Formation of Annular Protofibrillar Assembly by Cysteine Tripeptide: Unraveling the Interactions with NMR, FTIR, and Molecular Dynamics

Probing Peptide Assembly and Interaction via High-Resolution Imaging Techniques: A Mini Review

Peptide molecules, as fundamental structural units in biological systems, play pivotal roles in diverse biological processes and have garnered substantial attention in biomolecular self-assembly research. Their structural simplicity and high design flexibility make peptides key players in the development of novel biomaterials. High-resolution imaging techniques have provided profound insights into peptide assembly. Recently, the development of cutting-edge technologies, such as super-resolution microscopy (SRM) with unparalleled spatiotemporal resolution, has further advanced peptide assembly research. These advancements enable both the mechanistic exploration of peptide assembly pathways and the rational design of peptide-based functional materials. In this mini review, we systematically examine the structural diversity of peptide assemblies, including micelles, tubes, particles, fibers and hydrogel, as investigated by various high-resolution imaging techniques, with a focus on their assembly characterization and dynamic process. We also summarize the interaction networks of peptide assemblies with proteins, polymers and microbes, providing further insight into the interactions between peptide assemblies and other molecules. Furthermore, we emphasize the transformative role of high-resolution imaging techniques in addressing long-standing challenges in peptide nanotechnology. We anticipate that this review will accelerate the advancement of peptide assembly characterization, thereby fostering the creation of next-generation functional biomaterials.

Tunable Coassembly of Octaarginine with Thiazolyl Benzenesulfonamides Exerts Variable Antibacterial Activity

The cationic peptide octaarginine (R8) is a prominent cell-penetrating peptide and has been extensively researched as a carrier of diverse cell-destined cargo. In this work, we describe the coassembly of R8 with small molecule thiazolyl benzenesulfonamide (TBS) derivatives. Physical complexation of R8 with three TBS derivatives across a range of weight ratios results in the formation of a distinctive set of nano- and microstructures. A detailed structural characterization of the R8:TBS-derivative coassemblies has been performed by a combination of FTIR, XRD, SEM, and DSC. The major functional groups that facilitate coassembly include sulfonamide SO2 and NH groups of the TBS derivatives, and the guanidinium of R8, via a combination of cation-π and hydrogen-bonding interactions. The R8:4F-TBS coassembly displays singular topological features compared to R8:4Br-TBS and R8:4CH3-TBS complexes. These differences are attributed to the changes in the preferred orientation of the guanidino groups of R8 with respect to the π-surface of TBS derivatives. The modulation of forces of interaction across the R8:TBS-derivative coassemblies aligns with their respective thermal stabilities. The single-crystal structure of bare 4F-TBS has been subjected to Hirshfeld and 2D fingerprinting analysis and indicates notable variations from the crystal packing of the R8:4F-TBS coassembly. The structural differences among the R8:TBS-derivative coassemblies correlate with distinctive profiles of antibacterial activity in each case. The coassembled structures exert a variable extent of bacterial membrane disruption and damage based on the unique disposition of R8 and the potency of small molecule in each case. The aqueous suspension of R8:4F-TBS displays significant outer membrane disruption and bacterial killing compared with the other complexes. This work successfully demonstrates the hitherto unreported potential for coassembly of cell-penetrating peptides with other entities. The coassembly of R8 with small molecules highlights an attractive strategy for tuning the functional properties of each component.

Crystal to Hydrogel Transformation in S-Benzyl-L-Cysteine-Containing Cyclic Dipeptides - Nanostructure Elucidation and Applications

Cyclic dipeptides (CDPs) are crucial building blocks for a range of functional nanomaterials due to their simple chemical structure and high molecular stability. In this investigation, we synthesized a set of S-benzyl-L-cysteine-based CDPs (designated as P1-P6) and thoroughly examined their self-assembly behavior in a methanol-water solvent to elucidate the relationship between their structure and gelation properties. The hydrophobicity of the amino acids within the CDPs was gradually increased. The present study employed a comprehensive array of analytical techniques, including NMR, FT-IR, AFM, thioflavin-T, congo-red CD, X-ray crystallography, and biophysical calculations like Hirshfield Surface analysis and DFT analysis. These methods revealed that in addition to hydrogen bonding, the hydrophobic nature of the amino acid side chain significantly influences the propensity of CDPs to form hydrogels. Each CDP yielded distinct nanofibrillar networks rich in β-sheet structures, showcasing unique morphological features. Moreover, we explored the practical application of these CDP-based hydrogels in water purification by utilizing them to remove harmful organic dyes from contaminated water. This application underscores the potential of CDPs in addressing environmental challenges, offering a promising avenue for the future development of these materials in water treatment technologies.

The changed structures of Cyperus esculentus protein decide its modified physicochemical characters: Effects of ball-milling, high pressure homogenization and cold plasma treatments on structural and functional properties of the protein

Three physical treatments, including ball-milling (BM), high pressure homogenization (HPH) and cold plasma (CP) were applied to modify structural and functional properties of Cyperus esculentus protein (CEP). The results showed that three treatments significantly altered morphology and reduced particle size of CEP. Both primary and secondary structures of CEP were hardly changed, while disulfide bonds and hydrophobic forces between amino acid residues of CEP were interrupted by three treatments, releasing free sulfhydryls and hydrophobic groups. With the free moiety accumulation, the reformed interactions between them enhanced the crystallinity and thermostability of CEP. Besides, solubility and emulsifying properties of CEP were significantly improved within a certain range of treatment duration and intensity, and three treatments decreased water but increased oil holding capacity of CEP. Conclusively, the modified physicochemical properties of CEP were decided by the changed molecular structures of CEP, and different treatments may satisfy different processing requirements for the protein.

S-Benzyl Cysteine Based Cyclic Dipeptide Super Hydrogelator: Enhancing Efficacy of an Anticancer Drug via Sustainable Release

Peptide based low molecular weight supramolecular hydrogels hold promising aspects in various fields of application especially in biomaterial and biomedical sciences such as drug delivery, wound healing, tissue engineering, cell proliferation, etc due to their extreme biocompatibility. Unlike linear peptides, cyclic peptides have more structural rigidity and tolerance to enzymatic degradation and high environmental stability which make them even better candidates for the above said applications. Herein, a new small cyclic dipeptide (CDP) cyclo-(Leu-S-Bzl-Cys) (P1) consisting of L-leucine and S-benzyl protected L-cysteine was reported which formed hydrogel at physiological conditions (at 37^o C and pH=7.46). The hydrogel formed from the cyclic dipeptide P1 showed very good tolerance towards environmental parameters such as pH, temperature and was seen to be stable for more than a year without any deformation. The hydrogel was thermoreversible and stable in the pH range 6-12. Mechanical strength of P1 hydrogel was measured by rheology experiment. AFM and FE-SEM images revealed that in aqueous solvents P1 self-assembled into a highly cross-linked nanofibrillar network which immobilized water molecules inside the cages and formed the hydrogel. The self-assembled cyclic dipeptide acquired antiparallel β-sheet secondary structure which was evident from CD and FT-IR studies. The β-sheet arrangement and formation of amyloid fibrils were further established by ThT binding assay. Furthermore, P1 was able to form hydrogel in presence of anticancer drug 5-fluorouracil (5FU) and sustainable release of the drug from the hydrogel was measured in-vitro. The hydrogelator P1 showed almost no cytotoxicity towards human colorectal cancer cell line HCT116 up to a considerable high concentration and showed potential application in sustainable drug delivery. The co-assembly of 5FU and P1 hydrogel exhibited much better anticancer activity towards HCT116 cancer cell line than 5-fluorouracil alone and decreased the IC₅₀ dose of 5-fluorouracil to a much lower value.

Solvent-Assisted Tyrosine-Based Dipeptide Forms Low-Molecular Weight Gel: Preparation and Its Potential Use in Dye Removal and Oil Spillage Separation from Water

Low-molecular weight gelators (supramolecular, or simply molecular gels) are highly important molecular frameworks because of their potential application in drug delivery, catalysis, pollutant removal, sensing materials, and so forth. Herein, a small dipeptide composed of N-(tert-butoxycarbonyl)pentafluoro-l-phenylalanine and O-benzyl-l-tyrosine methyl ester was synthesized, and its gelation ability was investigated in different solvent systems. It was found that the dipeptide was unable to form gel with a single solvent, but a mixture of solvent systems was found to be suitable for the gelation of this dipeptide. Interestingly, water was found to be essential for gelation with the polar protic solvent, and long-chain hydrocarbon units such as, petroleum ether, kerosene, and diesel, were important for gelation with aromatic solvents. The structural insights of these gels were characterized by field-emission scanning electronic microscopy, atomic force microscopy, Fourier transform infrared analysis, and X-ray diffraction studies, and their mechanical strengths were characterized by rheological experiments. Both of the gels obtained from these two solvent systems were thermoreversible in nature, and these translucent gels had potential application for the treatment of waste water. The gel obtained from dipeptides with methanol-water was used to remove toxic dyes (crystal violet, Eriochrome Black T, and rhodamine B) from water. Furthermore, the gel obtained from dipeptide with assistance from toluene-petroleum ether was used as a phase-selective gelator for oil-spill recovery.

Graphene oxide wrapped melamine sponge as an efficient and recoverable adsorbent for Pb(II) removal from fly ash leachate

Lead is one of the most toxic elements, which has been well recognized for its negative effect on the environment and human beings. But, preliminary methods such as chemical precipitation, membrane separation etc. and commonly used adsorbents based on adsorption technology were found to be expensive and inefficient. In this study, we modify the surface of melamine sponge (MS) with polydopamine (PDA) and then coat with glutathione/graphene oxide (GG) as the adsorbent (MS@GG) to removal Pb(II) from aqueous solutions and fly ash leachate. The maximum adsorption capacity of MS@GG was calculated to be 349.7 mg Pb/g GG, and the reaction reached equilibrium in 30 min which were both higher than raw GG material and most previously reported adsorbents due to active sites on the surface of GG, as well as the unique macroporous and hydrophilic structure of MS. Meanwhile, based on its easy separation, by using HCl as the regeneration agent, the materials revealed good reproducibility. In addition, when MS@GG was applied for the removal of Pb(II) in fly ash leachate, the removal efficiency reached up to 99.24%, indicating that the novel MS@GG was the promising candidate adsorbent material for Pb(II) removal.

Investigation of the interaction of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase using inhibition kinetics, CD, FT-IR and molecular docking methods

Applying enzyme kinetics, spectroscopic, and molecular docking methods, the interaction properties of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase were systematically investigated. The α-glucosidase inhibitory activities (IC₅₀ = 0.40 mM) were significantly higher than that of acarbose (as control) and the spectrometric results revealed that 2,4-dimethoxy-6,7-dihydroxyphenanthrene inhibited α-glucosidase in a reversible and noncompetitive manner, which is that the inhibitor bind to the inactive region of α-glucosidase and could be separated from the bind sites. Hydrogen bond was the key interaction force obtained from the results of the molecular docking study, and the binding energy was -27.754 kJ/mol. The CD studies showed that the content of α-helix in α-glucosidase increased from 17.2% to 17.8% with the concentration varying of 2,4-dimethoxy-6,7-dihydroxyphenanthrene. The α-helix increasing trend (19.70% - 21.43%) of α-glucosidase secondary structure was further proved by Fourier transform infrared spectra (FT-IR) results and the FT-IR spectra of α-glucosidase resulted in obvious red shift with the addition of 2,4-dimethoxy-6,7-dihydroxyphenanthrene. All the measurements proved the interaction of 2,4-dimethoxy-6,7-dihydroxyphenanthrene with α-glucosidase and revealed the conformational change of α-glucosidase secondary structure.

Induction of adaptive immune response by self-aggregating peptides

INTRODUCTION

Recently, subunit vaccines are replacing some of the traditional vaccines because they offer a higher margin of safety. However, generally subunit vaccines have low antigenicity. Adjuvants are used in vaccine formulations to increase their immunogenicity, but current research suggests that adjuvants could induce serious side effects in susceptible individuals; therefore, the improvement of antigens and adjuvants is important.

AREAS COVERED

Here we reviewed some self-aggregating peptides (SAPs) used as antigen delivery systems. SAPs are based on a short sequence of amino acids, which have self-aggregating properties, inducing self-interaction among peptide molecules by means of non-covalent interactions to generate nanoparticles (NPs).

EXPERT COMMENTARY

SAPs increase the immunogenicity of fused/conjugated antigens because they can interact with antigen-presenting cells and induce adaptive immunity based on both humoral and cellular responses. As an example, we report an antigen delivery system based on SAPs forming NPs. These NPs are synthesized using a recombinant baculovirus. We fused the green fluorescent protein to the first 110 amino acids of polyhedrin protein from Autographa californica nucleopolyhedrovirus, which has self-aggregating properties. We showed that these NPs prompt high antibody levels without inducing inflammation, similarly to some SAPs reported here.

Guiding principles for peptide nanotechnology through directed discovery

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.