The conformational analysis of peptides using Fourier transform IR spectroscopy

Recognition of anion-water clusters by peptide-based supramolecular capsules

The biological and technological importance of anion-mediated processes has made the development of improved methods for the selective recognition of anions one of the most relevant research topics today. The hydration sphere of anions plays an important role in the functions performed by anions by forming a variety of cluster complexes. Here we describe a supramolecular capsule that recognizes hydrated anion clusters. These clusters are most likely composed of three ions that form hydrated C3 symmetry complexes that are entrapped within the supramolecular capsule of the same symmetry. The capsule is made of self-assembled α,γ-cyclic peptide containing amino acid with by five-membered rings and equipped with a tris(triazolylethyl)amine cap. To recognise the hydrated anion clusters, the hexapeptide capsule must disassemble to entrap them between its two subunits.

HydrogelFinder: A Foundation Model for Efficient Self-Assembling Peptide Discovery Guided by Non-Peptidal Small Molecules

Self-assembling peptides have numerous applications in medicine, food chemistry, and nanotechnology. However, their discovery has traditionally been serendipitous rather than driven by rational design. Here, HydrogelFinder, a foundation model is developed for the rational design of self-assembling peptides from scratch. This model explores the self-assembly properties by molecular structure, leveraging 1,377 self-assembling non-peptidal small molecules to navigate chemical space and improve structural diversity. Utilizing HydrogelFinder, 111 peptide candidates are generated and synthesized 17 peptides, subsequently experimentally validating the self-assembly and biophysical characteristics of nine peptides ranging from 1-10 amino acids-all achieved within a 19-day workflow. Notably, the two de novo-designed self-assembling peptides demonstrated low cytotoxicity and biocompatibility, as confirmed by live/dead assays. This work highlights the capacity of HydrogelFinder to diversify the design of self-assembling peptides through non-peptidal small molecules, offering a powerful toolkit and paradigm for future peptide discovery endeavors.

Secondary Structure Stabilization of Macrocyclic Antimicrobial Peptides via Cross-Link Swapping

Lactam cross-links have been employed to stabilize the helical secondary structure and enhance the activity and physiological stability of antimicrobial peptides; however, stabilization of β-sheets via lactamization has not been observed. In the present study, lactams between the side chains of C- and N-terminal residues have been used to stabilize the β-sheet conformation in a short ten-residue analogue of chicken angiogenin-4. Designed using a combination of molecular dynamics simulations and Markov state models, the lactam cross-linked peptides are shown to adopt stabilized β-sheet conformations consistent with simulated structures. Replacement of the peptide side-chain Cys-Cys disulfide by a lactam cross-link enhanced the broad-spectrum antibacterial activity compared to the parent peptide and exhibited greater propensity to induce proinflammatory activity in macrophages. The combination of molecular simulations and conformational and biological analyses of the synthetic peptides provides a useful paradigm for the rational design of therapeutically active peptides with constrained β-sheet structures.

Out-of-Equilibrium Mechanical Disruption of β-Amyloid-Like Fibers using Light-Driven Molecular Motors

Artificial molecular motors have the potential to generate mechanical work on their environment by producing autonomous unidirectional motions when supplied with a source of energy. However, the harnessing of this mechanical work to subsequently activate various endoenergetic processes that can be useful in materials science remains elusive. Here, it is shown that by integrating a light-driven rotary motor through hydrogen bonds in a β-amyloid-like structure forming supramolecular hydrogels, the mechanical work generated during the constant rotation of the molecular machine under UV irradiation is sufficient to disrupt the β-amyloid fibers and to trigger a gel-to-sol transition at macroscopic scale. This melting of the gel under UV irradiation occurs 25 °C below the temperature needed to melt it by solely using thermal activation. In the dark, a reversible sol-gel transition is observed as the system fully recovers its original microstructure, thus illustrating the possible access to new kinds of motorized materials that can be controlled by advanced out-of-equilibrium thermodynamics.

A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus, is the causative agent responsible for the spread of the COVID19 pandemic across the globe. The global impact of the COVID19 pandemic, the successful approval of vaccines for controlling the pandemic, and the further resurgence of COVID19 necessitate the exploration and validation of alternative therapeutic avenues targeting SARS-CoV-2. The initial entry and further invasion by SARS-CoV-2 require strong protein-protein interactions (PPIs) between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptors expressed on the cell surfaces of various tissues. In principle, disruption of the PPIs between the RBD of SARS-CoV-2 and the ACE2 receptor by designer peptides with optimized pharmacology appears to be an ideal choice for potentially preventing viral entry with minimal immunogenicity. In this context, the current study describes a short, synthetic designer peptide (codenamed SR16, ≤18 aa, molecular weight ≤2.5 kDa), which has a few noncoded amino acids, demonstrates a helical conformation in solution, and also engages the RBD of SARS-CoV-2 through a high-affinity interaction, as judged from a battery of biophysical studies. Further, the designer peptide demonstrates resistance to trypsin degradation, appears to be nontoxic to mammalian cells, and also does not induce hemolysis in freshly isolated human erythrocytes. In summary, SR16 appears to be an ideal peptide binder targeting the RBD of SARS-CoV-2, which has the potential for further optimization and development as an antiviral agent targeting SARS-CoV-2.

Tunable thermal diffusivity of silk protein assemblies based on their structural control and photo-induced chemical cross-linking

Silk, which has excellent mechanical properties and is lightweight, serves as a structural material in natural systems. However, the structural and functional applications of silk in artificial systems have been limited due to the difficulty in controlling its properties. In this study, we demonstrate the tunable thermal diffusivity of silk-based assemblies (films) based on secondary structural control and subsequent cross-linking. We found that the thermal diffusivity of the silk film is increased by the formation of β-sheet structures and dityrosine between Tyr residues adjacent to the β-sheet structures. Our results demonstrate the applicability of silk proteins as material components for thermally conductive biopolymer-based materials.

Chirality-Regulated Clusteroluminescence in Polypeptides

The low emission efficiency of clusteroluminogens restricts their practical applications in the fields of sensors and biological imaging. In this work, the clusteroluminescence of ordered/disordered polypeptides was observed, and the photoluminescence (PL) intensity of polypeptides can be modulated by the chirality of amino acid residues. Polyglutamates with different chiral compositions were synthesized, and the racemic polypeptides exhibited a significantly higher PL intensity than the enantiopure ones. This emission originates from the n-π* transition between C═O groups of polypeptides and is enhanced by clusterization of polypeptides. CD and Fourier transform infrared spectra demonstrated that the enantiopure and racemic polypeptides form α-helix and random coil structures, respectively. The disordered polypeptides can form more chain entanglements and interchain interactions because of their high flexibility, leading to more clusterizations and stronger PL intensity. The rigidity of ordered helical structures restrains the chain entanglements, and the formation of intrachain hydrogen bonds between amide groups of the backbone impairs the interchain interaction between polypeptides, resulting in lower PL intensity. The PL intensity of the polypeptides can also be manipulated by the addition of urea or trifluoroacetic acid. Our study not only elucidates the chirality/order-based structure-property relationship of clusteroluminescence in peptide-based polymers but also offers implications for the rational design of fluorescent peptides/proteins.

Molecular interactions and binding dynamics of Alpelisib with serum albumins: insights from multi-spectroscopic techniques and molecular docking

Alpelisib (ALP) is a potent anti-cancer drug showing promising activity against advanced breast cancers. Hence, profound understanding of its binding dynamics within the physiological system is vital. Herein, we have investigated interaction of ALP with human serum albumin (HSA) and bovine serum albumin (BSA) using spectroscopic techniques like absorption, fluorescence, time-resolved, synchronous and 3D-fluorescence, FRET, FT-IR, CD, and molecular docking studies. The intrinsic fluorescence of both BSA and HSA quenched significantly by ALP with an appreciable red shift in its emission maxima. Stern-Volmer analysis showed increase in Ksv with temperature indicating involvement of dynamic quenching process. This was further validated by no significant change in absorption spectrum of BSA and HSA (at 280 nm) upon ALP interaction, and by results of fluorescence time-resolved lifetime studies. ALP exhibited moderately strong binding affinity with BSA (of the order 106 M-1) and HSA (of the order 105 M-1), and the major forces accountable for stabilizing the interactions are hydrophobic forces. Competitive drug binding experiments and molecular docking suggested that ALP binds to site I in subdomain IIA of BSA and HSA. The Förster distance r was found to be less than 8 nm and 0.5 Ro < r < 1.5 Ro which suggests possible energy transfer between donors BSA/HSA and acceptor ALP. Synchronous and 3D-fluoresecnce, FT-IR and CD studies indicated that ALP induces conformational changes of BSA and HSA upon interaction.Communicated by Ramaswamy H. Sarma.

A self-standing superhydrophobic material formed by the self-assembly of an individual amino acid

HYPOTHESIS

There is a growing interest in designing superhydrophobic materials for many applications including self-clean surfaces, separation systems, and antifouling solutions. Peptides and amino acids offer attractive building blocks for these materials since they are biocompatible and biodegradable and can self-assemble into complex ordered structures.

EXPERIMENTS AND SIMULATIONS

We designed a self-standing superhydrophobic material through the self-assembly of an individual functionalized aromatic amino acid, Cbz-Phe(4F). The self-assembly of Cbz-Phe(4F) was investigated by experimental and computational methods. Moreover, when drop-casted three times on a solid support, it formed a self-standing superhydrophobic material. The mechanical properties and chemical stability of this self-standing superhydrophobic material were demonstrated.

FINDINGS

The designed Cbz-Phe(4F) self-assembled into fibrous structures in solution. Molecular dynamics (MD) simulations revealed that the fibrous backbone of Cbz-Phe(4F) aggregations was stabilized through hydrogen bonds, whereas the isotropic growth of the aggregates was driven by hydrophobic interactions. Importantly, when drop-casted three times on a solid support, it formed a self-standing superhydrophobic material. Moreover, this material had a high mechanical strength, with a Young's modulus of 53 GPa, resistance to enzymatic degradation, and thermal stability up to 200 ℃. This study provides a simple strategy to generate smart and functional materials by the simple self-assembly of functional individual amino acids.

A rationally engineered small antimicrobial peptide with potent antibacterial activity

Antimicrobial resistance (AMR) is a silent pandemic declared by the WHO that requires urgent attention in the post-COVID world. AMR is a critical public health concern worldwide, potentially affecting people at different stages of life, including the veterinary and agriculture industries. Notably, very few new-age antimicrobial agents are in the current developmental pipeline. Thus, the design, discovery, and development of new antimicrobial agents are required to address the menace of AMR. Antimicrobial peptides (AMPs) are an important class of antimicrobial agents for combating AMR due to their broad-spectrum activity and ability to evade AMR through a multimodal mechanism of action. However, molecular size, aggregability, proteolytic degradation, cytotoxicity, and hemolysis activity significantly limit the clinical application of natural AMPs. The de novo design and engineering of a short synthetic amphipathic AMP (≤16 aa, Mol. Wt. ≤ 2 kDa) with an unusual architecture comprised of coded and noncoded amino acids (NCAAs) is presented here, which demonstrates potent antibacterial activity against a few selected bacterial strains mentioned in the WHO priority list. The designer AMP is conformationally ordered in solution and effectively permeabilizes the outer and inner membranes, leading to bacterial growth inhibition and death. Additionally, the peptide is resistant to proteolysis and has negligible cytotoxicity and hemolysis activity up to 150 μM toward cultured human cell lines and erythrocytes. The designer AMP is unique and appears to be a potent therapeutic candidate, which can be subsequently subjected to preclinical studies to explicitly understand and address the menace of AMR.

A promising antifungal lipopeptide from Bacillus subtilis: its characterization and insight into the mode of action

Emerging resistance of fungal pathogens and challenges faced in drug development have prompted renewed investigations into novel antifungal lipopeptides. The antifungal lipopeptide AF3 reported here is a natural lipopeptide isolated and purified from Bacillus subtilis. The AF3 lipopeptide's secondary structure, functional groups, and the presence of amino acid residues typical of lipopeptides were determined by circular dichroism, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. The lipopeptide's low minimum inhibitory concentrations (MICs) of 4-8 mg/L against several fungal strains demonstrate its strong antifungal activity. Biocompatibility assays showed that ~ 80% of mammalian cells remained viable at a 2 × MIC concentration of AF3. The treated Candida albicans cells examined by scanning electron microscopy, transmission electron microscopy, and atomic force microscopy clearly showed ultrastructural alterations such as the loss of the cell shape and cell membrane integrity. The antifungal effect of AF3 resulted in membrane permeabilization facilitating the uptake of the fluorescent dyes-acridine orange (AO)/propidium iodide (PI) and FUN-1. Using 1,6-diphenyl-1,3,5-hexatriene (DPH) and 4-(2-[6-(dioctylamino)-2-naphthalenyl] ethenyl)-1-(3-sulfopropyl) pyridinium inner salt (di-8-ANEPPS), we observed that the binding of AF3 to the membrane bilayer results in membrane disruption and depolarization. Flow cytometry analyses revealed a direct correlation between lipopeptide activity, membrane permeabilization (~ 75% PI uptake), and reduced cell viability. An increase in 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA) fluorescence demonstrates endogenous reactive oxygen species production. Lipopeptide treatment appears to induce late-stage apoptosis and alterations to nuclear morphology, suggesting that AF3-induced membrane damage may lead to a cellular stress response. Taken together, this study illustrates antifungal lipopeptide's potential as an antifungal drug candidate. KEY POINTS: • The studied lipopeptide variant AF3 displayed potent antifungal activity against C. albicans • Its biological activity was stable to proteolysis • Analytical studies demonstrated that the lipopeptide is essentially membranotropic and able to cause membrane dysfunction, elevated ROS levels, apoptosis, and DNA damage.

Molecular Adhesion of a Pilus-Derived Peptide Involved in Pseudomonas aeruginosa Biofilm Formation on Non-Polar ZnO-Surfaces

Bacterial colonization and biofilm formation on abiotic surfaces are initiated by the adhesion of peptides and proteins. Understanding the adhesion of such peptides and proteins at a molecular level thus represents an important step toward controlling and suppressing biofilm formation on technological and medical materials. This study investigates the molecular adhesion of a pilus-derived peptide that facilitates biofilm formation of Pseudomonas aeruginosa, a multidrug-resistant opportunistic pathogen frequently encountered in healthcare settings. Single-molecule force spectroscopy (SMFS) was performed on chemically etched ZnO11 2 ‾ 0 ${\left(11\bar{2}0\right)}$ surfaces to gather insights about peptide adsorption force and its kinetics. Metal-free click chemistry for the fabrication of peptide-terminated SMFS cantilevers was performed on amine-terminated gold cantilevers and verified by X-ray photoelectron spectroscopy (XPS) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Atomic force microscopy (AFM) and XPS analyses reveal stable topographies and surface chemistries of the substrates that are not affected by SMFS. Rupture events described by the worm-like chain model (WLC) up to 600 pN were detected for the non-polar ZnO surfaces. The dissociation barrier energy at zero force ΔG(0), the transition state distance xb and bound-unbound dissociation rate at zero force koff (0) for the single crystalline substrate indicate that coordination and hydrogen bonds dominate the peptide/surface interaction.

Ultrashort Cationic Peptide Fmoc-FFK as Hydrogel Building Block for Potential Biomedical Applications

Fmoc-diphenylalanine (Fmoc-FF) is a low-molecular-weight peptide hydrogelator. This simple all-aromatic peptide can generate self-supporting hydrogel materials, which have been proposed as novel materials for diagnostic and pharmaceutical applications. Our knowledge of the molecular determinants of Fmoc-FF aggregation is used as a guide to design new peptide-based gelators, with features for the development of improved tools. Here, we enlarge the plethora of Fmoc-FF-based hydrogelated matrices by studying the properties of the Fmoc-FFK tripeptide, alone or in combination with Fmoc-FF. For multicomponent matrices, the relative weight ratios between Fmoc-FFK and Fmoc-FF (specifically, 1/1, 1/5, 1/10, and 1/20 w/w) are evaluated. All the systems and their multiscale organization are studied using different experimental techniques, including rheology, circular dichroism, Fourier transform infrared spectroscopy, and scanning electron microscopy (SEM). Preliminary profiles of biocompatibility for the studied systems are also described by testing them in vitro on HaCaT and 3T3-L1 cell lines. Additionally, the lysine (K) residue at the C-terminus of the Fmoc-FF moiety introduces into the supramolecular material chemical functions (amino groups) which may be useful for modification/derivatization with bioactive molecules of interest, including diagnostic probes, chelating agents, active pharmaceutical ingredients, or peptide nucleic acids.

Dual-Role Peptide with Capping and Cleavage Site Motifs in Nanoparticle-Based One-Pot Colorimetric and Electrochemical Protease Assay

A new method for enzyme substrate assembly and its use in proteolytic enzyme assays with colorimetric and electrochemical detection is presented. The novelty of the method is the use of dual-function synthetic peptide containing both gold clustering and protease-sensitive moieties, which not only induces the simple formation of the peptide-decorated gold nanoparticle test substrates but also allows for the detection of proteolysis in the same batch. Protease-treated nanoparticles with a destabilized peptide shell became more prone to electroactivity, and thus, the model enzyme plasmin activity could be quantified with stripping square wave voltammetry analysis as well, giving an alternative method to conduct aggregation-based assays. Spectrophotometric and electrochemical calibration data proved to be linear within the 40-100 nM active enzyme concentration range, with possible extensions of the dynamic range by varying substrate concentration. The simple initial components and the ease of synthesis make the assay substrate preparation economic and easy to implement. The possibility of cross-check analytical results with two independent measurement techniques in the same batch greatly increases the applicability of the proposed system.

Supramolecular presentation of bioinstructive peptides on soft multilayered nanobiomaterials stimulates neurite outgrowth

Peptide amphiphiles (PAs) have emerged as effective molecular building blocks for creating self-assembling nanobiomaterials for multiple biomedical applications. Herein, we report a straightforward approach to assemble soft bioinstructive platforms to recreate the native neural extracellular matrix (ECM) aiming for neuronal regeneration based on the electrostatic-driven supramolecular presentation of laminin-derived IKVAV-containing self-assembling PA (IKVAV-PA) on biocompatible multilayered nanoassemblies. Spectroscopic and microscopic techniques show that the co-assembly of positively charged low-molecular-weight IKVAV-PA with oppositely charged high-molecular-weight hyaluronic acid (HA) triggers the formation of ordered β-sheet structures denoting a one-dimensional nanofibrous network. The successful functionalization of poly(L-lysine)/HA layer-by-layer nanofilms with an outer positively charged layer of self-assembling IKVAV-PA is demonstrated by the quartz crystal microbalance with dissipation monitoring and the nanofibrous morphological properties revealed by atomic force microscopy. The bioactive ECM-mimetic supramolecular nanofilms promote the enhancement of primary neuronal cells' adhesion, viability, and morphology when compared to the PA without the IKVAV sequence and PA-free biopolymeric multilayered nanofilms, and stimulate neurite outgrowth. The nanofilms hold great promise as bioinstructive platforms for enabling the assembly of customized and robust multicomponent supramolecular biomaterials for neural tissue regeneration.

Neutraligands of C5a can potentially occlude the interaction of C5a with the complement receptors C5aR1 and C5aR2

The complement system is central to the rapid immune response witnessed in vertebrates and invertebrates, which plays a crucial role in physiology and pathophysiology. Complement activation fuels the proteolytic cascade, which produces several complement fragments that interacts with a distinct set of complement receptors. Among all the complement fragments, C5a is one of the most potent anaphylatoxins, which exerts solid pro-inflammatory responses in a myriad of tissues by binding to the complement receptors such as C5aR1 (CD88, C5aR) and C5aR2 (GPR77, C5L2), which are part of the rhodopsin subfamily of G-protein coupled receptors. In terms of signaling cascade, recruitment of C5aR1 or C5aR2 by C5a triggers the association of either G-proteins or β-arrestins, providing a protective response under normal physiological conditions and a destructive response under pathophysiological conditions. As a result, both deficiency and unregulated activation of the complement lead to clinical conditions that require therapeutic intervention. Indeed, complement therapeutics targeting either the complement fragments or the complement receptors are being actively pursued by both industry and academia. In this context, the model structural complex of C5a-C5aR1 interactions, followed by a biophysical evaluation of the model complex, has been elaborated on earlier. In addition, through the drug repurposing strategy, we have shown that small molecule drugs such as raloxifene and prednisone may act as neutraligands of C5a by effectively binding to C5a and altering its biologically active molecular conformation. Very recently, structural models illustrating the intermolecular interaction of C5a with C5aR2 have also been elaborated by our group. In the current study, we provide the biophysical validation of the C5a-C5aR2 model complex by recruiting major synthetic peptide fragments of C5aR2 against C5a. In addition, the ability of the selected neutraligands to hinder the interaction of C5a with the peptide fragments derived from both C5aR1 and C5aR2 has also been explored. Overall, the computational and experimental data provided in the current study supports the idea that small molecule drugs targeting C5a can potentially neutralize C5a's ability to interact effectively with its cognate complement receptors, which can be beneficial in modulating the destructive signaling response of C5a under pathological conditions.

Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes

Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.

Fluorescence Resonance Energy Transfer-Based Aptasensor Made of Carbon-Based Nanomaterials for Detecting Lactoferrin at Low Concentrations

Lactoferrin in the saliva is recently considered a biomarker for the diagnosis of Alzheimer's disease. In this paper, a solution-based, user-friendly biosensing system has been developed to quickly measure lactoferrin at low concentrations. This aptasensor is applied to the fluorescence resonance energy transfer (FRET) quenching mechanism, in which carbon quantum dots (CDs) act as the FRET donor; the FRET quenching element is made of graphene oxide (GO) nanosheets which show good quenching capability. CDs bioconjugated with a chosen aptamer (CDs-aptamer) have the strongest emission (λ_em) at 447 nm when excitation (λ_ex) is 365 nm. Due to the interaction of the aptamer and GO through the π-π* interaction, GO can approach CDs, resulting in FRET quenching. In the presence of lactoferrin, the fluorescence intensity of CDs-aptamer is restored as the binding affinity between lactoferrin and the aptamer is stronger than the π-π* interaction between the aptamer and GO. A linear relationship between the restored fluorescence intensity and the concentration of lactoferrin in artificial saliva with a range from 4 to 16 μg/mL is observed. The limit of detection of the solution-based aptasensor is estimated at 2.48 μg/mL. In addition, the sensing performance of the aptasensor made of carbon nanomaterials has been evaluated to test different proteins including major salivary proteins. The results show that this aptasensor has a high selectivity to detect LF with a low concentration, <16 μg/mL.

Unprecedented enhancement and preservation of the peroxidase activity of cytochrome-c packaged with ionic liquid-modified gold nanoparticles by offsetting temperature and time stresses

Inspired by the biocompatibility of ionic liquids and their dexterousness for the preservation of enzyme structure and activity, herein, the interactions of Cyt-c with naked AuNPs and four IL-mediated AuNPs, which were formed by the fabrication of ILs with common cation 1-ethyl-3-methyl-imidazolium (EMIM) and different anions, to obtain AuNP-IL1 [(BF4)^-1 anion], AuNP-IL2 [(CH₃OSO₃)^-1 anion], AuNP-IL3 [(CH₃CH₂OSO₃)^-1 anion], and (AuNP-IL4) [Cl^-1 anion], were studied. Through this work, the peroxidase activity observed in the presence of a lower concentration IL-AuNPs is exceptionally increased (16 fold). IL-AuNPs preferentially counteract the temperature gradient change and long-term solvent preservation effects while persistently maintaining the Cyt-c peroxidase activity without much depreciation. The hydrodynamic diameter (d_H) of the Cyt-c-AuNP system was obtained, which supported the TEM results. Furthermore, to evaluate the effect of Cyt-c interaction with the AuNPs, a Zeta potential analysis was performed. Taken together, the binding of IL-AuNPs with Cyt-c, diameter size analysis, zeta potential, structural integrity evaluation using the DichroWeb software and morphology results suggest the interaction order of the IL-AuNPs to be in a sequence of AuNP-IL2 > AuNP-IL3 > AuNP- IL4 > AuNP-IL1 > Naked AuNPs. Moreover, results indicate that the IL anions play a dominating role in the modulation of interactions between IL-mediated AuNPs and Cyt-c. The study strongly supports the promising character of sulfur-containing IL-mediated AuNPs for Cyt-c immobilization simultaneously opening new avenues for the application of greener and biocompatible nanoparticles with drug delivery and therapeutic applications.

Carbon Nanostructure-Based DNA Sensor Used for Quickly Detecting Breast Cancer-Associated Genes

The early diagnosis of breast cancer highly relies on the detection of mutant DNA at low concentrations. Förster resonance energy transfer (FRET) quenching may offer a solution to quickly detect a small amount of single-strand DNA (ssDNA) through the combination of nanomaterials with special luminescence and unique structures of DNA double helix structure. Here, carbon quantum dots (CDs) modified with Capture ssDNA act as the FRET donor which interact with the two-dimensional fluorescence quencher, i.e., graphene oxide nanosheets (GO), to detect breast cancer-associated Target ssDNA at a low concentration. CDs bioconjugated with the designed Capture ssDNA (named CDs-Capture ssDNA) have the maximum fluorescence intensity (I_max) at the emission (λ_em) = 510 nm. The fluorescence of CDs-Capture ssDNA is quenched, while they interact with GO due to the π-π* interaction between ssDNA and GO. In the presence of Target ssDNA, the I_max is restored because of the stronger interaction between Target ssDNA and CDs-Capture ssDNA through the hydrogen bond. The restored fluorescence intensity of CDs has a linear relationship with the concentration of Target ssDNA from 0.25 to 2.5 μM with a detection limit around 0.24 μM. The selectivity of the sensing system has been further evaluated by testing the 3-base mismatched and non-base matched in which efficient restoration of photoluminescence of the sensing system cannot be observed. This carbon nanostructure-based DNA sensing system offers a user-friendly and quick detection of single-strand DNA at lower concentration.

Natural Antimicrobial Peptides Self-assemble as α/β Chameleon Amyloids

Amyloid protein fibrils and some antimicrobial peptides (AMPs) share biophysical and structural properties. This observation suggests that ordered self-assembly can act as an AMP-regulating mechanism, and, vice versa, that human amyloids play a role in host defense against pathogens, as opposed to their common association with neurodegenerative and systemic diseases. Based on previous structural information on toxic amyloid peptides, we developed a sequence-based bioinformatics platform and, led by its predictions, experimentally identified 14 fibril-forming AMPs (ffAMPs) from living organisms, which demonstrated cross-β and cross-α amyloid properties. The results support the amyloid-antimicrobial link. The high prevalence of ffAMPs produced by amphibians and marine creatures among other species suggests that they confer unique advantageous properties in distinctive environments, potentially providing stability and adherence properties. Most of the newly identified 14 ffAMPs showed lipid-induced and/or time-dependent secondary structure transitions in the fibril form, indicating structural and functional cross-α/β chameleons. Specifically, ffAMP cytotoxicity against human cells correlated with the inherent or lipid-induced α-helical fibril structure. The findings raise hypotheses about the role of fibril secondary structure switching in regulation of processes, such as the transition between a stable storage conformation and an active state with toxicity against specific cell types.

Concerted Rolling and Penetration of Peptides during Membrane Binding

Peptide binding to membranes is common and fundamental in biochemistry and biophysics and critical for applications ranging from drug delivery to the treatment of bacterial infections. However, it is largely unclear, from a theoretical point of view, what peptides of different sequences and structures share in the membrane-binding and insertion process. In this work, we analyze three prototypical membrane-binding peptides (α-helical magainin, PGLa, and β-hairpin tachyplesin) during membrane binding, using molecular details provided by Markov state modeling and microsecond-long molecular dynamics simulations. By leveraging both geometric and data-driven collective variables that capture the essential physics of the amphiphilic and cationic peptide-membrane interactions, we reveal how the slowest kinetic process of membrane binding is the dynamic rolling of the peptide from an attached to a fully bound state. These results not only add fundamental knowledge of the theory of how peptides bind to biological membranes but also open new avenues to study general peptides in more complex environments for further applications.

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure

Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H₂O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H₂O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.

Investigating Membrane‐Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far‐Infrared Spectroscopy

Synchrotron radiation‐based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio‐molecular phenomena including folding‐mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near‐THz 400–40 cm⁻¹ range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature‐dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane‐induced and folding‐mediated activity of AMPs. The far‐FTIR study offers a direct and information‐rich probe of membrane‐related antimicrobial interactions.

Antiviral Activity of Peptide-Based Assemblies

The COVID-19 pandemic highlighted the importance of developing surfaces and coatings with antiviral activity. Here, we present, for the first time, peptide-based assemblies that can kill viruses. The minimal inhibitory concentration (MIC) of the assemblies is in the range tens of micrograms per milliliter. This value is 2 orders of magnitude smaller than the MIC of metal nanoparticles. When applied on a surface, by drop casting, the peptide spherical assemblies adhere to the surface and form an antiviral coating against both RNA- and DNA-based viruses including coronavirus. Our results show that the coating reduced the number of T4 bacteriophages (DNA-based virus) by 3 log, compared with an untreated surface and 6 log, when compared with a stock solution. Importantly, we showed that this coating completely inactivated canine coronavirus (RNA-based virus). This peptide-based coating can be useful wherever sterile surfaces are needed to reduce the risk of viral transmission.

Odd-Even Effect in Peptide SAMs-Competition of Secondary Structure and Molecule-Substrate Interaction

Peptide-based self-assembled monolayers (SAMs) are well known to be crucial for biocompatible surface formation on inorganic substrates applied for implants, biosensors, or tissue engineering. Moreover, recently these bioinspired nanostructures are also considered particularly interesting for molecular electronics applications due to their surprisingly high conductance and thickness-independent capacitance, which make them a very promising element of organic field-effect transistors (OFETs). Our structural analysis conducted for a series of prototypic homooligopeptides based on glycine (Gly) with cysteine (Cys) as a substrate bonding group chemisorbed on Au and Ag metal substrates (Gly_nCys/Au(Ag), n = 1–9) exhibits the formation by these monolayers secondary structure close to β-sheet conformation with pronounced odd–even structural effect strongly affecting packing density and conformation of molecules in the monolayer, which depend on the length of molecules and the type of metal substrate. Our experiments indicate that the origin of these structural effects is related to the either cooperative or competitive relationship between the type of secondary structure formed by these molecules and the directional character of their chemical bonding to the metal substrate. The current analysis opens up the opportunity for the rational design of these biologically inspired nanostructures, which is crucial both for mentioned biological and electronic applications.

The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure

The complex topologies of large multi-domain globular proteins make the study of their folding and assembly particularly demanding. It is often characterized by complex kinetics and undesired side reactions, such as aggregation. The structural simplicity of tandem-repeat proteins, which are characterized by the repetition of a basic structural motif and are stabilized exclusively by sequentially localized contacts, has provided opportunities for dissecting their folding landscapes. In this study, we focus on the Erwinia chrysanthemi pectin methylesterase (342 residues), an all-β pectinolytic enzyme with a right-handed parallel β-helix structure. Chemicals and pressure were chosen as denaturants and a variety of optical techniques were used in conjunction with stopped-flow equipment to investigate the folding mechanism of the enzyme at 25 °C. Under equilibrium conditions, both chemical- and pressure-induced unfolding show two-state transitions, with average conformational stability (ΔG° = 35 ± 5 kJ·mol⁻¹) but exceptionally high resistance to pressure (P_m = 800 ± 7 MPa). Stopped-flow kinetic experiments revealed a very rapid (τ < 1 ms) hydrophobic collapse accompanied by the formation of an extended secondary structure but did not reveal stable tertiary contacts. This is followed by three distinct cooperative phases and the significant population of two intermediate species. The kinetics followed by intrinsic fluorescence shows a lag phase, strongly indicating that these intermediates are productive species on a sequential folding pathway, for which we propose a plausible model. These combined data demonstrate that even a large repeat protein can fold in a highly cooperative manner.

Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Self-Templated, Enantioselective Assembly of an Amyloid-like Dipeptide into Multifunctional Hierarchical Helical Arrays

Chiral self-assembly of peptides has attracted great interest owing to their promising applications in biomedicine, chemistry, and materials science. However, compared with the rich knowledge about their chiral self-assembly at the molecular or nanoscale, the formation of long-range-ordered hierarchical helical arrays (HHAs) from simple peptides remains a formidable challenge. Herein, we report the self-templated assembly of an amyloid-like dipeptide into long-range-ordered HHAs by their spontaneous fibrillization and hierarchical helical assembly within a confined film. The chiral interactions between the peptide and diamines result in geometry frustration and the phase transition of self-assembling peptide films from achiral spherulite structures into chiral HHAs. By changing the chirality and enantioselective interactions, we can control the phase behavior, handedness, and chiroptics of the self-assembled HHAs precisely. Moreover, the redox activity of the HHAs allows the in situ decoration of nanoparticles with high catalytic activity. These results provide insights into the chiral self-assembly of peptides and the fabrication of highly ordered materials with complex architectures and promising applications in chiroptics and catalysis.

Infrared Microspectroscopy With Multivariate Analysis to Differentiate Oral Hyperplasia From Squamous Cell Carcinoma: A Proof of Concept for Early Diagnosis

BACKGROUND AND OBJECTIVES

Despite having numerous advances in therapeutics, mortality and morbidity due to oral cancer incidence are still very high. Early detection can improve the chances of survival in most patients. However, diagnosis at early stages can be challenging as premalignant conditions are usually asymptomatic. Currently, histological assessment remains the gold standard for diagnosis. Early diagnosis poses challenges to pathologists due to less severe morphological changes associated with early stages. Therefore, a fast and robust method of detection based on molecular changes is needed for early diagnosis. © 2021 Wiley Periodicals LLC.

STUDY DESIGN/MATERIAL AND METHODS

In the present study, Fourier transform infrared (FTIR) spectroscopic imaging has been used to differentiate early-stage oral hyperplasia from adjacent normal (AN) and oral squamous cell carcinoma (OSCC). Hyperplasia is often considered as an initial event in the pathogenesis of oral cancer and OSCC is the most common advanced stage of malignancy. Differentiating normal versus hyperplasia and hyperplasia versus OSCC can remain quite challenging on occasion using conventional staining as the histological assessment is based on morphological changes.

RESULTS

Unsupervised hierarchical cluster analysis (UHCA) has been performed on FTIR images of multiple tissues together that provided some degree of classification among tissue groups. The AN epithelium clustered distinctively using UHCA from both hyperplasia and grades 1 and 2 of OSCC. An increase in the content of DNA, denaturation of protein, and altered lipid structures were more clearly elucidated with spectral analysis.

CONCLUSION

This study demonstrates a simple strategy to differentiate early-stage oral hyperplasia from AN and OSCC using UHCA. This study also proposes a future alternative method where FTIR imaging can be used as a diagnostic tool for cancer at early stages.

Bio-Functionalized Chitosan for Bone Tissue Engineering

Hybrid biomaterials allow for the improvement of the biological properties of materials and have been successfully used for implantology in medical applications. The covalent and selective functionalization of materials with bioactive peptides provides favorable results in tissue engineering by supporting cell attachment to the biomaterial through biochemical cues and interaction with membrane receptors. Since the functionalization with bioactive peptides may alter the chemical and physical properties of the biomaterials, in this study we characterized the biological responses of differently functionalized chitosan analogs. Chitosan analogs were produced through the reaction of GRGDSPK (RGD) or FRHRNRKGY (HVP) sequences, both carrying an aldehyde-terminal group, to chitosan. The bio-functionalized polysaccharides, pure or "diluted" with chitosan, were chemically characterized in depth and evaluated for their antimicrobial activities and biocompatibility toward human primary osteoblast cells. The results obtained indicate that the bio-functionalization of chitosan increases human-osteoblast adhesion (p < 0.005) and proliferation (p < 0.005) as compared with chitosan. Overall, the 1:1 mixture of HVP functionalized-chitosan:chitosan is the best compromise between preserving the antibacterial properties of the material and supporting osteoblast differentiation and calcium deposition (p < 0.005 vs. RGD). In conclusion, our results reported that a selected concentration of HVP supported the biomimetic potential of functionalized chitosan better than RGD and preserved the antibacterial properties of chitosan.

Proton Dynamics of Water Diffusion in Shrimp Hydrolysates Flour and Effects of Moisture Absorption on Its Properties

Moisture absorbed into shrimp hydrolysates (SHs) flour profoundly affected its properties. The unstored hydrolysate flour was called SHs-0h and SHs stored for 30 h at 25 °C and 75% relative humidity was named SHs-30. During the process of storage, the moisture dynamics in SHs flour were investigated by dynamic vapor sorption (DVS) and low-field nuclear magnetic resonance (LF-NMR). The effects of moisture absorption on the radicals scavenging rates of SHs flour were evaluated by electron paramagnetic resonance (EPR). The effects of moisture absorption on secondary structure were studied by mid-infrared (MIR) spectroscopy and infrared microimaging spectroscopy. The changes of volatile components were monitored by purge and trap coupled with gas chromatography-mass spectrometry (PT-GC-MS). DVS results showed that the moisture absorption rate of SHs flour could reach a maximum of 88.93%. Meanwhile, the water was transformed into more stable water with shorter relaxation times. The porous structure of the SHs-30 h flour disappeared and became smoother compared to SH-0 h flour. DPPH (31.09 ± 0.54%) and OH (26.62 ± 1.14%) radicals scavenging rates of SHs-30 h significantly reduced (p < 0.05) compared to that of SHs-0 h flour. The vibrations of the MIR absorbance peaks were changed. Finally, eight volatile components disappeared and six new volatile compounds were found. This study provided a theory basis for moisture dynamics in peptide flour during the storage process.

The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid

Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.

Geometry encoded functional programming of tumor homing peptides for targeted drug delivery

Poly-peptide molecules have shown promising applications in drug delivery and tumor targeting. A series of tumor homing peptides were designed by exhaustively sampling low energy geometrical basins of amino acids at specific sites of a peptide molecule to induce a conformational lock. This peptide library was pruned to a limited set of eight molecules, employing electrostatic interactions, docking, and molecular dynamics simulations. These designed and optimized peptides were synthesized and tested on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS), and non-cancerous mammary epithelial cells (MCF-10A) using confocal microscopy and flow cytometry. Peptides show differential uptake in cancerous MDA-MB-231, HeLa, U2-OS, and non-cancerous MCF-10A cells. Confocal imaging verified their ability to penetrate even in 3D tumorospheres of MDA-MB-231 cells. Further, experiments of mitochondrial membrane potential depolarization and Caspase-3 activation confirmed that their cytotoxic effects are by apoptosis. Homing ability of the designed peptides in in vivo system and fluorescence imaging with clinical samples of human origin have further confirmed that the in vitro studies are qualitatively identical and quantitatively comparable in their ability to selectively recognize tumor cells. Overall, we present a roadmap for the functional programming of peptide-based homing and penetrating molecules that can perform selective tumor targeting.

Infrared spectroscopy probes ion binding geometries

Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.

Tuning the mechanistic pathways of peptide self-assembly by aromatic interactions

Herein, we have unravelled the key influence of aromatic interactions on the mechanistic pathways of peptide self-assembly by introducing suitable chromophores (pyrene vs. naphthalene). Although both self-assembled peptides are indistinguishable in their morphologies, this minor structural difference strongly affects the packing modes (parallel vs. antiparallel) and the corresponding self-assembly mechanism (cooperative vs. isodemsic).

Antibiotic Potential and Biophysical Characterization of Amphipathic β-Stranded [XZ]n Peptides With Alternating Cationic and Hydrophobic Residues

Cationic membrane-active peptides are considered to be promising candidates for antibiotic treatment. Many natural and artificial sequences show an antimicrobial activity when they are able to take on an amphipathic fold upon membrane binding, which in turn perturbs the integrity of the lipid bilayer. Most known structures are α-helices and β-hairpins, but also cyclic knots and other irregular conformations are known. Linear β-stranded antimicrobial peptides are not so common in nature, but numerous model sequences have been designed. Interestingly, many of them tend to be highly membranolytic, but also have a significant tendency to self-assemble into β-sheets by hydrogen-bonding. In this minireview we examine the literature on such amphipathic peptides consisting of simple repetitive sequences of alternating cationic and hydrophobic residues, and discuss their advantages and disadvantages. Their interactions with lipids have been characterized with a number of biophysical techniques—especially circular dichroism, fluorescence, and infrared—in order to determine their secondary structure, membrane binding, aggregation tendency, and ability to permeabilize vesicles. Their activities against bacteria, biofilms, erythrocytes, and human cells have also been studied using biological assays. In line with the main scope of this Special Issue, we attempt to correlate the biophysical results with the biological data, and in particular we discuss which properties (length, charge, aggregation tendency, etc.) of these simple model peptides are most relevant for their biological function. The overview presented here offers ideas for future experiments, and also suggests a few design rules for promising β-stranded peptides to develop efficient antimicrobial agents.

Self-Assembly of Peptide Chiral Nanostructures with Sequence-Encoded Enantioseparation Capability

Biopolymers such as polysaccharides and proteins have been widely used for the chiral separation of various components due to the intrinsic chirality of the polymers. Amyloid-like short peptides can also self-assemble into diverse chiral supramolecular nanostructures or polymers with precisely tailored architectures driving by noncovalent interactions. However, the use of such supramolecular nanostructures for the resolution and separation of chiral components remains largely unexplored. Here, we report that the self-assembled peptide supramolecular nanostructures can be used for the highly efficient chiral separation of various enantiomers. By rationally designing the constituent amino acid sequence of the peptides and the self-assembling environment, we can fabricate supramolecular polymers with distinct surface charges and architectures, including nanohelices, nanoribbons, nanosheets, nanofibrils, and nanospheres. The various supramolecular nanostructures were then used to resolve the racemic mixtures of α-methylbenzylamine, 2-phenylpropionic acid, and 1-phenylethanol. The results indicated that the self-assembled peptide polymers showed excellent enantioselective separation efficiency for different chiral molecules. The enantioselective separation efficiency of the peptide nanostructures can be tailored by changing their surface charges, morphology, and the constituent amino acid sequences of the peptides.

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

Peptide-based biopolymers represent highly promising biocompatible materials with multiple applications, such as tailored drug delivery, tissue engineering and regeneration, and as stimuli-responsive materials. Herein, we report the pH- and concentration-dependent self-assembly and conformational transformation of the newly synthesized octapeptide PEP-1. At pH 7.4, PEP-1 forms β-sheet-rich secondary structures into fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures and resulting morphologies due to electrostatic repulsion between charged amino acids. PEP-1 can also form helical or random-coil secondary structures at a relatively low concentration. The obtained pH-sensitive self-assembly behavior of the target octapeptide is expected to contribute to the development of novel drug nanocarrier assemblies.

Peptide-based delivery vectors with pre-defined geometrical locks

Design of peptide-based targeted delivery vectors with attributes of specificity and selective cellular targeting by fixing their topology and resulting electrostatic fingerprint is the objective of this study. We formulated our peptide design platform by utilizing the possibilities of side-chain induced geometric restrictions in a typical peptide molecule. Conceptually, we locked the conformation of the RGD/NGR motif of tumor homing peptides (THPs) by mutating glycine in these motifs with d-proline and tailed the peptides with a syndiotactic amphipathic segment for cellular penetration. The designed peptides were synthesized, characterized, and tested in vitro on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS) and non-cancer mammary epithelial cells (MCF-10A), by flow cytometry and confocal microscopy. The results showed differential cellular uptake in different cell types, as a result of the distinct electrostatic fingerprint encoded in their design. The uptake of serum pre-treated peptides by cells reveals the retention of peptide activity even after the incubation with serum. In addition, peptide-methotrexate (MTX) conjugates compared to the methotrexate drug showed enhanced apoptotic cell death in MTX-resistant MDA-MB-231 cells, indicating the increase in MTX bioavailability.

Isotopic Control over Self-Assembly in Supramolecular Gels

It is common to switch between H₂O and D₂O when examining peptide-based systems, with the assumption being that there are no effects from this change. Here, we describe the effect of changing from H₂O to D₂O in a number of low-molecular-weight dipeptide-based gels. Gels are formed by decreasing the pH. In most cases, there is little difference in the structures formed at high pH, but this is not universally true. On lowering the pH, the kinetics of gelation are affected and, in some cases, the structures underpinning the gel network are different. Where there are differences in the self-assembled structures, the resulting gel properties are different. We, therefore, show that isotopic control over gel properties is possible.

Hydroxyapatite Surfaces Functionalized with a Self-Assembling Peptide: XPS, RAIRS and NEXAFS Study

Hydroxyapatite (HAP) coatings can improve the biocompatibility and bioactivity of titanium alloys, such as Ti6Al4V, commonly used as material for orthopedic prostheses. In this framework, we have studied the surface of HAP coatings enriched with Mg and either Si or Ti deposited by RF magnetron sputtering on Ti6Al4V. HAP coatings have been furtherly functionalized by adsorption of a self-assembling peptide (SAP) on the HAP surface, with the aim of increasing the material bioactivity. The selected SAP (peptide sequence AbuEAbuEAbuKAbuKAbuEAbuEAbuKAbuK) is a self-complementary oligopeptide able to generate extended ordered structures by self-assembling in watery solutions. Samples were prepared by incubation of the HAP coatings in SAP solutions and subsequently analyzed by X-Ray Photoelectron Spectroscopy (XPS), Fourier Transform Infrared (FTIR) and Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopies, in order to determine the amount of adsorbed peptide, the peptide stability and the structure of the peptide overlayer on the HAP coatings as a function of the HAP substrate and of the pH of the mother SAP solution. Experimental data yielded evidence of SAP adsorption on the HAP surface, and peptide overlayers showed ordered structure and molecular orientation. The thickness of the SAP overlayer depends on the composition of the HAP coating.

Fourier-transform infrared spectroscopy for monitoring proteolytic reactions using dry-films treated with trifluoroacetic acid

In this study we explore the potential of using Fourier-transform infrared (FTIR) spectra of trifluoroacetate-protein and peptide complexes for monitoring proteolytic reactions. The idea of treating dry-films of protein hydrolysates with trifluoroacetic acid (TFA) prior to FTIR analysis is based on the unique properties of TFA. By adding a large excess of TFA to protein hydrolysate samples, the possible protonation sites of the proteins and peptides will be saturated. In addition, TFA has a low boiling point when protonated as well as complex-forming abilities. When forming TFA-treated dry-films of protein hydrolysates, the excess TFA will evaporate and the deprotonated acid (CF₃COO⁻) will interact as a counter ion with the positive charges on the sample materials. In the study, spectral changes in TFA-treated dry-films of protein hydrolysates from a pure protein and poultry by-products, were compared to the FTIR fingerprints of untreated dry-films. The results show that time-dependent information related to proteolytic reactions and, consequently, on the characteristics of the protein hydrolysates can be obtained. With additional developments, FTIR on dry-films treated with TFA may be regarded as a potential future tool for the analysis of all types of proteolytic reactions in the laboratory as well as in industry.