Peptide Anchor Research Articles

HLA‐DRB1 molecules and the presentation of anchor peptides from RhD, RhCE, and KEL proteins

Antigens from the Rh and Kell systems are recognized as the most immunogenic in clinical practice. This study evaluated the possible molecular mechanisms involved in the interaction of antigenic peptides with the DRB1 molecules, which help to explain the high frequency of anti-K and association of D + C antibodies in transfusion and incompatible pregnancy. We included 201 patients with antibodies against antigens from the Rh and Kell systems and compare them with 174,015 controls. HLA-DRB1 genotyping and in silico analysis were performed. The NetMHCIIpan software was used to identify RhD-, RhCE-, and KEL-derived anchor peptides that bind to DRB1 molecules. HLA-DRB1*15 is associated with an increased risk of D, C, E, and K alloimmunization, while the HLA-DRB1*01 and *12 alleles are overrepresented in patients with anti-C and anti-D, respectively. In silico analysis showed that three polymorphic points (60I, 68S, and 103S) common to C and D antigens can be presented by several DRB1 molecules, including DRB1*15:01. The DRB1*09:01 molecule, although not showing statistical significance, was able to interact strongly with almost all five anchor peptides from the sequence containing the polymorphic determinants of E antigen, except 217-WMFWPSVNS-225. The DRB1*15 molecule has specific physicochemical characteristics in residues 11P and 13R in the P4 pocket that can favor the response to various antigenic peptides. Anti-K alloimmunization is unrestricted for interaction with specific DRB1 molecules, which suggests that almost all individuals in our population have DRB1 molecules capable of binding to KEL-derived anchor peptides and produce anti-K when stimulated.

Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans.

Pathogens deploy a wide range of pathogenicity factors, including a plethora of proteases, to modify host tissue or manipulate host defences. Metalloproteases (MPs) have been implicated in virulence in several animal and plant pathogens. Here we investigated the repertoire of MPs in 46 stramenopile species including 37 oomycetes, 5 diatoms, and 4 brown algae. Screening their complete proteomes using hidden Markov models (HMMs) trained for MP detection resulted in over 4,000 MPs, with most species having between 65 and 100 putative MPs. Classification in clans and families according to the MEROPS database showed a highly diverse MP repertoire in each species. Analyses of domain composition, orthologous groups, distribution, and abundance within the stramenopile lineage revealed a few oomycete‐specific MPs and MPs potentially related to lifestyle. In‐depth analyses of MPs in the plant pathogen Phytophthora infestans revealed 91 MPs, divided over 21 protein families, including 25 MPs with a predicted signal peptide or signal anchor. Expression profiling showed different patterns of MP gene expression during pre‐infection and infection stages. When expressed in leaves of Nicotiana benthamiana, 12 MPs changed the sizes of lesions caused by inoculation with P. infestans; with 9 MPs the lesions were larger, suggesting a positive effect on the virulence of P. infestans, while 3 MPs had a negative effect, resulting in smaller lesions. To the best of our knowledge, this is the first systematic inventory of MPs in oomycetes and the first study pinpointing MPs as potential pathogenicity factors in Phytophthora.

Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner

Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.

Anchor peptides promote degradation of mixed plastics for recycling.

Resource stewardship and sustainable use of natural resources is mandatory for a circular plastic economy. The discovery of microbes and enzymes that can selectively degrade mixed-plastic waste enables to recycle plastics. Knowledge on how to achieve efficient and selective enzymatic plastic degradation is a key prerequisite for biocatalytic recycling of plastics. Wild-type natural polymer degrading enzymes such as cellulases pose often selective non-catalytic binding domains that facilitate a targeting and efficient degradation of polymeric substrates. Recently identified polyester hydrolases with synthetic polymer degrading activities, however, lack in general such selective domains. Inspired by nature, we herein report a protocol for the identification and engineering of anchor peptides which serve as non-catalytic binding domains specifically toward synthetic plastics. The identified anchor peptides hold the promise to be fused to known plastic degrading enzymes and thereby enhance the efficiency of biocatalytic plastic recycling processes.

Progenitor cell-derived exosomes endowed with VEGF plasmids enhance osteogenic induction and vascular remodeling in large segmental bone defects.

Large segmental bone regeneration remains a great challenge due to the lack of vascularization in newly formed bone. Conventional strategies primarily combine bone scaffolds with seed cells and growth factors to modulate osteogenesis and angiogenesis. Nevertheless, cell-based therapies have some intrinsic issues regarding immunogenicity, tumorigenesis, bioactivity and off-the-shelf transplantation. Exosomes are nano-sized (50-200 nm) extracellular vesicles with a complex composition of proteins, nucleic acids and lipids, which are attractive as therapeutic nanoparticles for disease treatment. Exosomes also have huge potential as desirable drug/gene delivery vectors in the field of regenerative medicine due to their excellent biocompatibility and efficient cellular internalization.Methods: We developed a cell-free tissue engineering system using functional exosomes in place of seed cells. Gene-activated engineered exosomes were constructed by using ATDC5-derived exosomes to encapsulate the VEGF gene. The specific exosomal anchor peptide CP05 acted as a flexible linker and effectively combined the engineered exosome nanoparticles with 3D-printed porous bone scaffolds.Results: Our findings demonstrated that engineered exosomes play dual roles as an osteogenic matrix to induce the osteogenic differentiation of mesenchymal stem cells and as a gene vector to controllably release the VEGF gene to remodel the vascular system. In vivo evaluation further verified that the engineered exosome-mediated bone scaffolds could effectively induce the bulk of vascularized bone regeneration.Conclusion: In our current work, we designed specifically engineered exosomes based on the requirements of vascularized bone repair in segmental bone defects. This work simultaneously illuminates the potential of functional exosomes in acellular tissue engineering.

Anchor peptides as innovative adjuvants reduce rain wash-off, but do not impair photosynthetic activity or cause oxidative damage in apple leaves

Anchor peptides as innovative adjuvants reduce rain wash-off, but do not impair photosynthetic activity or cause oxidative damage in apple leaves

Ratiometric antifouling electrochemiluminescence biosensor based on bi-functional peptides and low toxic quantum dots

It is a great challenge to detect the target selectively and accurately in complex biological samples. A ratiometric signal amplification strategy based on antifouling peptide is proposed to detect thrombin (TB) in this work. The electrode is modified with conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) and Au@Luminol. Then the bi-functional peptide anchors to the modified electrode and captures the low toxic electrochemiluminescence (ECL) probe. The bi-functional peptide includes a new antifouling sequence (DRDRDRDR) and a TB recognizable sequence (SGRPVLG), while the former can greatly reduce the non-specific adsorption in complex samples and the latter can be cleaved by TB. The new self-enhanced luminescence probe labeled as PAMAM-QDs is composed of low toxic and water-soluble CuInZnS/ZnS quantum dots (CIZS/ZnS QDs) and polyamidoamine (PAMAM) via amide bonds. Concentration of TB can be obtained via the ratio of the signals of ECLQDs/ECLAu@Luminol accurately and sensitively. The ECL biosensor with the detection line 1.82 fM can work from 10 fM to 1 nM. Thanks to the antifouling property of the designed peptide and the amplification of the new ECL probe, the biosensor can be used for quantifying TB in practical complex samples with high selectivity and sensitivity.

Recombinant Lactococcus Lactis Displaying Omp31 Antigen of Brucella melitensis Can Induce an Immunogenic Response in BALB/c Mice.

Since Brucella infection mostly occurs through the mucosal surfaces, immune response induced by vaccine that is delivered by a way of mucosal route can be drastically enhanced to control the brucellosis. Omp31is the major outer membrane protein of Brucella, and is considered as a protective antigen against Brucella infection. Accordingly, Lactococcus lactis has been used as an antigen-delivering vector to develop a vaccine-induced mucosal response for having a safer vaccination against brucellosis. A designed omp31 gene fused to the usp45 signal peptide and M6 cell wall anchor was sub cloned in the pNZ7021 expression vector, and a recombinant L. lactis displaying Omp31 was constructed. Omp31 protein expression was confirmed using Western blotting and immunofluorescence analysis. Animals were orally and intraperitoneally immunized with live or killed L. lactis expressing Omp31, respectively. The humoral and cellular immune responses were evaluated by measuring the specific cytokines and antibodies. sIgA, serum IgA, IgM, and total IgG antibodies significantly increased in the mice immunized with live recombinant L. lactis expressing Omp31 and also serum IgM, and total IgG antibodies significantly increased in mice immunized with killed recombinant L. lactis expressing Omp31. Among IgG subtypes, IgG2a response was significantly higher in both groups compared to IgG1. In mice groups immunized with recombinant L. lactis, the IFN-γ and IL-10 level elevated; however, there was no change in the level of IL-4. These results indicated that recombinants L. lactis induce both humoral and cellular immune responses in mice, and also vaccines based on L. lactis-derived live carriers are promising interventions against Brucella melitensis infections.

Organic dye anchor peptide conjugates as an advanced coloring agent for polypropylene yarn

Polypropylene as one of the world's top commodity polymers is also widely used in the textile industry. However, its non-polar nature and partially crystalline structure significantly complicate the process of industrial coloring of polypropylene. Currently, textiles made of polypropylene or with a significant proportion of polypropylene are dyed under quite harsh conditions, including the use of high pressures and temperatures, which makes this process energy intensive. This research presents a three-step synthesis of coloring agents, capable of adhering onto synthetic polypropylene yarns without harsh energy-consuming conditions. This is possible by encapsulation of organic pigments using trimethoxyphenylsilane, introduction of surface double bonds via modification of the silica shell with trimethoxysilylpropylmethacrylate and final attachment of highly adhesive anchor peptides using thiol-ene chemistry. We demonstrate the applicability of this approach by dyeing polypropylene yarns in a simple process under ambient conditions after giving a step-by-step guide for the synthesis of these new dyeing agents. Finally, the successful dyeing of the yarns is visualized, and its practicability is discussed.

Mesoporous Silica-Coated Gold Nanorods with Designable Anchor Peptides for Chemo-Photothermal Cancer Therapy

The incorporation of bioactive peptides often creates unprecedented opportunities in design of hierarchical nanocomposites, in this contribution we employed mesoporous silica-coated gold nanorods (...

Alarmin-painted exosomes elicit persistent antitumor immunity in large established tumors in mice

Treating large established tumors is challenging for dendritic cell (DC)-based immunotherapy. DC activation with tumor cell-derived exosomes (TEXs) carrying multiple tumor-associated antigen can enhance tumor recognition. Adding a potent adjuvant, high mobility group nucleosome-binding protein 1 (HMGN1), boosts DCs’ ability to activate T cells and improves vaccine efficiency. Here, we demonstrate that TEXs painted with the functional domain of HMGN1 (TEX-N1ND) via an exosomal anchor peptide potentiates DC immunogenicity. TEX-N1ND pulsed DCs (DCTEX-N1ND) elicit long-lasting antitumor immunity and tumor suppression in different syngeneic mouse models with large tumor burdens, most notably large, poorly immunogenic orthotopic hepatocellular carcinoma (HCC). DCTEX-N1ND show increased homing to lymphoid tissues and contribute to augmented memory T cells. Importantly, N1ND-painted serum exosomes from cancer patients also promote DC activation. Our study demonstrates the potency of TEX-N1ND to strengthen DC immunogenicity and to suppress large established tumors, and thus provides an avenue to improve DC-based immunotherapy.

Customizable Multiplex Antibody Array Immunoassays with Attomolar Sensitivities.

We have developed a customizable contact printed multiplex immunoassay capable of simultaneously measuring up to five analytes with attomolar sensitivities. This enzyme-linked immunosorbent assay (ELISA) was based on spotting different antibodies in a circular pattern at the bottom of a microtiter plate well. Unlike traditional antibody printing for ELISA that prints a capture antibody specific to a target of interest, in this ELISA we printed unique "anchor" antibodies at the well surface, each having a high affinity for a specific peptide target. By coupling each peptide to a unique assay capture antibody, this array of anchor antibodies enabled a customizable contact printed multiplex immunoassay workflow. As a proof of concept, we developed a 5-plex assay measuring interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), interleukin 22 (IL-22), and tumor necrosis factor alpha (TNF-α). Measurements of these five analytes in serum and plasma correlated well between the method utilizing the anchor antibodies and peptides and the traditional capture antibody printing approach, with r2 values of 0.99, 0.93, 0.99, 0.96, and 0.75 for IL-5, IL-6, IL-10, IL-22, and TNFα, respectively. This approach makes customizable multiplex ultrasensitive ELISA available to laboratories without access to the precision printing instrumentation and will be useful for antibody screening, custom assay development, biomarker detection, and protein profiling for diagnostic applications.

Multifunctional Heterogeneous Carbon Nanotube Nanocomposites Assembled by DNA-Binding Peptide Anchors.

Although carbon nanotubes (CNTs) are remarkable materials with many exceptional characteristics, their poor chemical functionality limits their potential applications. Herein, a strategy is proposed for functionalizing CNTs, which can be achieved with any functional group (FG) without degrading their intrinsic structure by using a deoxyribonucleic acid (DNA)-binding peptide (DBP) anchor. By employing a DBP tagged with a certain FG, such as thiol, biotin, and carboxyl acid, it is possible to introduce any FG with a controlled density on DNA-wrapped CNTs. Additionally, different types of FGs can be introduced on CNTs simultaneously, using DBPs tagged with different FGs. This method can be used to prepare CNT nanocomposites containing different types of nanoparticles (NPs), such as Au NPs, magnetic NPs, and quantum dots. The CNT nanocomposites decorated with these NPs can be used as reusable catalase-like nanocomposites with exceptional catalytic activities, owing to the synergistic effects of all the components. Additionally, the unique DBP-DNA interaction allows the on-demand detachment of the NPs attached to the CNT surface; further, it facilitates a CNT chirality-specific NP attachment and separation using the sequence-specific programmable characteristics of oligonucleotides. The proposed method provides a novel chemistry platform for constructing new functional CNTs suitable for diverse applications.

Rapid and Robust Coating Method to Render Polydimethylsiloxane Surfaces Cell-Adhesive.

Polydimethylsiloxane (PDMS) is a synthetic material with excellent properties for biomedical applications because of its easy fabrication method, high flexibility, permeability to oxygen, transparency, and potential to produce high-resolution structures in the case of lithography. However, PDMS needs to be modified to support homogeneous cell attachments and spreading. Even though many physical and chemical methods, like plasma treatment or extracellular matrix coatings, have been developed over the last decades to increase cell-surface interactions, these methods are still very time-consuming, often not efficient enough, complex, and can require several treatment steps. To overcome these issues, we present a novel, robust, and fast one-step PDMS coating method using engineered anchor peptides fused to the cell-adhesive peptide sequence (glycine-arginine-glycine-aspartate-serine, GRGDS). The anchor peptide attaches to the PDMS surface predominantly by hydrophobic interactions by simply dipping PDMS in a solution containing the anchor peptide, presenting the GRGDS sequence on the surface available for cell adhesion. The binding performance and kinetics of the anchor peptide to PDMS are characterized, and the coatings are optimized for efficient cell attachment of fibroblasts and endothelial cells. Additionally, the applicability is proven using PDMS-based directional nanotopographic gradients, showing a lower threshold of 5 μm wrinkles for fibroblast alignment.

Biocatalyst Immobilization by Anchor Peptides on an Additively Manufacturable Material

Additive manufacturing refers to manufacturing methods, which are being used to build up three-dimensional (3D) structures by adding a certain material stepwise onto a support. Nowadays, these manufacturing methods can be more material- and cost-efficient compared to conventional methods and allowing the defined production of a wide variety of 3D structures using computer aided design (CAD). A broad range of materials can be additively manufactured (AM) resulting in specific properties and highly diverse structures making them promising matrices for the utilization as enzyme carriers. The variety of materials offers the possibility to select materials with properties needed for particular biocatalytic processes. This is especially true for hybrid reactor concepts where multiple operations, including catalytic reactions and downstream processes, are combined into a single apparatus. For the enzymatic decarboxylation of ferulic acid, polyethylene terephthalate (PET) has been chosen as an additively manufacturable carrier material for the immobilization of phenolic acid decarboxylase (PAD) from Mycobacterium columbiense. The genetic fusion of PAD with anchor peptides enabled the adsorptive immobilization on PET. Starting from an immobilizate activity of 0.39 ± 0.19 U m–2 and a conversion of 19.2 ± 3.7% after 2 h the optimization of the peptide and spacer sequence between anchor peptide and PAD resulted in immobilizates with activities up to 1.80 ± 0.41 U m–2 and conversions of 59.9 ± 3.9% after 2 h. Moreover, within this study integrating an in situ product removal, enabled by an extraction with n-heptane, the altering of surface hydrophobicity of PET and a conversion of 88.0 ± 3.8% after 2 h could be observed.

Release of Fragrances from Cotton Functionalized with Carbohydrate-Binding Module Proteins.

Perspiration as a response to daily activity and physical exercise results in unpleasant odors that cause social unrest and embarrassment. To tackle it, functional textiles incorporating fragrances could be an effective clothing deodorizing product. This work presents two strategies for the release of β-citronellol from functionalized cotton with carbohydrate-binding module (CBM)-based complexes (OBP::GQ20::CBM/β-citronellol-approach 1 and CBM::GQ20::SP-DS3-liposome/β-citronellol-approach 2). CBM from Cellulomonas fimi was fused with the odorant-binding protein (OBP::GQ20::CBM) and with an anchor peptide with affinity to the liposome membrane (CBM::GQ20::SP-DS3). In approach 1, OBP fusion protein served as a fragrance container, whereas in approach 2, the fragrance was loaded into liposomes with a higher cargo capacity. The two strategies showed a differentiated β-citronellol release profile triggered by an acidic sweat solution. OBP::GQ20::CBM complex revealed a fast release (31.9% and 25.8% of the initial amount, after 1.5 and 24 h of exposure with acidic sweat solution, respectively), while the CBM::GQ20::SP-DS3-liposome complex demonstrated a slower and controlled release (5.9% and 10.5% of the initial amount, after 1.5 and 24 h of exposure with acidic sweat solution, respectively). Both strategies revealed high potential for textile functionalization aimed at controlled release of fragrances. The OBP::GQ20::CBM/β-citronellol complex is ideal for applications requiring fast release of a high amount of fragrance, whereas the CBM::GQ20::SP-DS3-liposome/β-citronellol complex is more suitable for prolonged and controlled release of a lower amount of β-citronellol.

TCR-induced alteration of primary MHC peptide anchor residue.

The HLA‐A*02:01‐restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T‐cells‐1 (MART‐1) protein, represents one of the best‐studied tumor associated T‐cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA‐A*02:01 and TCRs from clinically relevant T‐cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5‐HLA‐A*02:01‐AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide–MHC anchoring. This “flexing” at the TCR–peptide–MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well‐studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.

Folate receptor-specific cell-cell adhesion by using a folate-modified peptide-based anchor

We report here a folate-modified membrane anchor for cell surface modification to induce cell adhesion to target cells. The membrane anchor region, which was consisted of cationic lysine residues and palmitoyl group-modified residues, was modified with folate through an oligoethlene glycol linker. The peptide anchor was modified on to the cell membrane by using β-cyclodextrin as a solubilizer of the peptide anchor. After modification, the peptide anchor disappeared from the cell membrane via endocytotic uptake or dissociation from the cell membrane. However, the endocytosed peptide was represented on the cell surface via recycling endosome pathway. The obtained folate-modified cells successfully adhered on to target cells which expressed folate receptor α via ligand-receptor specific interaction and adhesion continued at least 4 hours.

Releasing the concept of HLA-allele specific peptide anchors in viral infections: A non-canonical naturally presented human cytomegalovirus-derived HLA-A*24:02 restricted peptide drives exquisite immunogenicity.

T‐cell receptors possess the unique ability to survey and respond to their permanently modified ligands, self HLA‐I molecules bound to non‐self peptides of various origin. This highly specific immune function is impaired following hematopoietic stem cell transplantation (HSCT) for a timespan of several months needed for the maturation of T‐cells. Especially, the progression of HCMV disease in immunocompromised patients induces life‐threatening situations. Therefore, the need for a new immune system that delivers vital and potent CD8+ T‐cells carrying TCRs that recognize even one human cytomegalovirus (HCMV) peptide/HLA molecule and clear the viral infection long term becomes obvious. The transcription and translation of HCMV proteins in the lytic cycle is a precisely regulated cascade of processes, therefore, it is a highly sensitive challenge to adjust the exact time point of HCMV‐peptide recruitment over self‐peptides. We utilized soluble HLA technology in HCMV‐infected fibroblasts and sequenced naturally sHLA‐A*24:02 presented HCMV‐derived peptides. One peptide of 14 AAs length derived from the IE2 antigen induced the strongest T‐cell responses; this peptide can be detected with a low ranking score in general peptide prediction databanks. These results highlight the need for elaborate and HLA‐allele specific peptide selection.

Bio‐Electrosynthesis of Vectorially Imprinted Polymer Nanofilms for Cytochrome P450cam

AbstractA new approach for synthesizing a “vectorially” imprinted polymer (VIP) is presented for the microbial cytochrome P450cam enzyme. A surface attached binding motif of a natural reaction partner of the target protein, putidaredoxin (Pdx), is the anchor to the underlying transducer. The 15 amino acid peptide anchor, which stems from the largest continuous amino acid chain within the binding site of Pdx was modified: (i) internal cysteines were replaced by serines to prevent disulfide bond formation; (ii) 2 ethylene glycol units were attached to the N‐terminus as a spacer region; and (iii) an N‐terminal cysteine was added to allow the immobilization on the gold electrode surface. Immobilization on GCE was achieved via an N‐(1‐pyrenyl)maleimide (NPM) cross‐linker. In this way oriented immobilization of P450cam was accomplished by binding it to a peptide‐modified gold or glassy carbon electrode (GCE) prior to the electrosynthesis of a polymer nanofilm around the immobilized target. This VIP nanofilm enabled reversible oriented docking of P450cam as it is indicated by the catalytic oxygen reduction via direct electron transfer between the enzyme and the underlying electrode. Catalysis of oxygen reduction by P450cam bound to the VIP‐modified GCE was used to measure rebinding to the VIP. The “mild” coupling of an oxidoreductase with the electrode may be appropriate for realizing electrode‐driven substrate conversion by instable P450 enzymes without the need of NADPH co‐factor.