DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra

Aggregation studies of alpha-lactalbumin induced by edible azo dyes with different sulfonyl group numbers: A comparative study

As an opaque and complex colloidal mixture, milk is usually present as a positively charged colloid under acidic conditions. Adding negatively charged colloids can lead to protein aggregation in milk. Alpha-lactalbumin (α-La) is an essential component of whey protein and has good physicochemical properties for functional food development. We combined spectroscopy, computer simulations, and other techniques to comparative analyze the mechanisms and characteristics of isolated α-La aggregation induced by CI Acid Red 27 (C27)/CI Acid Red 14 (FB) containing different sulfonyl groups in vitro. The results showed that C27/FB (5.25 × 10-5 mol·L-1 to 3.15 × 10-4 mol·L-1) induced the formation of fibril-like aggregates under acidic conditions (pH 2.0 and 4.0) mainly benefit from hydrophobic and electrostatic forces. Weakening and redshift of α-La's characteristics negative peak were observed (208 nm to 218 nm) on circular dichroism. β-Crosslinks self-assembly and reorganization of disulfide bonds occurred during protein fibrillation. Moreover, the different redshift intensity of Congo red binding to amyloid fibrils was observed to be induced by C27 (>551 nm) and FB (>536 nm), and the direct observation by TEM demonstrated the ability to induce protein fibrillation is C27 > FB. Edible azo dyes with more sulfonyl groups would possess a stronger ability to induce protein fibrillation.

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

Cricket Protein Isolate Extraction: Effect of Ammonium Sulfate on Physicochemical and Functional Properties of Proteins

Crickets are known to be a promising alternative protein source. However, a negative consumer bias and an off-flavor have become obstacles to the use of these insects in the food industry. In this study, we extracted the protein from commercial cricket powder by employing alkaline extraction-acid precipitation and including ammonium sulfate. The physicochemical and functional properties of the proteins were determined. It was found that, upon including 60% ammonium sulfate, the cricket protein isolate (CPI) had the highest protein content (~94%, w/w). The circular dichroism results indicated that a higher amount of ammonium sulfate drastically changed the secondary structure of the CPI by decreasing its α-helix content and enhancing its surface hydrophobicity. The lowest solubility of CPI was observed at pH 5. The CPI also showed better foaming properties and oil-holding capacity (OHC) compared with the cricket powder. In conclusion, adding ammonium sulfate affected the physicochemical and functional properties of the CPI, allowing it to be used as an alternative protein in protein-enriched foods and beverages.

Maillard reaction-based conjugation of Spirulina protein with maltodextrin using wet-heating route and characterisation of conjugates

Spirulina protein concentrate (SPC) was extracted from Spirulina biomass and its structure and technofunctional properties were modified through Maillard reaction with maltodextrin (MD). Wet-heating route was adapted and Maillard reaction was controlled within initial to intermediate stage by avoiding or minimising the formation of melanoidins. A glycation degree of up to 29.1 % was achieved after reaction between SPC and MD, and molecular weight of the SPC increased accordingly. The solubility of SPC was improved only in the pH range around its isoelectric point after conjugation. The antioxidative property of the SPC-MD conjugate was also improved as the DPPH radical scavenging activity increased 19.7 to 30.2 %. Oil-in-water emulsion stabilised by SPC-MD conjugate produced at 6 h had significantly reduced droplet size, increased surface charge, and higher physical stability in temperature range 25-60 °C. The outcome of this research will help broaden the application of SPC in food as emulsifier and encapsulating shell material.

The Interactional Characterization of Lentil Protein Isolate (LPI) with Cyanidin-3-O-Glucoside (C3G) and Their Effect on the Stability and Antioxidant Activity of C3G

The interaction between lentil protein isolate (LPI) and cyanidin-3-O-glucoside (C3G) was investigated via with UV−vis spectroscopy, circular dichroism, and fluorescence spectroscopy and the stability of anthocyanin was also evaluated. After LPI mixed with C3G, the turbidity and foaming capacity increased and the particle size and surface charge did not change significantly, while the surface hydrophobicity decreased significantly (p < 0.05). The fluorescence results indicated that C3G quenched the intrinsic of LPI by static quenching and LPI bound with C3G via hydrophobic effects with Ka of 3.24 × 106 M−1 at 298 K. The addition of LPI significantly (p < 0.05) slightly decreased the thermal and oxidation degradation of C3G by up to 90.23% and 54.20%, respectively, while their antioxidant activity was inhibited upon mixing. These alterations of physicochemical properties might be attributed to their structural changes during the interaction. The obtained results would be of help in stabilizing bioactive compounds and the development of functional foods.

A study on the catalytic activity of polypeptides toward the hydrolysis of glucoside compounds gastrodin, polydatin and esculin

The self-assembly of a series of catalytically active polypeptides toward hydrolysis of glucoside compounds, namely, gastrodin, polydatin and esculin was investigated. These active peptides are composed of two functional fragments: one is the hydrophobic sequence LHLHLRL, which forms assembling segments in the presence of Zn ions (Zn²⁺); another functional sequence of active peptides are catalytic sites such as Glu (E), Asp (D) and His (H), where carboxylic acids (-COOH) or imidazole groups act like scissors to cleave glucoside bonds of the compounds (according to the acid-base coupling mechanism). The effects of the amino acid sequence of the peptide, Zn²⁺ concentration, pH and the size or steric hindrance of glucoside compounds on the hydrolytic activity were studied. It was found that the crystalline structure of assembled peptides was crucial to provide the peptide with catalytic hydrolytic activity. Noncovalent interaction index was used to analyse the noncovalent interaction of PEs with glucoside compounds, including hydrogen bonds, van der Waals, and steric effect in the complexes. The binding energy of complexes, the direction and site of nucleophilic attack during deglycosylation processes were also investigated by molecular docking and the electron density Laplace function. This revealed that the differences in the hydrolytic activity of peptides toward glucoside compounds with different sizes originated from different hydrogen bond interactions between the peptides and substrates. These active peptides may find application in the preparation of drugs by de-glycosylation of natural compounds.

In vitro inhibition of acetylcholinesterase activity by yellow field pea (Pisum sativum) protein-derived peptides as revealed by kinetics and molecular docking

Compounds with structural similarities to the neurotransmitter (acetylcholine) are mostly used to inhibit the activity of acetylcholinesterase (AChE) in Alzheimer’s disease (AD) therapy. However, the existing drugs only alleviate symptoms of moderate to mild conditions and come with side effects; hence, the search is still on for potent and safer options. In this study, High performance liquid chromatography (HPLC) fractionations of AChE-inhibitory pea protein hydrolysates obtained from alcalase, flavourzyme and pepsin digestions were carried out followed by sequence identification of the most active fractions using mass spectrometry. Subsequently, 20 novel peptide sequences identified from the active fractions were synthesized and five peptides, QSQS, LQHNA, SQSRS, ETRSQ, PQDER (IC₅₀ = 1.53 – 1.61 μg/mL) were selected and analyzed for ability to change AChE protein conformation (fluorescence emission and circular dichroism), kinetics of enzyme inhibition, and enzyme-ligand binding configurations using molecular docking. The kinetics studies revealed different inhibition modes by the peptides with relatively low (<0.02 mM and <0.1 mM) inhibition constant and Michaelis constant, respectively, while maximum velocity was reduced. Conformational changes were confirmed by losses in fluorescence intensity and reduced α-helix content of AChE after interactions with different peptides. Molecular docking revealed binding of the peptides to both the catalytic anionic site and the peripheral anionic site. The five analyzed peptides all contained glutamine (Q) but sequences with Q in the penultimate N-terminal position (LQHNA, SQSRS, and PQDER) had stronger binding affinity. Results from the different analysis in this study confirm that the peptides obtained from enzymatic digestion of pea protein possess the potential to be used as novel AChE-inhibitory agents in AD management.

Electric Field Effect on Inhibiting the Co-fibrillation of Amyloid Peptides by Modulating the Aggregation Pathway

With the revelation of the close link between Alzheimer's disease (AD) and type II diabetes (T2D) and the possible assembly of multiple amyloid peptides therein, it is critical to understand and regulate the co-fibrillation pathway between related amyloid peptides. Here, we show experimentally and theoretically that electric field (EF) inhibited hybrid amyloid fibrillation of β-amyloid peptide (Aβ) and human islet amyloid peptide (hIAPP) by modulating the hetero-aggregation pathway. Experimental results confirm that the β-sheet secondary structure of amyloid peptides would be disrupted under small static EF and accompanied by transforming fibril aggregates into amorphous particles in vitro. Molecular dynamics simulations further demonstrate that even with the transformation of the secondary structure from β-sheet to random coil, the strong interaction between Aβ and hIAPP peptides would remain largely unaffected under the small static EF, leading to the formation of amorphous nanoparticles observed in the experiments. This inhibitory effect of EF on the co-fibrillation of multiple amyloid peptides might contribute to reducing the mutual deterioration of different degenerative diseases and show great potential for the noninvasive treatment of amyloid-related diseases.

Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1

SURP domains are exclusively found in splicing-related proteins in all eukaryotes. SF3A1, a component of the U2 snRNP, has two tandem SURP domains, SURP1, and SURP2. SURP2 is permanently associated with a specific short region of SF3A3 within the SF3A protein complex whereas, SURP1 binds to the splicing factor SF1 for recruitment of U2 snRNP to the early spliceosomal complex, from which SF1 is dissociated during complex conversion. Here, we determined the solution structure of the complex of SURP1 and the human SF1 fragment using nuclear magnetic resonance (NMR) methods. SURP1 adopts the canonical topology of α1-α2-3₁₀ -α3, in which α1 and α2 are connected by a single glycine residue in a particular backbone conformation, allowing the two α-helices to be fixed at an acute angle. A hydrophobic patch, which is part of the characteristic surface formed by α1 and α2, specifically contacts a hydrophobic cluster on a 16-residue α-helix of the SF1 fragment. Furthermore, whereas only hydrophobic interactions occurred between SURP2 and the SF3A3 fragment, several salt bridges and hydrogen bonds were found between the residues of SURP1 and the SF1 fragment. This finding was confirmed through mutational studies using bio-layer interferometry. The study also revealed that the dissociation constant between SURP1 and the SF1 fragment peptide was approximately 20 μM, indicating a weak or transient interaction. Collectively, these results indicate that the interplay between U2 snRNP and SF1 involves a transient interaction of SURP1, and this transient interaction appears to be common to most SURP domains, except for SURP2.

Expression, purification and characterisation of the recombinant possum lipocalin vulpeculin

BACKGROUND

Lipocalins are a large family of proteins, which possess a highly conserved eight-stranded antiparallel beta-barrel structure as distinctive trait. This family includes Major Urinary Proteins (MUPs) from rats and mouse, studied for their role in urinary protein-mediated chemosignalling. Vulpeculin has been identified as the most abundant protein in the urine of the common brushtail possum, Trichosurus vulpecula. On the basis of high similarity with other MUPS, we hypothesised that vulpeculin might have a role in possum chemosignalling and investigated its stability and binding ability.

METHODS

We expressed and purified vulpeculin using an E.coli-based system and confirmed correct folding by circular dichroism (CD) spectroscopy. Thermal stability was studied by CD and binding properties were investigated using two optical probes N-phenyl-naphthylamine (NPN) and 8-anilino-1-naphthalene sulphonic acid (ANS).

RESULTS

CD revealed a secondary structure typical of a predominantly β-sheet protein, consistent with the beta barrel structure of the lipocalin family. Vulpeculin showed a high level of thermostability, as assessed by CD, exhibiting a small shift in the secondary structure even at 95 °C. Binding assays indicated that vulpeculin cannot accommodate the NPN ligand but can bind ANS.

CONCLUSION

The urinary secretion, high degree of sequence similarity with other lipocalins, its beta sheet structure assessed by CD and potential to bind hydrophobic ligands in the hydrophobic cavity or an external hydrophobic pocket, suggest vulpeculin may be involved in possum chemosignalling.

GENERAL SIGNIFICANCE

This work represents a first step towards the further investigation of the newly discovered lipocalin and its role in possum chemosignalling.

Human Enzyme PADI4 Binds to the Nuclear Carrier Importin α3

PADI4 is a peptidyl-arginine deiminase (PADI) involved in the conversion of arginine to citrulline. PADI4 is present in macrophages, monocytes, granulocytes, and several cancer cells. It is the only PADI family member observed within both the nucleus and the cytoplasm. PADI4 has a predicted nuclear localization sequence (NLS) comprising residues Pro56 to Ser83, to allow for nuclear translocation. Recent predictors also suggest that the region Arg495 to Ile526 is a possible NLS. To understand how PADI4 is involved in cancer, we studied the ability of intact PADI4 to bind importin α3 (Impα3), a nuclear transport factor that plays tumor-promoting roles in several cancers, and its truncated species (ΔImpα3) without the importin-binding domain (IBB), by using fluorescence, circular dichroism (CD), and isothermal titration calorimetry (ITC). Furthermore, the binding of two peptides, encompassing the first and the second NLS regions, was also studied using the same methods and molecular docking simulations. PADI4 interacted with both importin species, with affinity constants of ~1–5 µM. The isolated peptides also interacted with both importins. The molecular simulations predict that the anchoring of both peptides takes place in the major binding site of Impα3 for the NLS of cargo proteins. These findings suggest that both NLS regions were essentially responsible for the binding of PADI4 to the two importin species. Our data are discussed within the framework of a cell mechanism of nuclear transport that is crucial in cancer.

Recombinant PilS: Cloning, Expression and Biochemical Characterization of a Pil-Fimbriae Subunit

Pil-fimbriae is a type IV pili member, which is a remarkably versatile component with a wide variety of functions, including motility, attachment to different surfaces, electrical conductance, DNA acquisition, and secretion of a broad range of structurally distinct protein substrates. Despite the previous functional characterization of Pil, more studies are required to understand the regulation of Pil expression and production, since the exact mechanisms involved in these steps are still unknown. Therefore it is extremely important to have a protein with the correct secondary and tertiary structure that will enable an accurate characterization and a specific antisera generation. For this reason, the aim of this work was to generate potential tools for further investigations to comprehend the mechanisms involved in Pil regulation and its role in pathogenic E. coli infections with the obtaining of a precise native-like recombinant PilS and the corresponding antisera. The pilS gene was successfully cloned into an expression vector, and recombinant PilS (rPilS) was efficiently solubilized and purified by metal affinity chromatography. Protein characterization analyses indicated that rPilS presented native-like secondary and tertiary structures after the refolding process. The generated anti-rPilS sera efficiently recognized recombinant and native proteins from atypical enteropathogenic E. coli strains.

Altering functional properties of rice protein hydrolysates by covalent conjugation with chlorogenic acid

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Rice protein hydrolysate was covalently conjugated to chlorogenic acid by three methods.

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Covalent conjugation resulted in an unfolded structure of rice protein hydrolysate.

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LYS might be the binding sites for chlorogenic acid grafted on rice protein hydrolysate.

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Conjugates formed by alkaline method exhibited highest functional property.

Proteins and phenolic compounds are common components in foods that readily interact with each other to yield complexes, leading to changes in the functional properties. In this study, we investigated the effect of covalent conjugation of rice protein hydrolysates (RPH) with chlorogenic acid (CA) on the structural and functional properties of RPH. Three RPH-CA conjugates were prepared by the alkaline, enzyme, and free radical methods, respectively. Covalent conjugation decreased the content of free amino, thiol, and tyrosine groups, and increased in the amount of CA bounds from 15.23 to 21.11 nmol/mg. Moreover, the circular dichroism analysis revealed that covalent conjugation resulted in an increase of random coils. The emulsifying activity and antioxidant capacity of RPH were also improved by the covalent conjugation with CA. This work provides a better understanding of the formation of hydrolysates-chlorogenic acid conjugates, contributing to improving the functional properties of foods.

BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy

Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu.

Identifying Heterozipper β-Sheet in Twisted Amyloid Aggregation

Amyloid peptide (AP) self-assembly is a hierarchical process. However, the mechanistic rule of guiding peptides to organize well-ordered nanostructure in a clear and precise manner remains poorly understood. Herein we explored the molecular insight of AP motif aggregates underlying hierarchical process with helical fibrillar structure by atomic force microscope, cryo-electron microscopy (cryo-EM), and molecular dynamics simulation. AP assembly encompasses well-ordered twisted fibrils with uniform morphology, size, and periodicity. More importantly, a heterozipper β-sheet was identified in a protofilament of AP assembly determined by cryo-EM with a high resolution of 3.5 Å. Each peptide heterozipper was further composed of two antiparallel β strands and arranged by an alternative manner in a protofilament. The hydrophobic core and hydrophilic area in each zipper played the significant role for peptide assembling. This work proposed and verified the rule facilitating the basic building unit to form twisted fibrils and gave the explanation of peptide hierarchical assembling.

Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy

Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. It is usable in a wide concentration range under various buffer conditions. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we propose an automatized binary disorder–order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. Moreover, the method can be used even for strong absorbing samples, such as the case of crowded environmental conditions, if the spectrum can be recorded down to the wavelength of 212 nm. We believe the classification method will be useful in identifying disorder and will also facilitate the growth of experimental data in IDP databases. The method is implemented on a webserver and freely available for academic users.

Fabrication and Characterization of Ultra-High-Pressure (UHP)-Induced Whey Protein Isolate/κ-Carrageenan Composite Emulsion Gels for the Delivery of Curcumin

The emulsion gels have attracted extensive interests due to their unique physical characters, remarkable stability, and control release properties of flavor and functional components compared to emulsions in liquid. In the current work, whey protein isolate (WPI)/κ-carrageenan (κ-CG) composite emulsion gels were fabricated based on the ultra-high-pressure (UHP) technology, in replacement of the traditional thermal, acid, or enzyme processing. Uniform composite emulsion gels could be fabricated by UHP above 400 MPa with minimum WPI and κ-CG concentrations of 8.0 and 1.0 wt%, respectively. The formation of UHP-induced emulsion gels is mostly attributed to the hydrophobic interaction and hydrogen bonding. The emulsion gels with different textures, rheology properties, and microstructures could be fabricated through adjusting the formulations (WPI concentration, κ-CG concentration, and oil phase fraction) as well as processing under different conditions (pressure and time). Afterward, curcumin-loaded emulsion gels were fabricated and subjected to an in vitro simulated gastrointestinal digestion in order to investigate the gastrointestinal fate of curcumin. In vitro simulated digestion results demonstrated that the UHP treatment significantly retarded the release of curcumin but had little impact on the bioaccessibility of curcumin. The results in this work provide useful information for the construction of emulsion gels through a non-thermal process, which showed great potential for the delivery of heat-sensitive bioactive components.

Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs

Background

Small angle scattering techniques are beginning to be more widely utilised for structural analysis of biological systems. However, applying these techniques to study membrane proteins still remains problematic, due to sample preparation requirements and analysis of the resulting data. The development of styrene-maleic acid co-polymers (SMA) to extract membrane proteins into nanodiscs for further study provides a suitable environment for structural analysis.

Methods

We use small angle neutron scattering (SANS) with three different contrasts to determine structural information for two different polymer nanodisc-incorporated proteins, Outer membrane protein F (OmpF) and gramicidin. Ab initio modelling was applied to generate protein/lipid structures from the SANS data. Other complementary structural methodologies, such as DLS, CD and TEM were compared alongside this data with known protein crystal structures.

Results

A single-phase model was constructed for gramicidin-containing nanodiscs, which showed dimer formation in the centre of the nanodisc. For OmpF-nanodiscs we were able to construct a multi-phase model, providing structural information on the protein/lipid and polymer components of the sample.

Conclusions

Polymer-nanodiscs can provide a suitable platform to investigate certain membrane proteins using SANS, alongside other structural methodologies. However, differences between the published crystal structure and OmpF-nanodiscs were observed, suggesting the nanodisc structure could be altering the folding of the protein.

General significance

Small angle scattering techniques can provide structural information on the protein and polymer nanodisc without requiring crystallisation of the protein. Additional complementary techniques, such as ab initio modelling, can generate alternative models both the protein and nanodisc system.

Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes

Understanding the interactions between peptides and lipid membranes could not only accelerate the development of antimicrobial peptides as treatments for infections but also be applied to finding targeted therapies for cancer and other diseases. However, designing biophysical experiments to study molecular interactions between flexible peptides and fluidic lipid membranes has been an ongoing challenge. Recently, with hardware advances, algorithm improvements, and more accurate parameterizations (i.e., force fields), all-atom molecular dynamics (MD) simulations have been used as a "computational microscope" to investigate the molecular interactions and mechanisms of membrane-active peptides in cell membranes (Chen et al., Curr Opin Struct Biol 61:160-166, 2020; Ulmschneider and Ulmschneider, Acc Chem Res 51(5):1106-1116, 2018; Dror et al., Annu Rev Biophys 41:429-452, 2012). In this chapter, we describe how to utilize MD simulations to predict and study peptide dynamics and how to validate the simulations by circular dichroism, intrinsic fluorescent probe, membrane leakage assay, electrical impedance, and isothermal titration calorimetry. Experimentally validated MD simulations open a new route towards peptide design starting from sequence and structure and leading to desirable functions.

Caseinolytic Proteins (Clp) in the Genus Klebsiella: Special Focus on ClpK

Caseinolytic proteins (Clp), which are present in both prokaryotes and eukaryotes, play a major role in cell protein quality control and survival of bacteria in harsh environmental conditions. Recently, a member of this protein family, ClpK was identified in a pathogenic strain of Klebsiella pneumoniae which was responsible for nosocomial infections. ClpK is linked to the thermal stress survival of this pathogen. The genome wide analysis of Clp proteins in Klebsiella spp. indicates that ClpK is present in only 34% of the investigated strains. This suggests that the uptake of the clpk gene is selective and may only be taken up by a pathogen that needs to survive harsh environmental conditions. In silico analyses and molecular dynamic simulations show that ClpK is mainly α-helical and is highly dynamic. ClpK was successfully expressed and purified to homogeneity using affinity and anion exchange chromatography. Biophysical characterization of ClpK showed that it is predominantly alpha-helical, and this is in agreement with in silico analysis of the protein structure. Furthermore, the purified protein is biologically active and hydrolyses ATP in a concentration- dependent manner.

Interaction characterization of zein with cyanidin-3-O-glucoside and its effect on the stability of mulberry anthocyanins and protein digestion

Ingredient interactions usually occur in food matrix, which may affect their functions and properties. This study aimed to investigate the interactive effects of mulberry and corn protein on pigment stability and zein digestibility. The interaction of main compounds in both ingredients, that is, cyanidin-3-O-glucoside (C3G) and zein, was characterized via their structural, morphological, thermal stability, and digestible properties using multi-spectroscopic techniques, scanning electron microscopy, high performance liquid chromatography, and in vitro digestion models. Results showed that zein exhibited a strong binding affinity for C3G via van der Waals forces and hydrogen bonds determined in fluorescence assays. The secondary structure of zein changed due to C3G binding, with a decrease in α-helix and an increase in β-sheet. The particle size of zein decreased after interacting with C3G. The zein complexation with mulberry anthocyanin-rich extracts in a simulative food system did not affect the digestibility of zein significantly but enhanced the thermal stability of pigments slightly. Specifically, anthocyanins did not change the susceptibility of zein to pepsin proteolysis, suggesting that binding sites of C3G might not be the cleavage sites of pepsins. These results provide important insight into the binding mechanism of zein and anthocyanins and might help guide the design of anthocyanin-based functional food. PRACTICAL APPLICATION: Zein, as a storage protein widely distributed in corn flour, was commonly co-existing with anthocyanins in starchy food. This study provides insights into the molecular interactions between zein and cyanidin-3-O-glucoside. However, the interaction might not impact the zein digestion but enhance anthocyanin thermal stability. The findings of this work could throw light on the selection of ingredients rich in zein and anthocyanins in the food industry.

A Rationally Designed Supercharged Protein-Enzyme Chimera Self-Assembles In Situ to Yield Bifunctional Composite Textiles

Catalytically active materials for the enhancement of personalized protective equipment (PPE) could be advantageous to help alleviate threats posed by neurotoxic organophosphorus compounds (OPs). Accordingly, a chimeric protein comprised of a supercharged green fluorescent protein (scGFP) and phosphotriesterase from Agrobacterium radiobacter (arPTE) was designed to drive the polymer surfactant (S^-)-mediated self-assembly of microclusters to produce robust, enzymatically active materials. The chimera scGFP-arPTE was structurally characterized via circular dichroism spectroscopy and synchrotron radiation small-angle X-ray scattering, and its biophysical properties were determined. Significantly, the chimera exhibited greater thermal stability than the native constituent proteins, as well as a higher catalytic turnover number (k_cat). Furthermore, scGFP-arPTE was electrostatically complexed with monomeric S^-, driving self-assembly into [scGFP-arPTE][S^-] nanoclusters, which could be dehydrated and cross-linked to yield enzymatically active [scGFP-arPTE][S^-] porous films with a high-order structure. Moreover, these clusters could self-assemble within cotton fibers to generate active composite textiles without the need for the pretreatment of the fabrics. Significantly, the resulting materials maintained the biophysical activities of both constituent proteins and displayed recyclable and persistent activity against the nerve agent simulant paraoxon.

Remarkably high solvatochromism in the circular dichroism spectra of the polyproline-II conformation: limitations or new opportunities?

Circular dichroism is a conventional method for studying the secondary structures of peptides and proteins and their transitions. While certain circular dichroism features are characteristic of α-helices and β-strands, the third most abundant secondary structure, the polyproline-II helix, does not exhibit a strictly conserved spectroscopic appearance. Due to its extended nature, the polyproline-II helix is highly accessible to the surrounding solvent; thus, the environment has a critical influence on the lineshape of the circular dichroism spectra of this structure. To showcase possible effects due to the medium, in this work, we report an experimental spectroscopic study of polyproline-II-forming oligomeric peptides in various environments: solvents, detergent micelles, and liposomes. Strikingly, the examination of an oligomeric peptide in a solvent series showed a remarkable 7 nm solvatochromic shift in the main negative band starting with hexafluoropropan-2-ol and moving to hexane. Furthermore, a previously predicted positive band below 200 nm was discovered in the spectra in nonpolar environments. In isotropic liposomes, the expected transition to the transmembrane state correlated with the appearance of a positive band at 228 nm. Our results demonstrate that changes in solvation should be taken into consideration when assessing the circular dichroism spectra of peptides expected to adopt the polyproline-II conformation. Although this precaution may complicate spectral analysis, characterization of solvent-induced spectral changes can generate new opportunities for testing the location of peptides in complex systems such as micelles or lipid bilayers.

Colanic Acid: Biosynthetic Overproduction by Engineering Escherichia coli and Physical Property Characterization

Colanic acid has promising applications in food, cosmetic, and healthcare fields. In this study, a recombinant WQM003/pRAU was constructed by deleting genes lon and hns and overexpressing genes rcsA and galU in E. coli MG1655Δ(L-Q). After systematic optimization of fermentation conditions, colanic acid yield in WQM003/pRAU reached 19.79 g/L, the highest yield reported so far. The colanic acid produced by WQM003/pRAU was purified and its structure and physical properties were determined. This colanic acid shows a triple-helical structure and is stable up to 102 °C, and its melting temperature is 253.9 °C. This colanic acid shows a sphere-like chain conformation in aqueous solution. The viscosity of this colanic acid solution is related to concentration, shear rate, salt, temperature, and pH. At high concentrations, this colanic acid shows both viscous and elastic behaviors. These results suggest that the colanic acid produced by WQM003/pRAU has broad application prospects.

Rapid preparation of nanodiscs for biophysical studies

Nanodiscs, which are disc-shaped entities that contain a central lipid bilayer encased by an annulus of amphipathic helices, have emerged as a leading native-like membrane mimic. The current approach for the formation of nanodiscs involves the creation of a mixed-micellar solution containing membrane scaffold protein, lipid, and detergent followed by a time consuming process (3-12 h) of dialysis and/or incubation with sorptive beads to remove the detergent molecules from the sample. In contrast, the methodology described herein provides a facile and rapid procedure for the preparation of nanodiscs in a matter of minutes (<15 min) using Sephadex® G-25 resin to remove the detergent from the sample. A panoply of biophysical techniques including analytical ultracentrifugation, dynamic light scattering, gel filtration chromatography, circular dichroism spectroscopy, and cryogenic electron microscopy were employed to unequivocally confirm that aggregates formed by this method are indeed nanodiscs. We believe that this method will be attractive for time-sensitive and high-throughput experiments.

Assessment of the Contribution of a Thermodynamic and Mechanical Destabilization of Myosin-Binding Protein C Domain C2 to the Pathomechanism of Hypertrophic Cardiomyopathy-Causing Double Mutation MYBPC3Δ25bp/D389V

Mutations in the gene encoding cardiac myosin-binding protein-C (MyBPC), a thick filament assembly protein that stabilizes sarcomeric structure and regulates cardiac function, are a common cause for the development of hypertrophic cardiomyopathy. About 10% of carriers of the Δ25bp variant of MYBPC3, which is common in individuals from South Asia, are also carriers of the D389V variant on the same allele. Compared with noncarriers and those with MYBPC3^Δ25bp alone, indicators for the development of hypertrophic cardiomyopathy occur with increased frequency in MYBPC3^Δ25bp/D389V carriers. Residue D389 lies in the IgI-like C2 domain that is part of the N-terminal region of MyBPC. To probe the effects of mutation D389V on structure, thermostability, and protein–protein interactions, we produced and characterized wild-type and mutant constructs corresponding to the isolated 10 kDa C2 domain and a 52 kDa N-terminal fragment that includes subdomains C0 to C2. Our results show marked reductions in the melting temperatures of D389V mutant constructs. Interactions of construct C0–C2 D389V with the cardiac isoforms of myosin-2 and actin remain unchanged. Molecular dynamics simulations reveal changes in the stiffness and conformer dynamics of domain C2 caused by mutation D389V. Our results suggest a pathomechanism for the development of HCM based on the toxic buildup of misfolded protein in young MYBPC3^Δ25bp/D389V carriers that is supplanted and enhanced by C-zone haploinsufficiency at older ages.

Novel antimicrobial cecropins derived from O. curvicornis and D. satanas dung beetles

Antibiotic resistance is an increasing global problem and therapeutic alternatives to traditional antibiotics are needed. Antimicrobial and host defense peptides represent an attractive source for new therapeutic strategies, given their wide range of activities including antimicrobial, antitumoral and immunomodulatory. Insects produce several families of these peptides, including cecropins. Herein, we characterized the sequence, structure, and biological activity of three cecropins called satanin 1, 2, and curvicin, found in the transcriptome of two dung beetle species Dichotomius satanas and Onthophagus curvicornis. Sequence and circular dichroism analyses show that they have typical features of the cecropin family: short length (38-39 amino acids), positive charge, and amphipathic α-helical structure. They are active mainly against Gram-negative bacteria (3.12-12.5 μg/mL), with low toxicity on eukaryotic cells resulting in high therapeutic indexes (TI > 30). Peptides also showed effects on TNFα production in LPS-stimulated PBMCs. The biological activity of Satanin 1, 2 and Curvicin makes them interesting leads for antimicrobial strategies.

Interfacial Interactions within Amyloid Protein Corona Based on 2D MoS2 Nanosheets

The interfacial interaction within the amyloid protein corona based on MoS₂ nanomaterial is crucial, both for understanding the biological effects of MoS₂ nanomaterial and the evolution of amyloid diseases. The specific nano-bio interface phenomenon of human islet amyloid peptide (hIAPP) and MoS₂ nanosheet was investigated by using theoretical and experimental methods. The MoS₂ nanosheet enables the attraction of hIAPP monomer, dimer, and oligomer on its surface through van der Waals forces. Especially, the means of interaction between two hIAPP peptides might be changed by MoS₂ nanosheet. In addition, it is interesting to find that the hIAPP oligomer can stably interact with the MoS₂ nanosheet in one unique "standing" binding mode with an entire exposed β-sheet surface. All the interaction modes on the surface of MoS₂ nanosheet can be the essence of amyloid protein corona that may provide the venue to facilitate the fibrillation of hIAPP proteins. Further, it was verified experimentally that MoS₂ nanosheets could accelerate the fibrillation of hIAPP at a certain concentration mainly based on the newly formed nano-bio interface. In general, our results provide insight into the molecular interaction mechanism of the nano-bio interface within the amyloid protein corona, and shed light on the pathway of amyloid protein aggregation that is related to the evolution of amyloid diseases.

Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction

A neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs, and increased significantly after the animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na⁺, K⁺-ATPase activity in the posterior (6th) gills. Furthermore, the solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy, revealing that it has an N-terminal tail, three α-helices (α2, Gly⁹-Asn²⁸; α3, His³⁴-Gly³⁸; and α5, Glu⁶²-Arg⁷²), and a π-helix (π4, Cys⁴³-Tyr⁵⁴), and is structurally constrained by a pattern of disulfide bonds (Cys⁷-Cys⁴³, Cys²³-Cys³⁹, and Cys²⁶-Cys⁵²), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substitution, and the resulting mutants were functionally tested using the gill Na⁺, K⁺-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, and G73) are located at either end of the sequence, which are sterically close to each other and presumably constitute the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily, revealing a folding pattern, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand-receptor binding specificity.

Key Physicochemical Determinants in the Antimicrobial Peptide RiLK1 Promote Amphipathic Structures

Antimicrobial peptides (AMPs) represent a skilled class of new antibiotics, due to their broad range of activity, rapid killing, and low bacterial resistance. Many efforts have been made to discover AMPs with improved performances, i.e., high antimicrobial activity, low cytotoxicity against human cells, stability against proteolytic degradation, and low costs of production. In the design of new AMPs, several physicochemical features, such as hydrophobicity, net positive charge, propensity to assume amphipathic conformation, and self-assembling properties, must be considered. Starting from the sequence of the dodecapeptide 1018-K6, we designed a new 10-aminoacid peptide, namely RiLK1, which is highly effective against both fungi and Gram-positive and -negative bacteria at low micromolar concentrations without causing human cell cytotoxicity. In order to find the structural reasons explaining the improved performance of RiLK1 versus 1018-K6, a comparative analysis of the two peptides was carried out with a combination of CD, NMR, and fluorescence spectroscopies, while their self-assembling properties were analyzed by optical and atomic force microscopies. Interestingly, the different spectroscopic and microscopic profiles exhibited by the two peptides, including the propensity of RiLK1 to adopt helix arrangements in contrast to 1018-K6, could explain the improved bactericidal, antifungal, and anti-biofilm activities shown by the new peptide against a panel of food pathogens.

Comparative Study of the Structural and Functional Properties of Membrane-Isolated and Isoelectric pH Precipitated Green Lentil Seed Protein Isolates

The demand for isolated seed proteins continues to increase but functionality in food systems can be greatly dependent on the extraction method. In this work, we report the physicochemical and functional properties of lentil seed proteins isolated using various protocols. Lentil flour was defatted followed by protein extraction using isoelectric pH precipitation (ISO) as well as NaOH (MEM_NaOH) and NaCl (MEM_NaCl) extractions coupled with membrane ultrafiltration. The MEM_NaCl had significantly (p < 0.05) higher protein content (90.28%) than the ISO (86.13%) and MEM_NaOH (82.55%). At pH 3-5, the ISO was less soluble (2.26-11.84%) when compared to the MEM_NaOH (25.74-27.22%) and MEM_NaCl (27.78-40.98%). However, the ISO had higher yield and protein digestibility (48.45% and 89.82%) than MEM_NaOH (35.05% and 77.87%) and MEM_NaCl (13.35% and 77.61%), respectively. Near-UV circular dichroism spectra showed that the MEM_NaOH had loose tertiary conformation at pH 3, 5, 7 and 9 while ISO and MEM_NaCl had more compact structures at pH 7 and 9. The three protein isolates formed better emulsions (lower oil droplet sizes) at pH 7 and 9 when compared to pH 3 and 5. In contrast, foaming capacity was better at pH 5 than pH 3, 7, and 9.

Effect of pulsed light treatment on enzymes and protein allergens associated with their structural changes: a review

The pulsed light (PL) technique is used for food and surface decontamination widely. The sterilization effect of PL is well known and identified as the photo-chemical effect. Besides, PL is used to inactivate enzymes, reduce the immunoreactivity of proteins, and change protein function properties at a laboratory level. The current study aims to review the effect of PL on proteins by highlighting the differences between proteins in buffer solutions or food systems. Although PL is known as a non-thermal technique, most studies done on food systems, food temperature raised considerably. Therefore, PL inactivated many enzymes in buffer solution non-thermally, while mostly with a high increase in temperature of a food system. PL reduced food allergens several folds in some foods. However, immunoreactivity responses of some protein were increased after PL treatment. Also, the current study covers the conformational changes of proteins that occur because of PL treatment. Therefore, some techniques used to follow proteins structural changes such as polyacrylamide gel electrophoresis (SDS-PAGE), high-performance liquid chromatography (HPLC), Fourier-transform infrared spectroscopy (FTIR), etc. were defined. Studies reported that PL altered proteins structure differently. For example, some studies reported that PL degraded some proteins, while other studies suggested that PL aggregated proteins. Also, there were contrary results regarding α-helix and ß-sheet concentration for the treated proteins. In conclusion, some techniques, such as amino acid sequencing, specially when some small new fragments proteins appeared on SDS-PAGE, should be used to detect the effect of PL on proteins precisely.

In Situ Monitored Vortex Fluidic-Mediated Protein Refolding/Unfolding Using an Aggregation-Induced Emission Bioprobe

Protein folding is important for protein homeostasis/proteostasis in the human body. We have established the ability to manipulate protein unfolding/refolding for β-lactoglobulin using the induced mechanical energy in the thin film microfluidic vortex fluidic device (VFD) with monitoring as such using an aggregation-induced emission luminogen (AIEgen), TPE-MI. When denaturant (guanidine hydrochloride) is present with β-lactoglobulin, the VFD accelerates the denaturation reaction in a controlled way. Conversely, rapid renaturation of the unfolded protein occurs in the VFD in the absence of the denaturant. The novel TPE-MI reacts with exposed cysteine thiol when the protein unfolds, as established with an increase in fluorescence intensity. TPE-MI provides an easy and accurate way to monitor the protein folding, with comparable results established using conventional circular dichroism. The controlled VFD-mediated protein folding coupled with in situ bioprobe AIEgen monitoring is a viable methodology for studying the denaturing of proteins.

DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data

Circular dichroism (CD) spectroscopy is a widely‐used method for characterizing the secondary structures of proteins. The well‐established and highly used analysis website, DichroWeb (located at: http://dichroweb.cryst.bbk.ac.uk/html/home.shtml) enables the facile quantitative determination of helix, sheet, and other secondary structure contents of proteins based on their CD spectra. DichroWeb includes a range of reference datasets and algorithms, plus graphical and quantitative methods for determining the quality of the analyses produced. This article describes the current website content, usage and accessibility, as well as the many upgraded features now present in this highly popular tool that was originally created nearly two decades ago.

Development of a Novel Bi-Enzymatic Nanobiocatalyst for the Efficient Bioconversion of Oleuropein to Hydroxytyrosol

Lipase A from Candida antarctica (CalA) and β-glucosidase from Thermotoga maritima (bgl) were covalently co-immobilized onto the surface of chitosan-coated magnetic nanoparticles (CS-MNPs). Several parameters regarding the co-immobilization procedure (glutaraldehyde concentration, incubation time, CS-MNPs to enzyme mass ratio and bgl to CalA mass ratio) were evaluated and optimized. The developed nanobiocatalyst was characterized by various spectroscopic techniques. Biochemical parameters such as kinetic constants and thermal stability were also evaluated. The nanobiocatalytic system revealed an increase in the Km constant followed by a decrease in Vmax value compared with the native enzymes, while a significant increase (>5-fold higher) of the thermal stability of the immobilized CalA, both in individual and in co-immobilized form, was observed after 24 h incubation at 60 °C. Finally, the nanobiocatalyst was efficiently applied for the bioconversion of oleuropein to hydroxytyrosol, one of the most powerful naturally derived antioxidants, and it could be recycled for up to 10 reaction cycles (240 h of constant operation) at 60 °C, retaining more than 50% of its initial activity.

Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention

Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro and punctate-like structures in vivo. A ninety-four amino acid sequence within the PRD1 domain, PRD1-core, displays high propensity towards aggregation and associated amyloid characteristics. PRD1-core is characterized using electron microscopy, X-ray diffraction, and solution-state NMR deuterium exchange experiments. Secondary structure elements deduced from solid-state NMR reveal a β-rich core comprising of forty amino acids at the N-terminus of PRD1-core. The synthesized twenty-three amino acid long peptide containing the longest rigid segment (E124-H145) of the PRD1-core rapidly self-aggregates and forms fibrils, indicating a limited aggregation-prone region that could potentially activate the aggregation of the full-length protein. This study provides the first step in identifying the structural trigger for the CPEB3 aggregation process.

Effects of compaction and storage conditions on stability of intravenous immunoglobulin - Implication on developing oral tablets of biologics

Biological products, such as therapeutic proteins, vaccines and cell - based therapeutics have a rapidly growing global market. Monoclonal antibody represents a major portion of the biologics market. For biologics that target gastrointestinal tract, the oral delivery route offers many advantages, such as better patient compliance, easy administration and increased stability, over the parental route of administration. To lay the ground work for the oral delivery of biologics, we studied the solid state properties and effects of compaction pressure, particle size, and storage relative humidity on the stability of immunoglobulin G (IVIG). We employed complementary analytical and biophysical techniques, such as size exclusion chromatography and Dynamic light scattering to characterize the aggregates, circular dichroism and solid state Fourier-transform infrared spectroscopy to evaluate protein secondary structure and nano-DSC to probe thermal stability of protein conformations. Our results showed storage relative humidity could induce conformational changes and aggregation of IVIG. However, the IVIG binding activity did not significantly change with relative humidity. The commonly used compaction pressures did not promote protein aggregation, but noticeably reduced binding activity.

The nuclear localization sequence of the epigenetic factor RYBP binds to human importin α3

RYBP (Ring1 and YY1 binding protein, UniProt ID: Q8N488) is an epigenetic factor with a key role during embryonic development; it does also show an apoptotic function and an ubiquitin binding activity. RYBP is an intrinsically disordered protein (IDP), with a Zn-finger domain at its N-terminal region, which folds upon binding to DNA. It is predicted that RYBP has a nuclear localization sequence (NLS), comprising residues Asn58 to Lys83, to allow for nuclear translocation. We studied in this work the ability of intact RYBP to bind Impα3 and its truncated species, ΔImpα3, without the importin binding domain (IBB), by using fluorescence and circular dichroism (CD). Furthermore, the binding of the peptide matching the isolated NLS region of RYBP (NLS-RYBP) was also studied using the same methods and isothermal titration calorimetry (ITC), and in silico molecular docking. Moreover, we carried out experiments with NLS-RYBP in the absence or in the presence of NaCl (140 mM). Our results show that RYBP interacted with Impα3 and ΔImpα3, causing protein precipitation. The NLS-RYBP also interacted with both importin species (dissociation constant in the low micromolar range), at low or high ionic strength, as shown by intrinsic fluorescence and ITC. These findings indicate that the NLS region, which was mainly unfolded in isolation in solution, was essentially responsible for the binding of RYBP to each of the importin species. Furthermore, the molecular simulations predict that the anchoring of NLS-RYBP takes place in the major binding site for the NLS of cargo proteins bound to Impα3. Taken together, our findings pinpoint the theoretical predictions of the NLS region in RYBP and, more importantly, suggest that this IDP relies on an importin for its nuclear translocation.

α-Synuclein mutation impairs processing of endomembrane compartments and promotes exocytosis and seeding of α-synuclein pathology

Neuronal loss in Parkinson's disease (PD) is associated with impaired proteostasis and accumulation of α-syn microaggregates in dopaminergic neurons. These microaggregates promote seeding of α-synuclein (α-syn) pathology between synaptically linked neurons. However, the mechanism by which seeding is initiated is not clear. Using human pluripotent stem cell (hPSC) models of PD that allow comparison of SNCA mutant cells with isogenic controls, we find that SNCA mutant neurons accumulate α-syn deposits that cluster to multiple endomembrane compartments, specifically multivesicular bodies (MVBs) and lysosomes. We demonstrate that A53T and E46K α-syn variants bind and sequester LC3B monomers into detergent-insoluble microaggregates on the surface of late endosomes, increasing α-syn excretion via exosomes and promoting seeding of α-syn from SNCA mutant neurons to wild-type (WT) isogenic controls. Finally, we show that constitutive inactivation of LC3B promotes α-syn accumulation and seeding, while LC3B activation inhibits these events, offering mechanistic insight into the spread of synucleinopathy in PD.

The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy

Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.