Interaction Of Peptides Research Articles

Antimicrobial peptide interactions with bacterial cell membranes

Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptides including magainin 2 and protegrin 1 with α-helix and β-sheet secondary structures were selected to investigate their interactions with different lipid bilayers such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), POPC/POPG (7:3), POPC/POPS (7:3), POPG/POPE(1:3), and POPG/POPE(3:1). The obtained structures of the AMPs illustrated that protegrin 1 cannot maintain its secondary structure in the solution phase in contrast to magainin 2. The head groups of the lipid units play a key role in the stability of the lipid bilayers. The head parts of the lipid membranes by increasing the internal H-bond contribute to membrane compactness. The POPG and POPS units inside the POPC/POPG and POPC/POPS membranes increase the order of the POPC units. The cationic residues of the AMPs form remarkable electrostatic interactions with the negatively charged membrane surfaces, which play a key role in the stabilization process of the peptide secondary structures. The Arg residues of protegrin 1 and the Gly1, Lys4, Lys10, Lys11, Lys14, and Glu19 of the magainin 2 have the most important roles in the complexation process. The values of Gibbs binding energies (ΔG) indicate that the complexation process between AMPs and different bacterial membranes is favorable from the thermodynamic viewpoint and AMPs could form stable complexes with the lipid bilayers. As a result of ΔG values, protegrin 1 forms a more stable complex with POPG/POPE(3:1), while the α-helix has more affinity to the POPG/POPE(1:3) bacterial membranes. Therefore, it can be considered that β-sheet and α-helix AMPs are more effective against gram-positive and gram-negative bacteria, respectively. The results of this study can provide useful details about the antimicrobial peptide interactions with the bacterial cell, which can be employed for designing new antimicrobial materials with greater efficiency. Communicated by Ramaswamy H. Sarma

Quillaja and Sapindus saponins influence on effect on solubilization of Polymyxin B peptide antibiotic in aqueous solutions

Knowing and understanding the interactions between surfactants and pharmaceuticals is crucial for the proper and efficient design of drug delivery systems. The goal of such systems is to ensure that the drug is as bioavailable to cells as possible. The subject of this study was the effect of natural surfactants, saponins from Quillaja saponaria Mol. and Sapindus mukorossi L., on the behavior of the antibiotic Polymyxin B in aqueous solutions at 30 °C and atmospheric pressure. The conducted research showed that the tested surfactants in the concentration range up to 5 mg mL−1 did not affect the solubility of the antibiotic, but increased the value of the octanol–water partition coefficient (Kow). At concentrations of plant saponins from both sources, Kow slightly increased from 0.19 (control sample) to 0.40 (at 5 mg mL−1). The presence of surfactants also led to changes in the particle size distribution of Polymyxin B solutions and also in their zeta potential values. There was also a clear effect of saponins on the freezing point of the Polymyxin solution, but no significant changes in the melting point were observed. The collected results provide new knowledge about the interactions of plant surfactants and peptides based on the example of Polymyxin B, which opens wider possibilities for their use in drug delivery systems.

A transferrin receptor targeting dual-modal MR/NIR fluorescent imaging probe for glioblastoma diagnosis.

The prognosis of glioblastoma (GBM) remains challenging, primarily due to the lack of a precise, effective imaging technique for comprehensively characterization. Addressing GBM diagnostic challenges, our study introduces an innovative dual-modal imaging that merges near-infrared (NIR) fluorescent imaging with magnetic resonance imaging (MRI). This method employs superparamagnetic iron oxide nanoparticles coated with NIR fluorescent dyes, specifically Cyanine 7, and targeted peptides. This synthetic probe facilitates MRI functionality through superparamagnetic iron oxide nanoparticles, provides NIR imaging capability via Cyanine 7 and enhances tumor targeting trough peptide interactions, offering a comprehensive diagnostic tool for GBM. Notably, the probe traverses the blood-brain barrier, targeting GBM in vivo via peptides, producing clear and discernible images in both modalities. Cytotoxicity and histopathology assessments confirm the probe's favorable safety profile. These findings suggest that the dual-modal MR\NIR fluorescent imaging probe could revolutionize GBM prognosis and survival rates, which can also be extended to other tumors type.

The critical role of aromatic residues in the binding of the SARS-CoV-2 fusion peptide to phospholipid bilayer membranes.

Based on the SARS-CoV-2 fusion peptide (FP) structure determined from the NMR experiment, we created six FP models under different environmental conditions to explore the effects of salt and cholesterol on FP-membrane binding. The all-atom molecular dynamics (MD) simulation results indicated that ionic environments notably impact the FP structure as well as the stability of the helical elements within the peptide. Our findings highlighted the unpredictable influence of ions on the secondary structures and dynamics of the FP, emphasizing the complexity and sensitivity of the peptide's conformations to ionic conditions. When exploring the peptide's interaction with a cholesterol-free phospholipid bilayer membrane, we found that the helical elements of the FP remain stable irrespective of the salt type (Na+ or Ca2+). This result emphasizes the crucial role of phospholipid bilayer membranes in supporting the secondary structures of the FP. The MD simulation results showed that Ca2+ ions facilitated deeper membrane penetration than Na+ ions, highlighting the critical role of calcium ions in the FP-membrane binding. Our study indicates the essential role of the aromatic residues (such as Phe833 and Tyr837) in the FP-membrane binding process. Finally, we investigated the FP-membrane binding patterns in the presence of cholesterol. The MD simulation results demonstrated that the coupling of Ca2+ ions and cholesterol would also benefit the FP-membrane binding. Furthermore, our findings reveal that while the type of ion and cholesterol content exert varied and unpredictable influences on FP-membrane binding patterns, aromatic residues like tyrosine (Tyr) and phenylalanine (Phe) play an essential role in FP-membrane binding. In particular, deep mutational scanning (DMS) experiments have confirmed that mutating phenylalanine in the FP significantly decreases viral mutational fitness, emphasizing the pivotal role of phenylalanine residues in membrane fusion. This knowledge can aid in developing more effective therapeutic strategies targeting the viral fusion peptide and its key amino acids, ultimately contributing to developing treatments and vaccines against the virus.

High-Throughput Screening for LC3/GABARAP Binders Utilizing the Fluorescence Polarization Assay.

The characterization of interactions between autophagy modifiers (Atg8-family proteins) and their natural ligands (peptides and proteins) or small molecules is important for a detailed understanding of selective autophagy mechanisms and for the design of potential Atg8 inhibitors that affect the autophagy processes in cells. The fluorescence polarization (FP) assay is a rapid, cost-effective, and robust method that provides affinity and selectivity information for small molecules and peptide ligands targeting human Atg8 proteins.This chapter introduces the basic principles of FP assays. In addition, a case study on peptide interaction with human Atg8 proteins (LC3/GABARAPs) is described. Finally, data analysis and quality control of FP assaysare discussed for the proper calculation of Ki values for the measured compounds.

Thermodynamic Characterization of LC3/GABARAP:Ligand Interactions by Isothermal Titration Calorimetry.

Isothermal titration calorimetry (ITC) is a widely used technique for the characterization of protein-protein and protein-ligand interactions. It provides information on the stoichiometry, affinity, and thermodynamic driving forces of interactions. This chapter exemplifies the use of ITC to investigate interactions between human autophagy modifiers (LC3/GABARAP proteins) and their interaction partners, the LIR motif-containing sequences. The purpose of this report is to present a detailed protocol for the production of LC3/GABARAP-interacting LIR peptides using E. coli expression systems. In addition, we outline the design of ITC experiments using the LC3/GABARAP:peptide interactions as an example. Comprehensive troubleshooting notes are provided to facilitate the adaptation of these protocols to different ligand-receptor systems. The methodology outlined for studying protein-ligand interactions will help to avoid common errors and misinterpretations of experimental results.

Application of a modern theoretical approach to the study of the interaction of KR-12 peptides derived from human cathelicidins with Cu(II) ions.

The human cationic antimicrobial protein (hCAP) corresponding to the overlapping sequences of 151-162 of hCAP named KR-12 peptide is the smallest portion of the only type of human Cathelicidin, which has been shown to be modifiable into a more effective antimicrobial. In this study, an in silico analysis, supported by potentiometric titration and isothermal titration calorimetry techniques, was performed to identify potential Cu(II) binding sites of KR-12. The analysis of the presented data at the given theoretical level (GFN2-xTB/ALPB) revealed which peptide chain fragments are involved in the most favourable KR-12-Cu(II) binding mode. Based on a quantum chemical approach, the most favourable coordination modes of Cu(II) to peptides are proposed together with the discussion of the chemical nature of the interactions. The presented results demonstrated that KR-12 interacts with metal ions mostly via the main chain's oxygen atoms; however, the two types of amino acids that are expected to be vital for the interaction of Cu(II) are D (aspartic acid) and R29 (arginine). It was demonstrated that in order to explain the complexity of the interaction process in peptide-metal ion systems, the use of theoretical methods is sometimes necessary to explain the details of the experimental results and provide an in-depth understanding of these dynamic systems.

Strategy for Experimental Studies of Target Protein Interactomics

It is known that intermolecular interactions of proteins and peptides play a critical role in life processes. Such interactions can be either directly related to the implementation of various functions or play the role of a regulator. Currently, there is no doubt that the majority of proteins function as part of various molecular complexes, the formation of which occurs due to protein-protein interactions (PPIs), the totality of which can be defined as the “protein interactome”. Protein subinteractome studies are critical for studying the functions and regulatory mechanisms of unknown or poorly annotated proteins, understanding the architecture of intracellular molecular machines, and the design of PPI modulators. Previously, we used combinations of experimental approaches, as well as analytical and preparative methods, to study the subinteractomes of functionally different cellular proteins, which allowed us to identify the protein subinteractomes of several clinically significant human proteins. The purpose of this work was to conceptualize the principles of the experimental platform we developed for studying protein subinteractomes and to describe its features in detail.

Marine bioactive peptides with anticancer potential, a narrative review.

In this paper, we explore marine bioactive peptides with anticancer potential sourced from various marine organisms, including tunicates, sea sponges, and mollusks. Peptides like Stylisin and Papuamides have been isolated, identified, and modified to enhance their activity, with many advancing to clinical trials due to their diverse biological activities, promising prospects in medicine. Enzymatic hydrolysis is a favored method for extracting peptides from marine proteins, particularly from sponges known for their rich bioactive compounds. Compounds such as Jaspamide and Homophymins exhibit potent cytotoxic activity against cancer cells, underscoring their therapeutic potential. Additionally, peptides from ascidians and mollusks, such as Aplidine and Kahalalide F, demonstrate significant anticancer properties. This study also explores peptides influencing apoptosis, microtubule dynamics, and angiogenesis, providing insights into potential mechanisms for cancer treatment. While peptides like Neovastat and mycothiazole target known pathways, others such as patellamides act through unknown mechanisms, highlighting the intricate interactions of marine peptides with cancer cells. Overall, marine-derived peptides show promise as valuable candidates for developing novel anticancer therapies.

Molecular dynamics simulation of the interactions of antimicrobial peptides with phospholipids of the inner membrane of gram-negative bacteria

Molecular dynamics simulation of the interactions of antimicrobial peptides with phospholipids of the inner membrane of gram-negative bacteria

Engineering the interaction of short antimicrobial peptides with bacterial barriers

Designing short antimicrobial peptides and tuning their interaction with bacterial barriers.

Porous organic cages as inhibitors of Aβ42 peptide aggregation: a simulation study.

The aggregation of Aβ monomers into oligomers with β-sheet structures is an important cause of Alzheimer's disease (AD), while the Aβ42 peptide is more toxic and prone to aggregate. It is of great significance to study the inhibition mechanism of Aβ42 monomer aggregation and find excellent inhibitors for the treatment of AD. Research in recent years has focused on small molecule compounds and nanoparticles, but they all have certain limitations. As a new type of porous material, a porous organic cage (POC) has potential application feasibility in the biomedical field due to its unique physicochemical properties. In this work, molecular dynamics simulations were used for the first time to explore the interaction and conformational transformation of the Aβ42 peptide in CC3 crystals with different morphologies (planar and spherical). The results show that the adsorption of the Aβ42 peptide on different CC3 crystals is mainly achieved through strong van der Waals forces. During the simulations, the Aβ42 peptide undergoes various degrees of structural changes. Compared to that in water, this binding induces more irregular structures, such as turns and 3-helices, and inhibits the production of β-sheets, while enhancing the overall backbone rigidity of the Aβ42 peptide. The transformation analysis of peptide conformation is further complemented by free energy landscape and cluster analysis. These findings provide a strong basis for CC3 crystals as novel inhibitors to inhibit the toxicity and aggregation of the Aβ42 peptide.

Reinforcement of nanofibrillar hydrogels via cyclodextrin and self-assembling peptide interactions for controlled drug delivery

The Fmoc-GFFG/SBE-β-CD@HCPT hydrogel exploits host–guest interactions between Fmoc-GFFG and SBE-β-CD, resulting in enhanced viscoelastic strength of hydrogel and sustained release of HCPT.

Recalculating the Route: Repositioning Antimicrobial Peptides for Cancer Treatment.

Resistance to antimicrobial drugs has been considered a public health problem. Likewise, the increasing resistance of cancer cells to drugs currently used in therapy has also become a problem. Therefore, the research and development of synthetic peptides bring a new perspective on the emergence of new drugs for treating this resistance since bioinformatics provides a means to optimize these molecules and save time and costs in research. Peptides have several mechanisms of action, such as forming pores on the cell membrane and inhibiting protein synthesis. Some studies report the use of antimicrobial peptides with the potential for action against cancer cells, suggesting a repositioning of antimicrobial peptides to fight back cancer resistance. There is an alteration in the microenvironment, making its net charge negative for the survival and growth of cancer cells. The changes in glycoproteins favor the membrane to have a more negative charge, favoring the interaction between the cells and the peptide, thus making possible the repositioning of these antimicrobial peptides against cancer. Here, we will discuss the mechanism of action, targets and effects of peptides, comparison between microbial and cancer cells, and proteomic changes caused by the interaction of peptides and cells.

PepCNN deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and language model features

Protein–peptide interactions play a crucial role in various cellular processes and are implicated in abnormal cellular behaviors leading to diseases such as cancer. Therefore, understanding these interactions is vital for both functional genomics and drug discovery efforts. Despite a significant increase in the availability of protein–peptide complexes, experimental methods for studying these interactions remain laborious, time-consuming, and expensive. Computational methods offer a complementary approach but often fall short in terms of prediction accuracy. To address these challenges, we introduce PepCNN, a deep learning-based prediction model that incorporates structural and sequence-based information from primary protein sequences. By utilizing a combination of half-sphere exposure, position specific scoring matrices from multiple-sequence alignment tool, and embedding from a pre-trained protein language model, PepCNN outperforms state-of-the-art methods in terms of specificity, precision, and AUC. The PepCNN software and datasets are publicly available at https://github.com/abelavit/PepCNN.git.

Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity

Hyaluronan is a natural carbohydrate polymer with a negative charge that fosters gel-like conditions crucial for its cellular functions and industrial applications. As a recognized ligand for proteins, understanding their mutual interactions provides solid ground to tune hyaluronan's gel properties using biocompatible peptides. This work employs NMR and molecular dynamics simulations to identify molecular motifs relevant to hyaluronan–peptide interactions using arginine, lysine, and glycine oligopeptides. Arginine-rich peptides exhibit the strongest binding to hyaluronan according to chemical shift perturbation measurements, followed distantly by the similarly charged lysine. This difference highlights the significance of electrostatics and the peculiarities of the guanidinium side chain in arginine, capable of non-polar interactions that further stabilize the binding. Additional nuclear Overhauser effect measurements do not show stable interaction partners, precluding strong and well-defined complexes. Finally, molecular simulations support our findings and show an extended but significant interaction region, especially for arginine, responsible for the observed enhanced binding, which can also promote cross-linking of hyaluronan polymers. Our findings pave the way for optimizing biocompatible peptides to alter hyaluronan gels' properties efficiently and also explain why hyaluronan–protein interaction typically involves positively charged arginine-rich regions also capable of forming hydrogen bonds and non-polar interactions.

Biophysical Insights into the Antitumoral Activity of Crotalicidin against Breast Cancer Model Membranes.

Bioactive peptides have emerged as promising therapeutic agents with antimicrobial, antifungal, antiparasitic, and, recently, antitumoral properties with a mechanism of action based on membrane destabilization and cell death, often involving a conformational change in the peptide. This biophysical study aims to provide preliminary insights into the membrane-level antitumoral mode of action of crotalicidin, a cationic host defense peptide from rattlesnake venom, toward breast cancer cell lines. The lipid composition of breast cancer cell lines was obtained after lipid extraction and quantification to prepare representative cell membrane models. Membrane-peptide interaction studies were performed using differential scanning calorimetry and Fourier-transform infrared spectroscopy. The outcome evidences the potential antitumoral activity and selectivity of crotalicidin toward breast cancer cell lines and suggests a mechanism initiated by the electrostatic interaction of the peptide with the lipid bilayer surface and posterior conformation change with membrane intercalation between the acyl chains in negatively charged lipid systems. This research provides valuable information that clears up the antitumoral mode of action of crotalicidin.

Characterization of AT-02, a pan-amyloid-binding peptide fusion immunoglobulin with high binding potency, complement activation, and immune cell stimulation

Abstract Background Cardiac amyloidosis is an ominous manifestation of systemic amyloidosis, notably in AL and ATTR-associated types, resulting in a restrictive hypertrophic cardiomyopathy with electrical conduction and atrioventricular strain dysfunction (1). Amyloid is not naturally cleared by the immune system due to the presence of extracellular matrix components in the deposits (2). However, recruiting and stimulating the innate immune system, notably phagocytic macrophages, is a promising strategy to effect amyloid removal. To facilitate this, we have generated AT-02, a humanized IgG1 incorporating the pan-amyloid-binding peptide, p5R (3), at the light chain C-terminus. This reagent binds diverse types of amyloid via the peptide interactions and retains immunomodulatory capacity. Purpose The goal of these studies was to characterize the bioactivity of AT-02 that underlies its potential therapeutic activity. Methods AT-02 was produced from a CHO pool using a perfusion cell culture production process, purified by Protein A, anion exchange, and cation exchange chromatographies, and characterized by mass spectrometry and SDS-capillary electrophoresis. AT-02 was biotinylated and used for immunohistochemical detection of both AL and ATTR amyloidosis in formalin fixed tissues (Figure 1A). Binding to heparin (as a surrogate for amyloid-associated hypersulfated heparan sulfate proteoglycans) and synthetic AL fibrils was studied using both ELISA and surface plasmon resonance assays (Figure 1B). Activation of complement following binding to amyloid substrates was determined using a C5b9 liberation assay in the presence of human plasma. The effect of AT-02 on amyloid fibril growth was determined using a fluorescence fibril elongation assay. In vivo clearance of amyloid and cell activation was demonstrated using a murine model of AL amyloidoma. Results AT-02 bound human cardiac amyloid in tissue sections with high specificity and intensity. The potency for heparin and synthetic amyloid fibrils, as well as human cardiac amyloid extracts, was sub-nanomolar in the ELISA assay with kinetics consistent with a high affinity antibody. In the presence of plasma, complement activation of amyloid-bound AT-02 was significantly higher as compared to controls, and the reagent inhibited synthetic amyloid fibril growth by ∼40%. Treatment of human amyloid with AT-02 expedited phagocytosis by murine macrophages in vivo and enhanced the intensity of immune response to the implanted amyloid. Conclusion Clearance of cardiac amyloid is a significant clinical unmet need for patients with systemic amyloidosis. The humanized IgG1-peptide fusion, AT-02, potently binds cardiac amyloid and may serve as an opsonin and induce macrophage-mediated phagocytosis and clearance of cardiac amyloid deposits.

Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains.

Heterologous interactions between different amyloid-forming proteins, also called cross-interactions, may have a critical impact on disease-related amyloid formation. β-hairpin conformers of amyloid-forming proteins have been shown to affect homologous interactions in the amyloid self-assembly process. Here, we applied two β-hairpin-forming peptides derived from immunoglobulin light chains as models to test how heterologous β-hairpins modulate the fibril formation of Parkinson's disease-associated protein α-synuclein (αSyn). The peptides SMAhp and LENhp comprise β-strands C and C' of the κ4 antibodies SMA and LEN, which are associated with light chain amyloidosis and multiple myeloma, respectively. SMAhp and LENhp bind with high affinity to the β-hairpin-binding protein β-wrapin AS10 according to isothermal titration calorimetry and NMR spectroscopy. The addition of SMAhp and LENhp affects the kinetics of αSyn aggregation monitored by Thioflavin T (ThT) fluorescence, with the effect depending on assay conditions, salt concentration, and the applied β-hairpin peptide. In the absence of agitation, substoichiometric concentrations of the hairpin peptides strongly reduce the lag time of αSyn aggregation, suggesting that they support the nucleation of αSyn amyloid fibrils. The effect is also observed for the aggregation of αSyn fragments lacking the N-terminus or the C-terminus, indicating that the promotion of nucleation involves the interaction of hairpin peptides with the hydrophobic non-amyloid-β component (NAC) region.

Ion-exchange purification, nano-HPLC–MS/MS identification and molecular dynamics simulation of novel umami peptides from fermented grain wine (Huangjiu)

Huangjiu is a traditional Chinese fermented rice wine with abundant peptides, but the umami peptides are little known due to the wine’s complex matrix. Herein, the target umami fraction was enriched with sensory-guided separation coupled with ultrafiltration, ion-exchange, and gel chromatography purification. A total of 1901 peptides were identified from gel F1 fraction with nano-HPLC–MS/MS. Eight novel umami peptides DWDPHGL, VPEPEPH, LTPEPEH, GANQLDPR, FREE, LDFR, QEGW, and RDH were filtered by virtual screening and sensory evaluation. They exhibited thermal stability at 373.15 K and the taste thresholds in water were between 0.29 and 0.65 mmol/L. Among them, RDH was crucial, due to a relatively high dose over threshold (DoT) factor (1.12). Molecular docking results showed that residues ASP147, SER148, ARG151, TYR220, SER276, and ALA302 contributed most to the interaction of peptide and T1R1. Moreover, molecular dynamics simulation and weak interaction analysis suggested the important role of intramolecular forces in peptide thermal stability.