a final thermal precipitation. The result is a purified native protein target, without the requirement for affinity apparatus or protease removal of the tag. This protocol describes the required cloning methods to insert a given target into the expression vector, as well as the general method for purifying the resulting expressed protein.

Circular dichroism and UV-resonance Raman investigation of the temperature dependence of the conformations of linear and cyclic elastin

We used electronic circular dichroism (CD) and UV resonance Raman (UVRR) spectroscopy at 204 nm excitation to examine the temperature dependence of conformational changes in cyclic and linear elastin peptides. We utilize CD spectroscopy to study global conformation changes in elastin peptides, while UVRR is utilized to probe the local conformation and hydrogen bonding of Val and Pro peptide bonds. Our results indicate that at 20 degrees C cyclic elastin predominantly populates distorted beta-strand, beta-type II and beta-type III turn conformations. At 60 degrees C, the beta-type II turn population increases, while the distorted beta-strand population decreases. Linear elastin predominantly adopts distorted beta-strand and beta-type III turn conformations with some beta-type II turn population at 20 degrees C. Increasing temperature to 60 degrees C results in a small increase in the turn population.

Molecular and supramolecular structural studies on human tropoelastin sequences

One of the unusual properties of elastin is its ability to coacervate, which has been proposed to play an important role in the alignment of monomeric elastin for cross-linking into the polymeric elastin matrix. The temperature at which this transition takes place depends on several factors including protein concentration, ionic strength, and pH. Previously, polypeptide sequences encoded by different exons of the human tropoelastin gene have been analyzed for their ability to coacervate and to self-assemble. Few of them were indeed able to coacervate and only one, that encoded by exon 30 (EX30), gave amyloid fibers. In this article, we report on two chemically synthesized peptides-a decapeptide and an octadecapeptide-whose sequences are contained in the longer EX30 peptide and on a polypeptide (EX1-7) of 125 amino-acid residues corresponding to the sequence coded by the exons 1-7 and on a polypeptide (EX2-7) of 99 amino-acid residues encoded by exons 2-7 of human tropoelastin obtained by recombinant DNA techniques. Molecular and supramolecular structural characterization of these peptides showed that a minimum sequence of approximately 20 amino acids is needed to form amyloid fibers in the exon 30-derived peptides. The N-terminal region of mature tropoelastin (EX2-7) gives rise to a coacervate and forms elastinlike fibers, whereas the polypeptide sequence containing the signal peptide (EX1-7) forms mainly amyloid fibers. Circular dichroism spectra show that beta-structure is ubiquitous in all the sequences studied, suggesting that the presence of a beta-structure is a necessary, although not sufficient, requirement for the appearance of amyloid fibers.

Genetically engineered polymers: status and prospects for controlled release

Genetic engineering methodology has enabled the synthesis of protein-based polymers with precisely controlled structures. Protein-based polymers have well-defined molecular weights, monomer compositions, sequences and stereochemistries. The incorporation of tailor-made motifs at specified locations by recombinant techniques allows the formation of hydrogels, sensitivity to environmental stimuli, complexation with drugs and nucleic acids, biorecognition and biodegradation. Accordingly, a special interest has emerged for the use of protein-based polymers for controlled drug and gene delivery, tissue engineering and other biomedical applications. This article is a review of genetically engineered polymers, their physicochemical characteristics, synthetic strategies used to produce them and their biomedical applications with emphasis on controlled release.

Evaluation of methods for measuring amino acid hydrophobicities and interactions

The concept of hydrophobicity has been addressed by researchers in all aspects of science, particularly in the fields of biology and chemistry. Over the past several decades, the study of the hydrophobicity of biomolecules, particularly amino acids has resulted in the development of a variety of hydrophobicity scales. In this review, we discuss the various methods of measuring amino acid hydrophobicity and provide explanations for the wide range of rankings that exist among these published scales. A discussion of the literature on amino acid interactions is also presented. Only a surprisingly small number of papers exist in this rather important area of research; measuring pairwise amino acid interactions will aid in understanding structural aspects of proteins.

Differential scanning calorimetry study of the hydrophobic hydration of the elastin-based polypentapeptide, poly(VPGVG), from deficiency to excess of water

The polypentapeptide of elastin, poly(VPGVG), has become an interesting model polypeptide in understanding the mechanism of protein folding and assembly. Due to its simple amino acid composition and the predominance of apolar side chains, this polymer shows strong hydrophobic-hydration phenomena. This paper explores, by calorimetric methods, the nature and structure of the clathrate-like arrangements that take place, surrounding the apolar side chains of the polymer. The performance of these methods, especially differential scanning calorimetry, has a well-gained reputation. In this work, the development of the clathrate-like structures around this model polymer has been followed from water deficiency to water-excess states. Two main conclusions have been obtained from the data obtained. First, there is an upper limit of about 170 water molecules per pentamer as the number of water molecules required to form all the possible clathrate-like structures. Second, these structures exist as an inhomogeneous population with energies spreading in a significantly broad range, which is likely related to differences in geometrical parameters (bond lengths and angles) of the clathrate structure.

Retention mechanism of beta-blockers on an immobilized cellulase. Relative importance of the hydrophobic and ionic contributions to their enantioselective and nonselective interactions

The adsorption isotherms of the enantiomers of three beta-blockers, metoprolol, alprenolol, and propranolol, were measured on cellobiohydrolase I (CBH I) immobilized on silicagel, in the concentration range between 0.25 microM and 1.7 mM, at pH = 5.0, 5.5, and 6.0. In agreement with previous results, these data are accounted for by a two-sites physical model and fit closely to a Bilangmuir equation. The saturation capacities and the binding constants were determined for each enantiomer on the chiral and the nonchiral sites. The chiral sites are shown to be strongly ionic, in contrast to the nonchiral ones, which are mainly hydrophobic. However, the chiral binding of (S)-propranolol is endothermic, with a high adsorption entropy, in contrast to the chiral interactions of (R)-propranolol and to the nonchiral interactions, which are all exothermic. This indicates that hydrophobic interactions also play a role in the chiral binding. The dependence of the adsorption parameters on the hydrophobicity of the solute is discussed and interpreted in terms of the retention mechanism. The results are compared with the structure of the protein, recently elucidated by X-ray crystallography.

Characterizations of critical processes in liquid-liquid phase separation of the elastomeric protein-water system: microscopic observations and light scattering measurements

Biological self-assembly process of tropoelastin in an extracellular space, viewed as a key step of the elastogenesis, can be mimicked by the temperature-dependent coacervation of the elastin-related polypeptide-water system. Early and late stages of the phase separation behavior of the bovine neck ligamental alpha-elastin-water system were examined respectively by the laser light scattering photometry and phase contrast microscopy. Changes in the hydrodynamic size of molecular assemblies and visible microcoacervate droplet size were traced as a function of the concentration of alpha-elastin and temperature. Near the critical point, alpha-elastin concentration of 0.11 mg/mL and temperature of 21.5 degrees C, the phase separation was initiated after fast increase of the hydrodynamic size of primary aggregates as scattering particles and followed by the appearance of larger microcoacervate droplets with a broad size distribution. Whereas in the off-critical region, slow decrease of the hydrodynamic size of primary particles induced phase separation with smaller droplets of a narrow size distribution. Observation of the phase separation processes in the alpha-elastin-water system with metal chlorides and hydrophobic synthetic model polypeptide-water system indicated that the fast and slow molecular assembly processes were based on the fundamental hydrophobic interactions and involvements of electrostatic interactions between charged amino acid residues, respectively.

Role of hydrophobic and hydrophilic forces in peptide-protein interaction: new advances

A considerable part of important biological processes is governed by the noncovalent association of peptides and proteins. Various types of intermolecular forces may be involved in the formation of these molecular assemblies. This review gives a brief account of the physicochemical bases of interactive forces, with special emphasis on their impact on various peptide-protein interactions; summarizes the newest biochemical and biophysical methods for the study of such interactions; and discusses the role of various hydrophilic and hydrophobic forces in peptide-protein interactions in various fields of life sciences, such as immunology, enzymology, receptor binding, and toxicology.

Resolution of proteins on a phenyl-Superose HR5/5 column and its application to examining the conformation homogeneity of refolded recombinant staphylococcal nuclease

In order to examine the effect of amino acid substitutions on protein retention in hydrophobic interaction chromatography and the resolution of a phenyl-Superose HR5/5 column, two groups of staphylococcal nucleases, named Y113/W140 (wild-type), Y113W/W140 and Y113/W140F, Y113W/W140F, were produced by substituting tryptophan (W) for tyrosine (Y) at residue 113 and phenylalanine (F) for tryptophan (W) at residue 140. For each group, the proteins have the same amino acid at residue 140, but a different amino acid at residue 113. The solvent perturbation of nuclease fluorescence and 1,8-anilinoaphthalene-8-sulfonate binding studies showed that the substitutions do not change the side-chain positions of amino acids at residues 113 and 140. Chromatography of the proteins on the Phenyl-Superose HR5/5 column showed that the proteins with tryptophan at residue 113 have longer retention times than the proteins having tyrosine at residue 113; the proteins with the same amino acid at residue 113 have almost the same retention time regardless of substituting phenylalanine for tryptophan at residue 140. The studies clearly indicate that not all amino acid substitutions have an effect on protein retention; the contribution to retention of a given amino acid substitution depends on its position in a protein. Single amino acid substitutions at the exterior surface of a protein, which change the strength of hydrophobic interaction, can affect the protein retention in hydrophobic interaction chromatography. Staphylococcal nuclease and its mutants with only one amino acid difference on their surfaces can be discriminated by the phenyl-Superose column.(ABSTRACT TRUNCATED AT 250 WORDS)