Peptide Adsorption Research Articles

Strain-Dependent Adsorption of Pseudomonas aeruginosa-Derived Adhesin-Like Peptides at Abiotic Surfaces

Implant-associated infections are an increasingly severe burden on healthcare systems worldwide and many research activities currently focus on inhibiting microbial colonization of biomedically relevant surfaces. To obtain molecular-level understanding of the involved processes and interactions, we investigate the adsorption of synthetic adhesin-like peptide sequences derived from the type IV pili of the Pseudomonas aeruginosa strains PAK and PAO at abiotic model surfaces, i.e., Au, SiO2, and oxidized Ti. These peptides correspond to the sequences of the receptor-binding domain 128–144 of the major pilin protein, which is known to facilitate P. aeruginosa adhesion at biotic and abiotic surfaces. Using quartz crystal microbalance with dissipation monitoring (QCM-D), we find that peptide adsorption is material- as well as strain-dependent. At the Au surface, PAO(128–144) shows drastically stronger adsorption than PAK(128–144), whereas adsorption of both peptides is markedly reduced at the oxide surfaces with less drastic differences between the two sequences. These observations suggest that peptide adsorption is influenced by not only the peptide sequence, but also peptide conformation. Our results furthermore highlight the importance of molecular-level investigations to understand and ultimately control microbial colonization of surfaces.

Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides.

Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides.

The amphipathic α-helix is a common motif for peptide adsorption to membranes. Many physiologically relevant events involving membrane-adsorbed peptides occur over time and size scales readily accessible to coarse-grain molecular dynamics simulations. This methodological suitability, however, comes with a number of pitfalls. Here, I exemplify a multi-step adsorption equilibration procedure on the antimicrobial peptide Magainin 2. It involves careful control of peptide freedom to promote optimal membrane adsorption before other interactions are allowed. This shortens preparation times prior to production simulations while avoiding divergence into unrealistic or artifactual configurations.

Application of Alanine Scanning to Determination of Amino Acids Essential for Peptide Adsorption at the Solid/Solution Interface and Binding to the Receptor: Surface-Enhanced Raman/Infrared Spectroscopy versus Bioactivity Assays.

The article describes the application of the alanine-scanning technique used in combination with Raman, surface-enhanced Raman, attenuated total reflection Fourier transform infrared, and surface-enhanced infrared absorption (SEIRA) spectroscopies, which allowed defining the role of individual amino acid residues in the C-terminal 6–14 fragment of the bombesin chain (BN6–14) on the path of its adsorption on the surface of Ag (AgNPs) and Au nanoparticles (AuNPs). A reliable analysis of the SEIRA spectra of these peptides was possible, thanks to a curve fitting of these spectra. By combining alanine-scanning with biological activity studies using cell lines overexpressing bombesin receptors and the intracellular inositol monophosphate assay, it was possible to determine which peptide side chains play a significant role in binding a peptide to membrane-bound G protein-coupled receptors (GPCRs). Based on the analysis of spectral profiles and bioactivity results, conclusions for the specific peptide–metal and peptide–GPCR interactions were drawn and compared.

Selective adsorption of egg white hydrolysates onto activated carbon: Establishment of physicochemical mechanisms for removing phenylalanine

Previously, it was shown that activated carbon can remove phenylalanine from egg white hydrolysates to produce a low phenylalanine peptide ingredient that can be used by individuals suffering from phenylketonuria. However, the factors impacting the selective adsorption of phenylalanine and peptides to activated carbon is not fully understood, which is holding back the optimization of this process. In this research, two activated carbons with different morphologies and electrical characteristics were used to adsorb egg white hydrolysates with different degrees of hydrolysis. The selective adsorption behavior of the different constituents within the hydrolysates was studied to identify the nature of the adsorption mechanisms involved. The results showed that aromatic amino acids and components with higher molecular weight were preferentially adsorbed. Moreover, the main driving force for adsorption was hydrophobic attraction, followed by hydrogen bonding and electrostatic interactions. These results could facilitate the preparation of medical foods for patients with phenylketonuria.

Simulating Peptide Monolayer Formation: GnRH-I on Silica.

Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.

Modulatory Effects of Acidic pH and Membrane Potential on the Adsorption of pH-Sensitive Peptides to Anionic Lipid Membrane.

Anionic lipid membrane electrostatic potential and solution pH can influence cationic peptide adsorption to these bilayers, especially those containing simultaneously acid and basic residues. Here, we investigate the effects of the pH solution on MP1 (IDWKKLLDAAKQIL-NH2) adsorption to anionic (7POPC:3POPG) lipid vesicles in comparison to its analog H-MP1, with histidines substituting lysines. We used the association of adsorption isotherms and constant pH molecular dynamic simulations (CpHMD) to explore the effects of membrane potential and pH on peptides’ adsorption on this lipid membrane. We analyzed the fluorescence and zeta potential adsorption isotherms using the Gouy–Chapman theory. In CpHMD simulations for the peptides in solution and adsorbed on the lipid bilayer, we used the conformations obtained by conventional MD simulations at a μs timescale. Non-equilibrium Monte Carlo simulations provided the protonation states of acidic and basic residues. CpHMD showed average pKa shifts of two to three units, resulting in a higher net charge for the analog than for MP1, strongly modulating the peptide adsorption. The fractions of the protonation of acidic and basic residues and the peptides’ net charges obtained from the analysis of the adsorption isotherms were in reasonable agreement with those from CpHMD. MP1 adsorption was almost insensitive to solution pH. H-MP1 was much more sensitive to partitioning, at acidic pH, with an affinity ten times higher than in neutral ones.

Reducing metal-ion mediated adsorption of acidic peptides in RPLC-based assays using hybrid silica chromatographic surfaces

In this study we evaluate column hardware exhibiting a novel hybrid silica surface in its ability to mitigate metal-induced adsorption artifacts such as chromatographic peak tailing for acidic amino acid residue containing peptides. Using a conventional reversed-phase liquid chromatography (RPLC)-based method, chromatographic performance of a peptide map was compared using a traditional stainless-steel column and an equivalent column bearing a novel hybrid silica surface. Tailing factors for six peptides containing acidic amino acid residues (Tf ≥ 1.50) were observed to be reduced up to 80% to a nominal value Tf ≤ 1.2 with R.S.D. % ≤ 4%. Furthermore, recovery for two of the identified peptides exhibited increased recovery in addition to reduced peak tailing when using the column bearing the hybrid silica surface. Performance was unaffected for peaks where there were no implications of metal induced effects. Collectively, this study demonstrates that the novel hybrid silica surface can effectively reduce peak tailing for acidic residue containing peptides.

Characterization of Biological Material Adsorption to the Surface of Nanoparticles without a Prior Separation Step: a Case Study of Glioblastoma-Targeting Peptide and Lipid Nanocapsules.

PurposeCurrent preclinical therapeutic strategies involving nanomedicine require increasingly sophisticated nanosystems and the characterization of the complexity of such nanoassemblies is becoming a major issue. Accurate characterization is often the factor that can accelerate the translational approaches of nanomedicines and their pharmaceutical development to reach the clinic faster. We conducted a case study involving the adsorption of the NFL-TBS.40–63 (NFL) peptide (derived from neurofilaments) to the surface of lipid nanocapsules (LNCs) (a combined nanosystem used to target glioblastoma cells) to develop an analytical approach combining the separation and the quantification in a single step, leading to the characterization of the proportion of free peptide and thus the proportion of peptide adsorbed to the lipid nanocapsule surface.MethodsLNC suspensions, NFL peptide solution and LNC/NFL peptide mixtures were characterized using a Size-Exclusion Chromatography method (with a chromatographic apparatus). In addition, this method was compared to centrifugal-filtration devices, currently used in literature for this case study.ResultsCombining the steps for separation and characterization in one single sequence improved the accuracy and robustness of the data and led to reproducible results. Moreover the data deviation observed for the centrifugal-filtration devices demonstrated the limits for this increasingly used characterization approach, explained by the poor separation quality and highlighting the importance for the method optimization. The high potential of the technique was shown, proving that H-bond and/or electrostatic interactions mediate adsorption of the NFL peptide to the surface of LNCs.ConclusionsUsed only as a characterization tool, the process using chromatographic apparatus is less time and solvent consuming than classical Size-Exclusion Chromatography columns only used for separation. It could be a promising tool for the scientific community for characterizing the interactions of other combinations of nanosystems and active biological agents.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11095-021-03034-8.

Practical Protocol for Optimization of Suppression of Peptide Adsorption in the Sensitive Quantitative LC-MS Using Calibration Curve Parameters

Practical Protocol for Optimization of Suppression of Peptide Adsorption in the Sensitive Quantitative LC-MS Using Calibration Curve Parameters

Corrosion inhibition properties of small peptides: DFT and Monte Carlo simulation studies

Using the computational methods of Density Functional Theory (DFT) and Monte Carlo (MC), we investigated the potential and mechanism of corrosion inhibition of iron, copper and aluminum by small peptides of aliphatic amino acids (AAs), such as L-alanine (Ala) dipeptide and tripeptide. The article provides an assessment of the local and global descriptors of the reactivity of Ala in neutral and protonated forms and its changes when combining Ala into di- and tripeptides. There was established a boost in the inhibitory effect of di- and tripeptides, due to an increase in the number of reaction centers of the molecular structure. The authors calculated the adsorption energies, and determined the most stable low energy configurations for the adsorption of alanine amino acids and small peptides on Fe (110), Cu (111), and Al (111) surfaces. It has been established that Ala and Ala-derived peptides can be absorbed on these substrates by chemisorption, predominantly located on epitaxial grooves. The absolute values of the adsorption energy between these inhibitors on the studied metal surfaces rise with an increase in the number of amino acid residues. The stronger adsorption of small peptides is also indicated by a decrease in the shortest bond lengths between the layer of on-surface Fe, Cu and Al atoms and the nearest inhibitor atoms that are characterized by the following sequence: Ala > Ala-Ala > Ala-Ala-Ala. The peptides have the best adsorption ability to the iron surface, which characterizes their highest inhibitory efficiency from a theoretical point of view. The results of the studies performed have demonstrated promising prospects for the use of small peptides as effective “green” corrosion inhibitors.

α-Helical peptides on plasma-treated polymers promote ciliation of airway epithelial cells

Airway respiratory epithelium forms a physical barrier through intercellular tight junctions, which prevents debris from passing through to the internal environment while ciliated epithelial cells expel particulate-trapping mucus up the airway. Polymeric solutions to loss of airway structure and integrity have been unable to fully restore functional epithelium. We hypothesised that plasma treatment of polymers would permit adsorption of α-helical peptides and that this would promote functional differentiation of airway epithelial cells. Five candidate plasma compositions are compared; Air, N2, H2, H2:N2 and Air:N2. X-ray photoelectron spectroscopy shows changes in at% N and C 1s peaks after plasma treatment while electron microscopy indicates successful adsorption of hydrogelating self-assembling fibres (hSAF) on all samples. Subsequently, adsorbed hSAFs support human nasal epithelial cell attachment and proliferation and induce differentiation at an air-liquid interface. Transepithelial measurements show that the cells form tight junctions and produce cilia beating at the normal expected frequency of 10–11 Hz after 28 days in culture. The synthetic peptide system described in this study offers potential superiority as an epithelial regeneration substrate over present “gold-standard” materials, such as collagen, as they are controllable and can be chemically functionalised to support a variety of in vivo environments. Using the hSAF peptides described here in combination with plasma-treated polymeric surfaces could offer a way of improving the functionality and integration of implantable polymers for aerodigestive tract reconstruction and regeneration.

Sensitive mass spectrometric determination of kinin-kallikrein system peptides in light of COVID-19

The outbreak of COVID-19 has raised interest in the kinin–kallikrein system. Viral blockade of the angiotensin-converting enzyme 2 impedes degradation of the active kinin des-Arg(9)-bradykinin, which thus increasingly activates bradykinin receptors known to promote inflammation, cough, and edema—symptoms that are commonly observed in COVID-19. However, lean and reliable investigation of the postulated alterations is currently hindered by non-specific peptide adsorption, lacking sensitivity, and cross-reactivity of applicable assays. Here, an LC–MS/MS method was established to determine the following kinins in respiratory lavage fluids: kallidin, bradykinin, des-Arg(10)-kallidin, des-Arg(9)-bradykinin, bradykinin 1-7, bradykinin 2-9 and bradykinin 1-5. This method was fully validated according to regulatory bioanalytical guidelines of the European Medicine Agency and the US Food and Drug Administration and has a broad calibration curve range (up to a factor of 103), encompassing low quantification limits of 4.4–22.8 pg/mL (depending on the individual kinin). The application of the developed LC–MS/MS method to nasal lavage fluid allowed for the rapid (~ 2 h), comprehensive and low-volume (100 µL) determination of kinins. Hence, this novel assay may support current efforts to investigate the pathophysiology of COVID-19, but can also be extended to other diseases.

Accurate prediction for adsorption rate of peptides with high ACE-inhibitory activity from sericin hydrolysate on thiophene hypercross-linked polymer using CoMSIA in 3D-QSAR model

Efficient screening of angiotensin converting enzyme inhibitory (ACE-I) peptides from agricultural or edible sources attract increasing attention. However, their purification process from the complex natural system is still semi-empirical or even uncontrollable, which has seriously reduced their screening efficiency. Herein, inspired by the prediction of ACE-I activity, 3D-QSAR was proposed to predict the adsorption performance of peptides from sericin hydrolysate (SH) having high ACE-I activity on porous hypercross-linked polymers according to their molecular structures. Thiophene hypercross-linked polymer (T-HCP) possessing better screening capacity for ACE-I peptides was chosen as our research object in this work. The sequence and relative adsorption rate of 101 peptides in SH were analyzed by LC-MS and was used as a database to construct the relationship of peptide’s chemical structure and adsorption performance on T-HCP by Comparative molecular similarity indices analysis (CoMSIA) from 3D-QSAR. Optimum CoMSIA revealed that enhanced interaction of hydrophobicity and H-bond between T-HCP and the peptide was conducive to increase the adsorption performance of di- to hexa- peptides. Based on these relationships, the adsorption capability of 24 designed peptides with distinguished hydrophobic and H-bond fields was predicted on T-HCP by using optimum CoMSIA and the results of half of these were verified, which showed high consistency with their predicted adsorption rate. Interestingly, these peptides having higher adsorption capacities on T-HCP also possessed higher ACE-I activity. This can be attributed to the high concentration of aromatic surface with π-π interaction and weak-polar CSC group with H-bond interaction on T-HCP material, which is ideal for the selective adsorption of peptides with higher ACE-I activity from SH. This study provides important theoretical guidance for the industrial screening of bio-functional peptides from complex protein mixtures.

Analysis of binding modes of biopanning heptapeptides with specific affinity to chitosan wrapped MSN

In this work, we demonstrated for the first time that six short heptapeptides screened out by biopanning strategy show affinity binding to chitosan wrapped mesoporous silica nanoparticle (CS/MSN). The interaction between peptide and chitosan-wrapped MSN (CS/MSN) was carefully analyzed with the aid of DLS and ELISA characterization. The results show that π-π stacking and hydrogen bonds account for the strong adsorption under neutral as well as acidic conditions. While hydrophilic and electrostatic interaction are the major modes of the peptide under alkaline condition. These different interaction modes involved in the adsorption of peptides onto CS/MSN could vividly mimic the binding of peptide with chitosan in physiological conditions and help to deeply understand the process of protein adsorption on nanomaterials.

The efficient enrichment of marine peptides from the protein hydrolysate of the marine worm Urechis unicinctus by using mesoporous materials MCM-41, SBA-15 and CMK-3.

Peptides found in marine life have various specific activities due to their special growth environment, and there is increasing interest in the isolation and concentration of these biofunctional compounds. In this study, the protein hydrolysate of the marine worm Urechis unicinctus was prepared by enzymolysis and enriched by using mesoporous materials of silica MCM-41 and SBA-15 and carbon CMK-3. The differences in pore structures and elemental composition of these materials lead to differences in surface area and hydrophobicity. The adsorption capacities of peptides were 459.5 mg g-1, 431.3 mg g-1, and 626.3 mg g-1 for MCM-41, SBA-15 and CMK-3, respectively. Adsorption kinetics studies showed that the pseudo-second-order model fit the adsorption process better, where both external mass transfer and intraparticle diffusion affected the adsorption, while the Langmuir model better fit the adsorption of peptides on MCM-41 and SBA-15 and the Freundlich model was more suitable for CMK-3. Aqueous acetonitrile (ACN, 50/50, v/v) yielded the most extracted peptides. MALDI-TOF mass spectrometry of the extracted peptides showed that the three mesoporous materials, especially the CMK-3, gave good enrichment results. This study demonstrates the great potential of mesoporous materials in the enrichment of marine biofunctional peptides.

Adsorption of Amyloid Beta Peptide by Metal-Organic Frameworks.

Metal–organic frameworks (MOFs) are capable of adsorbing a wide range of molecules. In addition to the more commonly investigated small molecules, researchers have demonstrated that MOFs adsorb much larger molecules, such as proteins and peptides. We have investigated whether MOFs are capable of adsorbing amyloid beta peptide. Amyloid beta plays a pivotal role in the progression of Alzheimer’s disease because individual copies of the peptides can aggregate, forming neurotoxic oligomers and the amyloid plaques found in brains of Alzheimer’s patients. After synthesizing a number of commonly studied MOFs, their adsorption capabilities were tested. We found that the MOFs tested readily adsorbed small amounts of amyloid beta (as determined by gel electrophoresis). It was determined that in most cases, adsorption occurs rapidly, with complete adsorption within minutes of incubation. Overall adsorption capacity was found to vary between different MOFs as well. Once adsorbed, amyloid beta peptide can subsequently be eluted from some MOFs by treatment with acetonitrile/water solutions, though retention strength varied between different MOFs. In some cases, MOFs that showed complete adsorption also saw high levels of peptide elution, but others showed little to no elution of the peptide. Together these data can help us begin to understand the interactions between amyloid beta and MOFs.

Passive Internalization of Bioactive β-Casein Peptides into Phospholipid (POPC) Bilayers. Free Energy Landscapes from Unbiased Equilibrium MD Simulations at μs-Time Scale

Absorption of bioactive peptides in the intestinal epithelium take place in the apical or the basolateral tight junctions of the cells. Depending on the peptide size and hydrophobicity, translocation mechanisms involve processes of passive diffusion, active transport by peptide-cotransporters such as members of the PepT family, and transcytosis by internalization vesicles. In this work, we investigated passive diffusion of bioactive peptides of 6, 17, and 30 amino acids into lipid bilayers of (POPC) phospholipid molecules. We initially selected these three peptides because such fragments are produced by partial hydrolysis of β-casein (BCN), and because of their physiological functions: BCN6 is an agonist of opioid receptors; BCN17 is an inhibitor of thrombin and angiotensin-converting enzymes, and BCN30 promotes secretion of the protective mucin barrier in the intestine. Our computational set up consisted of unbiased equilibrium molecular dynamics simulations, at the μs-time scale, using an all-atom force field. Each peptide was allowed to freely fold and unfold, as well as enter and exit the lipid bilayer, which allows determination of peptide affinity for the bilayer interface and hydrophobic core. Passive internalization of BCN6 (YPVEPF), BCN17 (YQEPVLGPVR GPFPIIV), and BCN30 (GVSKVKEAMA PKHKEMPFPK YPVEPFTESQ) displayed different dynamics at the bilayer interface: the BCN6 peptide attached and detached throughout the simulation trajectory; BCN17 and BCN30 attached irreversibly to the bilayer interface, respectively, with N- and C-terminus fragments in close contact with lipid molecules. Quenching of tyrosine fluorescence data suggest interfacial interactions of BCN6, BCN17 and BCN30 in POPC lipid bilayers, consistent with the proposed modeling set up. This approach gave valuable information of peptide insertion and folding at a lipid bilayer, allowing to explore the initial stages of the peptide adsorption at the interface, and providing a model for evaluation of amphipathic properties of potential biofunctional peptides.

N-terminal acetylation of a mastoparan-like peptide enhances PE/PG segregation in model membranes

The synthetic peptides L1A and its acetylated analog (acL1A) display potent Gram-negative bactericidal activities without being hemolytic. We have gathered evidence that the N-terminal acetylation of L1A enhances the lytic activity in anionic vesicles with high capability to insert into and disturb lipid packing of model membranes. Here, the impact of L1A and acL1A was evaluated on a model membrane that mimics the cytoplasmic membrane of Gram-negative bacteria, which is rich in phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), using 3:1 mixture of POPE/DOPG and a variety of techniques. We followed peptide adsorption and penetration by zeta potential determination of large unilamellar vesicles, accessibility of tryptophan residue to acrylamide by quenching assays, and Gibbs isotherms. The secondary structure of the peptide on the membranes was assessed using circular dichroism. Peptide mixing ability with the lipids and phase segregation was assessed by the observation of Langmuir monolayers with fluorescence microscopy, as well as with differential scanning calorimetry thermograms of multilamellar vesicles. All in all, the results indicate that both peptides adsorb and penetrate POPE/DOPG membranes with similar affinities, decreasing the surface charge, and adopting alpha structures. Both peptides mix with DOPG and demix from POPE, and consequently, persist at the interface to larger surface pressures in the presence of PG than in pure PE monolayers. This selective degree of mixing of the peptides with PE and PG leads to peptide-induced segregation of PG from PE, being the less charged peptide, acL1A, able to segregate the lipids more efficiently.

Effect of surface structure on peptide adsorption on soft surfaces

Understanding protein adsorption onto material surfaces is a major challenge in the design of biomaterials. While this has been long studied, knowledge of how the nanoscale surface structure affects protein adsorption is still lacking. Using molecular dynamics simulations the effect of nanoscale structure, specifically alternating hydrophobic and hydrophilic stripes, on the adsorption of LK-peptides onto surfaces is investigated. Strongest adsorption is found for surfaces with larger hydrophobic regions, which allow the peptides to minimise unfavourable contacts with hydrophilic regions. This information may be used to understand the relationship between protein adsorption and surface structure, allowing for control over biocompatibility and anti-fouling behaviour.