Charged Amino Acids Research Articles

Electrostatically Mediated Attractive Self-Interactions and Reversible Self-Association of Fc-Fusion Proteins.

Attractive self-interactions and reversible self-association are implicated in many problematic solution behaviors for therapeutic proteins, such as irreversible aggregation, elevated viscosity, phase separation, and opalescence. Protein self-interactions and reversible oligomerization of two Fc-fusion proteins (monovalent and bivalent) and the corresponding fusion partner protein were characterized experimentally with static and dynamic light scattering as a function of pH (5 and 6.5) and ionic strength (10 mM to at least 300 mM). The fusion partner protein and monovalent Fc-fusion each displayed net attractive electrostatic self-interactions at pH 6.5 and net repulsive electrostatic self-interactions at pH 5. Solutions of the bivalent Fc-fusion contained higher molecular weight species that prevented quantification of typical interaction parameters (B22 and kD). All three of the proteins displayed reversible self-association at pH 6.5, where oligomers dissociated with increased ionic strength. Coarse-grained molecular simulations were used to model the self-interactions measured experimentally, assess net self-interactions for the bivalent Fc-fusion, and probe the specific electrostatic interactions between charged amino acids that were involved in attractive electrostatic self-interactions. Mayer-weighted pairwise electrostatic energies from the simulations suggested that attractive electrostatic self-interactions at pH 6.5 for the two Fc-fusion proteins were due to cross-domain interactions between the fusion partner domain(s) and the Fc domain.

Charge cluster occurrence in land plants’ mitochondrial proteomes with functional and structural insights

The Charge Clusters (CCs) are involved in key functions and are distributed according to the organism, the protein’s type, and the charge of amino acids. In the present study, we have explored the occurrence, position, and annotation as a first large-scale study of the CCs in land plants mitochondrial proteomes. A new python script was used for data curation. The Finding Clusters Charge in Protein Sequences Program was performed after adjusting the reading window size. A 44316 protein sequences belonging to 52 species of land plants were analysed. The occurrence of Negative Charge Clusters (NCCs) (1.2%) is two times more frequent than the Positive Charge Clusters (PCCs) (0.64%). Moreover, 39 and 30 NCCs were conserved in 88 and 41 proteins in intra and in inter proteomes respectively, while 14 and 21 PCCs were conserved in 53 and 85 protein sequences in intra and inter proteomes consecutively. Sequences carrying mixed CCs are rare (0.12%). Despite this low abundance, CCs play a crucial role in protein function. The CCs tend to be located mainly in the terminal regions of proteins which guarantees specific protein targeting and import into the mitochondria. In addition, the functional annotation of CCs according to Gene Ontology shows that CCs are involved in binding functions of either proteins or macromolecules which are deployed in different metabolic and cellular processes such as RNA editing and transcription. This study may provide valuable information while considering the CCs in understanding the environmental adaptation of plants. Communicated by Ramaswamy H. Sarma

Charged Amino Acids in the Transmembrane Helix Strongly Affect the Enzyme Activity of Aromatase.

Estrogens play critical roles in embryonic development, gonadal sex differentiation, behavior, and reproduction in vertebrates and in several human cancers. Estrogens are synthesized from testosterone and androstenedione by the endoplasmic reticulum membrane-bound P450 aromatase/cytochrome P450 oxidoreductase complex (CYP19/CPR). Here, we report the characterization of novel mammalian CYP19 isoforms encoded by CYP19 gene copies. These CYP19 isoforms are all defined by a combination of mutations in the N-terminal transmembrane helix (E42K, D43N) and in helix C of the catalytic domain (P146T, F147Y). The mutant CYP19 isoforms show increased androgen conversion due to the KN transmembrane helix. In addition, the TY substitutions in helix C result in a substrate preference for androstenedione. Our structural models suggest that CYP19 mutants may interact differently with the membrane (affecting substrate uptake) and with CPR (affecting electron transfer), providing structural clues for the catalytic differences.

Self-Assembling Polypeptides in Complex Coacervation.

Intracellular compartmentalization plays a pivotal role in cellular function, with membrane-bound organelles and membrane-less biomolecular "condensates" playing key roles. These condensates, formed through liquid-liquid phase separation (LLPS), enable selective compartmentalization without the barrier of a lipid bilayer, thereby facilitating rapid formation and dissolution in response to stimuli. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs), which are often rich in charged and polar amino acid sequences, scaffold many condensates, often in conjunction with RNA.Comprehending the impact of IDP/IDR sequences on phase separation poses a challenge due to the extensive chemical diversity resulting from the myriad amino acids and post-translational modifications. To tackle this hurdle, one approach has been to investigate LLPS in simplified polypeptide systems, which offer a narrower scope within the chemical space for exploration. This strategy is supported by studies that have demonstrated how IDP function can largely be understood based on general chemical features, such as clusters or patterns of charged amino acids, rather than residue-level effects, and the ways in which these kinds of motifs give rise to an ensemble of conformations.Our laboratory has utilized complex coacervates assembled from oppositely charged polypeptides as a simplified material analogue to the complexity of liquid-liquid phase separated biological condensates. Complex coacervation is an associative LLPS that occurs due to the electrostatic complexation of oppositely charged macro-ions. This process is believed to be driven by the entropic gains resulting from the release of bound counterions and the reorganization of water upon complex formation. Apart from their direct applicability to IDPs, polypeptides also serve as excellent model polymers for investigating molecular interactions due to the wide range of available side-chain functionalities and the capacity to finely regulate their sequence, thus enabling precise control over interactions with guest molecules.Here, we discuss fundamental studies examining how charge patterning, hydrophobicity, chirality, and architecture affect the phase separation of polypeptide-based complex coacervates. These efforts have leveraged a combination of experimental and computational approaches that provide insight into molecular level interactions. We also examine how these parameters affect the ability of complex coacervates to incorporate globular proteins and viruses. These efforts couple directly with our fundamental studies into coacervate formation, as such "guest" molecules should not be considered as experiencing simple encapsulation and are instead active participants in the electrostatic assembly of coacervate materials. Interestingly, we observed trends in the incorporation of proteins and viruses into coacervates formed using different chain length polypeptides that are not well explained by simple electrostatic arguments and may be the result of more complex interactions between globular and polymeric species. Additionally, we describe experimental evidence supporting the potential for complex coacervates to improve the thermal stability of embedded biomolecules, such as viral vaccines.Ultimately, peptide-based coacervates have the potential to help unravel the physics behind biological condensates, while paving the way for innovative methods in compartmentalization, purification, and biomolecule stabilization. These advancements could have implications spanning medicine to biocatalysis.

The current landscape of the antimicrobial peptide melittin and its therapeutic potential.

Melittin, a main component of bee venom, is a cationic amphiphilic peptide with a linear α-helix structure. It has been reported that melittin can exert pharmacological effects, such as antitumor, antiviral and anti-inflammatory effects in vitro and in vivo. In particular, melittin may be beneficial for the treatment of diseases for which no specific clinical therapeutic agents exist. Melittin can effectively enhance the therapeutic properties of some first-line drugs. Elucidating the mechanism underlying melittin-mediated biological function can provide valuable insights for the application of melittin in disease intervention. However, in melittin, the positively charged amino acids enables it to directly punching holes in cell membranes. The hemolysis in red cells and the cytotoxicity triggered by melittin limit its applications. Melittin-based nanomodification, immuno-conjugation, structural regulation and gene technology strategies have been demonstrated to enhance the specificity, reduce the cytotoxicity and limit the off-target cytolysis of melittin, which suggests the potential of melittin to be used clinically. This article summarizes research progress on antiviral, antitumor and anti-inflammatory properties of melittin, and discusses the strategies of melittin-modification for its future potential clinical applications in preventing drug resistance, enhancing the selectivity to target cells and alleviating cytotoxic effects to normal cells.

Thermodynamics of Metal-Acetate Interactions.

Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C4 parameters for the 12-6-4 LJ nonbonded model to be used with three widely employed water models (Transferable Intermolecular Potential with 3 Points (TIP3P), Simple Point Charge Extended (SPC/E), and Optimal Point Charge (OPC) water models). These parameters can accurately match the experimental binding free energy between 11 metal ions and acetate. These parameters can be applied to the study of metalloproteins and transition metal ion channels and transporters, as acetate serves as a representative of the negatively charged amino acid side chains from aspartate and glutamate.

Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining

Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap.Key points• Six new opine dehydrogenases have been discovered from a hot spring metagenome• The newly identified enzymes display a unique substrate scope• Substrate specificity is governed by two correlated active-site residues

An extensive ion-pair/hydrogen-bond network contributes to the thermostability of the MutL ATPase domain from Aquifex aeolicus.

Proteins from hyperthermophiles often contain a large number of ionic interactions. Close examination of the previously determined crystal structure of the ATPase domain of MutL from a hyperthermophile, Aquifex aeolicus, revealed that the domain contains a continuous ion-pair/hydrogen-bond network consisting of 11 charged amino acid residues on a β-sheet. Mutations were introduced to disrupt the network, showing that the more extensively the network was disrupted, the greater the thermostability of the protein was decreased. Based on urea denaturation analysis, a thermodynamic parameter, energy for the conformational stability, was evaluated, which indicated that amino acid residues in the network contributed additively to the protein stability. A continuous network rather than a cluster of isolated interactions would pay less entropic penalty upon fixing the side chains to make the same number of ion pairs/hydrogen bonds, which might contribute more favorably to the structural formation of thermostable proteins.

High Quantum Yield Amino Acid Carbon Quantum Dots with Unparalleled Refractive Index.

Carbon quantum dots (CQDs) are one of the most promising types of fluorescent nanomaterials due to their exceptional water solubility, excellent optical properties, biocompatibility, chemical inertness, excellent refractive index, and photostability. Nitrogen-containing CQDs, which include amino acid based CQDs, are especially attractive due to their high quantum yield, thermal stability, and potential biomedical applications. Recent studies have attempted to improve the preparation of amino acid based CQDs. However, the highest quantum yield obtained for these dots was only 44%. Furthermore, the refractive indices of amino acid derived CQDs were not determined. Here, we systematically explored the performance of CQDs prepared from all 20 coded amino acids using modified hydrothermal techniques allowing more passivation layers on the surface of the dots to optimize their performance. Intriguingly, we obtained the highest refractive indices ever reported for any CQDs. The values differed among the amino acids, with the highest refractive indices found for positively charged amino acids including arginine-CQDs (∼2.1), histidine-CQDs (∼2.0), and lysine-CQDs (∼1.8). Furthermore, the arginine-CQDs reported here showed a nearly 2-fold increase in the quantum yield (∼86%) and a longer decay time (∼8.0 ns) compared to previous reports. In addition, we also demonstrated that all amino acid based CQD materials displayed excitation-dependent emission profiles (from UV to visible) and were photostable, water-soluble, noncytotoxic, and excellent for high contrast live cell imaging or bioimaging. These results indicate that amino acid based CQD materials are high-refractive-index materials applicable for optoelectronic devices, bioimaging, biosensing, and studying cellular organelles in vivo. This extraordinary RI may be highly useful for exploring cellular elements with different densities.

Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages.

Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution. We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment. The data underlying the article are available in the Supplementary material.

Structure-guided directed evolution of deacetylase leads to increased specificity of chloroacetamides and effective production of chloroamines

O-3-chloro-2-propenyl hydroxylamine (chloroamine) is the primary material for the production of cyclohexenone herbicides, such as clethodim, which are widely used in agricultural production due to their high efficiency, low toxicity, and good environmental safety. In this study, a bioenzymatic strategy is proposed for the synthesis of chloroamines in order to address the polluting nature of traditional chemical synthesis. Using easily synthesized chloroacetamides as the model substrate, histone deacetylase 10 (zHDAC10) from zebrafish was used as the biocatalyst for the deacetylation process, resulting in the production of chloroamides. Through a structure-directed mutagenesis and site saturation mutagenesis strategy, a zHDAC10-M2 (A24RE274K) was created, leading to approximately an 8-fold enhancement of activity in comparison to the zHDAC10-WT, with a high catalytic efficiency of 40 mM and a 24-hour conversion of over 94% on a 100-mL preparative scale. Structural analysis and molecular dynamics showed that the mutation of 24 and 274 sites to positively charged amino acids enabled them to form hydrogen bonds with the terminal Cl of chloroamines, thereby stabilizing the state of the substrate in the active pocket and thus improving the catalytic efficiency. The biosynthetic route established in this study provides a new promising way for the production of chloroamines.

An atomistic scale simulation study of structural properties in the silk-fibrohexamerin complex.

The use of Bombyx mori silk fibroin in composite materials has been extensively explored in many studies, owing to its remarkable mechanical properties. Recently, the N-glycan-engineered P25 protein was utilized to improve the mechanical properties of silk. However, the mechanism by which N-glycan-engineered P25 protein enhances the mechanical properties of silk remains unclear. This study analyzed the interaction between the P25 protein and silkworm silk using quantum mechanics/molecular mechanics multiscale simulations and discovered stronger hydrogen bonding between the amorphous domain and the P25 protein. The results confirmed that glycoengineering of the mannose molecule in N-glycan in orders of three, five, and seven increased the hydrogen bonding of the amorphous structures. However, P25 has fewer binding interactions with the crystalline domain. Silk amino acids and mannose molecules were analyzed using QM simulations, and hydroxyl and charged amino acids in the amorphous domains were found to have relatively higher reactivity with mannose molecules in N-glycans than basic and aliphatic amino acids in the crystalline domain. This study demonstrates how the N-glycan-engineered P25 protein can improve the mechanical properties of silk fibroin and identifies a key factor for N-glycan-engineered proteins.

On the Role and Structural Outlook of Carboxy-Terminal Domain of Anabaena Sensory Rhodopsin

Anabaena Sensory Rhodopsin, ASR represents a small family of sensory rhodopsins among a vast family of microbial rhodopsins. In contrast to other microbial sensory rhodopsins, which are known to mediate photostimulated signal relay using cognate membrane transducer, ASR interacts to plausible soluble oligomeric transducer protein. Though the atomic resolution structure ASR is available, it only included only the transmembrane domain. Interestingly the available structure is remarkably different from other microbial sensory rhodopsins, with presence of water. Additionally, the sequence of missing cytoplasmic domain contains a series of positively charged Arginine residues in it. Authors have outlined the influence of this domain in addition to flexible structural outlook using Deep Mind’s Nova Fold-2. Authors propose that charged amino acids are vital in ASR-transducer interaction. Subsequent attempts to explore the molecular basis of ASR and cognate transducer binding would be vital to understand the unique photo-mediated signal cascade in Anabaena PCC 7120.

DRGD-linked charged EKKE dimeric dodecapeptide: pH-based amyloid nanostructures and their application in lead and uranium binding.

Peptides have been reported to undergo self-assembly into diverse nanostructures, influenced by several parameters, including their amino acid sequence, pH, charge, solvent, and temperature. Inspired by natural systems, researchers have developed biomimetic peptides capable of self-assembling into supramolecular functional structures. The present study explored a newly designed peptide sequence, EKKEDRGDEKKE, where E = glutamic acid, K = lysine, D = aspartic acid, G = glycine, and R = arginine, with a metal binding DRGD sequence incorporated between the exclusively charged EKKE peptide. We investigated the formation and the potential of the EKKEDRGDEKKE peptide in retaining the structure and morphology adopted by the individual EKKE peptide. According to a combination of experimental techniques such as thioflavin T fluorescence, field emission-scanning electron microscopy, atomic force microscopy, and circular dichroism, it was evident that the EKKEDRGDEKKE peptide displayed a pH-dependent propensity to adopt amyloid-like structures. Furthermore, the self-assembled entities formed under acidic, basic, and neutral conditions exhibited morphological variations, which resembled that observed for the exclusively charged EKKE peptide. Furthermore, the incorporation of the functional DRGD motif resulted in promising binding to two toxic metal ions, lead (Pb) and uranium (U), as evidenced by a range of spectroscopic techniques, including UV-visible spectroscopy, atomic absorption spectroscopy, fluorescence spectroscopy, and X-ray photoelectron spectroscopy. The use of the amyloid-forming EKKEDRGDEKKE scaffold can also be extended to potential biomedical applications.

ХАРАКТЕРИСТИКА И ВЛИЯНИЕ МИКРОКАПСУЛЯЦИИ НА СТАБИЛЬНОСТЬ БИОПЕПТИДА В МОДЕЛИ IN VITRO

One of the ways to prevent the development of oxidative stress is the oral use of bioactive peptides. To ensure the targeted release of biologically active substances in the body, they are microcapsulated. The aim of the research is to characterize, predict, evaluate the antioxidant properties of a biopeptide and study the effect of microcapsulation on its stability in a model of the gastrointestinal tract. The molecular mass distribution of the peptide was evaluated by mass spectrometric method. Identification and characterization of the peptide was carried out using Protein NCBI and ARD databases. The antioxidant activity of the peptide was determined by DPPH, ABTS and FRAP methods. The microencapsulation of the peptide was carried out in a pseudo-boiling layer of 10 % maltodextrin solution. As a result of research, a peptide was isolated from trypsin hydrolysate of cow colostrum, its molecular weight, amino acid sequence, charge, hydrophobicity, isoelectric point, two- and three-dimensional structure were determined. Based on the obtained physicochemical characteristics of the peptide, a hypothesis about its antioxidant properties has been proposed, which has been confirmed in in vitro studies. It is proved that the microcapsulation of the peptide into a protective layer of maltodextrin ensures its stability in the model of the oral cavity and stomach and targeted release in the intestine in vitro.

Interaction of Au(III) with amino acids: a vade mecum for medicinal chemistry and nanotechnology.

Au(III) is highly reactive. At odds with its reduced counterpart, Au(I), it is hardly present in structural databases. And yet, it is the starting reactant to form gold nanoclusters (AuNCs) and the constitutive component of a new class of drugs. Its reactivity is a world apart from that of the iso-electronic Pt(II) species. Rather than DNA, it targets proteins. Its interaction with amino acid residues is manifold. It can strongly interact with the residue backbones, amino acid side chains and protein ends, it can form appropriate complexes whose stabilization energy reaches up to more than 40 kcal mol-1, it can affect the pKa of amino acid residues, and it can promote charge transfer from the residues to the amount that it is reduced. Here, quantum chemical calculations provide quantitative information on all the processes where Au(III) can be involved. A myriad of structural arrangements are examined in order to determine the strongest interactions and quantify the amount of charge transfer between protonated and deprotonated residues and Au(III). The calculated interaction energies of the amino acid side chains with Au(III) quantitatively reproduce the experimental tendency of Au(III) to interact with selenocysteine, cysteine and histidine and negatively charged amino acids such as Glu and Asp. Also, aromatic residues such as tyrosine and tryptophan strongly interact with Au(III). In proteins, basic pH plays a role in the deprotonation of cysteine, lysine and tyrosine and strongly increases the binding affinity of Au(III) toward these amino acids. The amino acid residues in the protein can also trigger the reduction of Au(III) ions. Sulfur-containing amino acids (cysteine and methionine) and selenocysteine provide almost one electron to Au(III) upon binding. Tyrosine also shows a considerable tendency to act as a reductant. Other amino acids, commonly identified in Au-protein adducts, such as Ser, Trp, Thr, Gln, Glu, Asn, Asp, Lys, Arg and His, possess a notable reducing power toward Au(III). These results and their discussion form a vade mecum that can find application in medicinal chemistry and nanotech applications of Au(III).

Conformational control of antimicrobial peptide amphiphilicity: consequences for boosting membrane interactions and antimicrobial effects of photocatalytic TiO2 nanoparticles.

This study reports on the effects of conformationally controlled amphiphilicity of antimicrobial peptides (AMPs) on their ability to coat TiO2 nanoparticles (NPs) and boost the photocatalytic antimicrobial effects of such NPs. For this, TiO2 NPs were combined with AMP EFK17 (EFKRIVQRIKDFLRNLV), displaying a disordered conformation in aqueous solution but helix formation on interaction with bacterial membranes. The membrane-bound helix is amphiphilic, with all polar and charged amino acid residues located at one side and all non-polar and hydrophobic residues on the other. In contrast, the d-enantiomer variant EFK17-d (E(dF)KR(dI)VQR(dI)KD(dF)LRNLV) is unable to form the amphiphilic helix on bacterial membrane interaction, whereas the W-residues in EFK17-W (EWKRWVQRWKDFLRNLV) boost hydrophobic interactions of the amphiphilic helix. Circular dichroism results showed the effects displayed for the free peptide, to also be present for peptide-coated TiO2 NPs, causing peptide binding to decrease in the order EFK17-W > EFK17 > EFK17-d. Notably, the formation of reactive oxygen species (ROS) by the TiO2 NPs was essentially unaffected by the presence of peptide coating, for all the peptides investigated, and the coatings stabilized over hours of UV exposure. Photocatalytic membrane degradation from TiO2 NPs coated with EFK17-W and EFK17 was promoted for bacteria-like model bilayers containing anionic phosphatidylglycerol but suppressed in mammalian-like bilayers formed by zwitterionic phosphatidylcholine and cholesterol. Structural aspects of these effects were further investigated by neutron reflectometry with clear variations observed between the bacteria- and mammalian-like model bilayers for the three peptides. Mirroring these results in bacteria-like model membranes, combining TiO2 NPs with EFK17-W and EFK17, but not with non-adsorbing EFK17-d, resulted in boosted antimicrobial effects of the resulting cationic composite NPs already in darkness, effects enhanced further on UV illumination.

Combinations of charged amino acids and glycine as enhancers of the antibacterial properties of chicken lysozyme

Combinations of charged amino acids and glycine as enhancers of the antibacterial properties of chicken lysozyme

Разработка нового антимикробного пептида

The properties of antimicrobial peptides as substances with high biological activity are considered; they can also be used as functional ingredients and (or) preservative substances in food product composition for preventive and specialized purposes. A new antimicrobial peptide consisting of 20 amino acid residues was developed; during the work, suitable amino acid sequences were selected, physical and chemical characteristics were optimized, and activity against target microorganisms was assessed. The inclusion of positively charged amino acids, such as lysine and arginine, which increase the cationicity of antimicrobial peptides and therefore increase their selectivity towards microbial membranes, is considered. The percentage content of each amino acid is as follows, %: Val – 5, Leu – 25, Cys – 5, Ala – 20, Trp – 5, Gly – 5, Ser – 5, His – 5, Lys – 20 and Arg – 5. General hydrophobicity ratio determined by APD is 60%, the charge is + 5.25. The peptide has a molecular weight of 2 206.761 Da, protein binding potential (Bohmann index) of 0.23 kcal/mol. The peptide can form alpha helices and has at least 8 elements on a single hydrophobic surface. According to data obtained from the APD database, the peptide can interact with bacterial membranes and is antimicrobial. The following known antimicrobial peptides are closest in physical and chemical characteristics to the created peptide: AP 00500, AP 03880 and AP 03383. The developed peptide can be classified as a cationic alpha-helical hydrophobic antimicrobial peptide.

A robust and versatile host-guest peptide toolbox for developing highly stable and specific quantum dot-based peptide probes for imaging extracellular matrices and cells.

Multiplex fluorescence imaging plays a vital role in precision medicine for targeting complex diseases with diverse biomolecular signatures. Quantum dot (QD) probes with vibrant colors are promising candidates for multiplex imaging, but their stability and specificity are frequently compromised by the current tedious post-modification process. We have herein developed a robust and versatile host-guest peptide (HGP) toolbox for creating highly stable and specific QD-based peptide probes for imaging extracellular matrices and cells. The HGP system comprises a host peptide and a guest peptide with a shared sequence pattern of cysteine and negatively charged amino acids, allowing for QD stabilization and specificity towards targeted biomarkers. HGP has been demonstrated as a convenient one-step approach to construct hydrophilic QD-based peptide probes with superior stability under various conditions. Six multicolor HGP-modified QDs have been developed to specifically target extracellular matrix proteins such as collagen, laminin, and nidogen, as well as major cellular elements like the membrane, nucleus, and cytoplasm, providing an efficient tool for real-time monitoring of high-resolution interactions between cancer cells and the extracellular matrix. The HGP system represents a next-generation approach to developing QDs with unprecedented stability and specificity, holding great potential in multiplex imaging and precision medicine.