Longer Peptides Research Articles

Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model.

Protein and peptide aggregation is a ubiquitous phenomenon with implications in medicine, pharmaceutical industry, and materials science. An important issue in peptide aggregation is the molecular mechanism of aggregate nucleation and growth. In many experimental studies, sigmoidal kinetics curves show a clear lag phase ascribed to nucleation; however, experimental studies also show downhill kinetics curves, where the monomers decay continuously and no lag phase can be seen. In this work, we study peptide aggregation kinetics using a coarse-grained implicit solvent model introduced in our previous work. Our simulations explore the hypothesis that the interplay between interchain attraction and intrachain bending stiffness controls the aggregation kinetics and transient aggregate morphologies. Indeed, our model reproduces the aggregation modes seen in experiment: no observed aggregation, nucleated aggregation, and rapid downhill aggregation. We find that the interaction strength is the primary parameter determining the aggregation mode, whereas the stiffness is a secondary parameter modulating the transient morphologies and aggregation rates: more attractive and stiff chains aggregate more rapidly and the transient morphologies are more ordered. We also explore the effects of the initial monomer concentration and the chain length. As the concentration decreases, the aggregation mode shifts from downhill to nucleated and no-aggregation. This concentration effect is in line with an experimental observation that the transition between downhill and nucleated kinetics is concentration-dependent. We find that longer peptides can aggregate at conditions where short peptides do not aggregate at all. It supports an experimental observation that the elongation of a homopeptide, e.g., polyglutamine, can increase the aggregation propensity.

X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5.

C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.

Elucidation of the structure of supramolecular polymorphs in peptide nanofibres using Raman spectroscopy

AbstractPeptide fibre formation via molecular self‐assembly is a key step in a range of cellular processes and increasingly considered as an approach to produce supramolecular biomaterials. We previously demonstrated the self‐assembly of the tripeptide lysine‐dityrosine (KYY) as a substrate for the formation of proton‐conducting melanin‐like materials. Point based Raman scattering is one of several techniques which were used to characterise the secondary structure of the KYY nanofibre but as is often the case with this type of fibre, the spectra are rather complex and in addition there were variations in intensity between samples making interpretation difficult. Using Raman mapping we show that, as a drop of KYY in solution dries, it self‐assembles into two different fibre forms and the simpler spectra obtained for each are easier to interpret. The tyrosine amide marker bands, 852 and 828 cm−1, are present in both forms with similar intensities indicating the formation of a similar secondary structure in both forms with some stacking of the tyrosine rings. However, the tyrosine marker bands at 1614 and 1661 cm−1 vary considerably in intensity between the two forms. It is concluded that both forms consist of stacked polypeptide units joined by hydrogen bonds to form structures similar to β‐sheet structures in longer peptides. There are other clear differences such the large intensity difference in the lysine side chain band at 1330 cm−1 and the relative intensities of the bands at 982 and 1034 cm−1. These differences are attributed to changes in the conformation of tyrosine side chains causing different electron withdrawing effects on the ring.

MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism

BackgroundAccurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learning algorithms and mass spectrometry data have indeed showed improvement on the average predicting power for class I HLA-peptide interaction. However, their prediction performances show great variability over individual HLA alleles and peptides with different lengths, which is particularly the case for HLA-C alleles due to the limited amount of experimental data. To meet the increasing demand for attaining the most accurate HLA-peptide binding prediction for individual patient in the real-world clinical studies, more advanced deep learning framework with higher prediction accuracy for HLA-C alleles and longer peptides is highly desirable.ResultsWe present a pan-allele HLA-peptide binding prediction framework—MATHLA which integrates bi-directional long short-term memory network and multiple head attention mechanism. This model achieves better prediction accuracy in both fivefold cross-validation test and independent test dataset. In addition, this model is superior over existing tools regarding to the prediction accuracy for longer ligand ranging from 11 to 15 amino acids. Moreover, our model also shows a significant improvement for HLA-C-peptide-binding prediction. By investigating multiple-head attention weight scores, we depicted possible interaction patterns between three HLA I supergroups and their cognate peptides.ConclusionOur method demonstrates the necessity of further development of deep learning algorithm in improving and interpreting HLA-peptide binding prediction in parallel to increasing the amount of high-quality HLA ligandome data.

Unconventional Peptide Presentation by Classical MHC Class I and Implications for T and NK Cell Activation.

T cell-mediated immune recognition of peptides is initiated upon binding of the antigen receptor on T cells (TCR) to the peptide-MHC complex. TCRs are typically restricted by a particular MHC allele, while polymorphism within the MHC molecule can affect the spectrum of peptides that are bound and presented to the TCR. Classical MHC Class I molecules have a confined binding groove that restricts the length of the presented peptides to typically 8–11 amino acids. Both N- and C-termini of the peptide are bound within binding pockets, allowing the TCR to dock in a diagonal orientation above the MHC-peptide complex. Longer peptides have been observed to bind either in a bulged or zig-zag orientation within the binding groove. More recently, unconventional peptide presentation has been reported for different MHC I molecules. Here, either N- or C-terminal amino acid additions to conventionally presented peptides induced a structural change either within the MHC I molecule that opened the confined binding groove or within the peptide itself, allowing the peptide ends to protrude into the solvent. Since both TCRs on T cells and killer immunoglobulin receptors on Natural Killer (NK) cells contact the MHC I molecule above or at the periphery of the peptide binding groove, unconventionally presented peptides could modulate both T cell and NK cell responses. We will highlight recent advances in our understanding of the functional consequences of unconventional peptide presentation in cellular immunity.

Crown ethers as shift reagents in peptide epimer differentiation \u2013conclusions from examination of ac-(H)FRW-NH2 petide sequences

Crown ethers with different ring sizes and substituents (18-crown-6, dibenzo-18-crown-6, dicyclohexano-18-crown-6, a chiral tetracarboxylic acid-18-crown-6 ether, dibenzo-21-crown-7, and dibenzo-30-crown-10) were evaluated as shift reagents to differentiate epimeric model peptides (tri-and tetrapeptides) using ion mobility mass spectrometry (IM-MS). The stable associates of peptide epimers with crown ethers were detected and examined using traveling-wave ion mobility time-of-flight mass spectrometer (Synapt G2-S HDMS) equipped with an electrospray ion source. The overall decrease of the epimer separation upon crown ether complexation was observed. The increase of the effectiveness of the microsolvation of a basic moiety - guanidine or ammonium group in the peptide had no or little effect on the epimer discrimination. Any increase of the epimer separation, which referred to the specific association mode between crown substituents and a given peptide sequence, was drastically reduced for the longer peptide sequence (tetrapeptide). The obtained results suggest that the application of the crown ethers as shift reagents in ion mobility mass spectrometry is limited to the formation of complexes differing in stoichiometry rather than it refers to a specific coordination mode between a crown ether and a peptide molecule.

Antifungal and Antibiofilm Activities and the Mechanism of Action of Repeating Lysine-Tryptophan Peptides against Candida albicans.

The rapid increase in the emergence of antifungal-resistant Candida albicans strains is becoming a serious health concern. Because antimicrobial peptides (AMPs) may provide a potential alternative to conventional antifungal agents, we have synthesized a series of peptides with a varying number of lysine and tryptophan repeats (KWn-NH2). The antifungal activity of these peptides increased with peptide length, but only the longest KW5 peptide displayed cytotoxicity towards a human keratinocyte cell line. The KW4 and KW5 peptides exhibited strong antifungal activity against C. albicans, even under conditions of high-salt and acidic pH, or the addition of fungal cell wall components. Moreover, KW4 inhibited biofilm formation by a fluconazole-resistant C. albicans strain. Circular dichroism and fluorescence spectroscopy indicated that fungal liposomes could interact with the longer peptides but that they did not release the fluorescent dye calcein. Subsequently, fluorescence assays with different dyes revealed that KW4 did not disrupt the membrane integrity of intact fungal cells. Scanning electron microscopy showed no changes in fungal morphology, while laser-scanning confocal microscopy indicated that KW4 can localize into the cytosol of C. albicans. Gel retardation assays revealed that KW4 can bind to fungal RNA as a potential intracellular target. Taken together, our data indicate that KW4 can inhibit cellular functions by binding to RNA and DNA after it has been translocated into the cell, resulting in the eradication of C. albicans.

Identification of an immunogenic DKK1 long peptide for immunotherapy of human multiple myeloma

Dickkopf-1 (DKK1), broadly expressed by tumor cells from human multiple myeloma (MM) and other cancers but absent from most normal tissues, may be an ideal target for immunotherapy. Our previous studies have shown that DKK1 (peptide)-specific cytotoxic T lymphocytes can effectively lyse primary MM cells in vitro. To develop DKK1-based vaccines that can be easily and inexpensively made and used by all patients, we identified a DKK1 long peptide (LP), DKK13-76-LP, that contains 74 amino acids and epitopes that can potentially bind to all major MHC class I and II molecules. Using HLA-A*0201- and HLA-DR*4-transgenic mouse models, we found that DKK1-specific CD4+ and CD8+ T-cell responses, detected by DKK1 short peptide (P20 and P66v)-HLA-A*0201 tetramer staining and cytotoxic assay for CD8+ T cells or by carboxyfluorescein diacetate succinimidyl ester (CSFE) dilution and IFN-g secretion for CD4+ T cells, respectively, can be induced in vivo by immunizing mice with the DKK13-76-LP. In addition, DKK13-76-LP also induced anti-DKK1 humoral immunity in the transgenic mice and the DKK1 antibodies were functional. Finally, DKK13-76-LP stimulated human blood T cells ex vivo to generate DKK1-specific CD4+ and CD8+ T-cell responses from 8 out of 10 MM patients with different MHC backgrounds. The generated DKK1-specific CD8+ cells efficiently lysed autologous MM cells from these patients. Thus, these results confirm the immunogenicity of the DKK13-76-LP in eliciting DKK1-specific CD4+ and CD8+ T-cell responses in vitro and in vivo, and suggest that the DKK13-76-LP can be used for immunotherapy of MM and other cancers.

N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists.

Recently, it was reported that tetrapeptides cyclized via lactam bond between the amino terminus and a glutamic residue in position 4 (termed here N-lock) can nucleate helix formation in longer peptides. We applied such strategy to derive N-locked covalent BH3 peptides that were designed to selectively target the anti-apoptotic protein Bfl-1. The resulting agents were soluble in aqueous buffer and displayed a remarkable (low nanomolar) affinity for Bfl-1 and cellular activity. The crystal structure of the complex between such N-locked covalent peptide and Bfl-1 provided insights on the geometry of the N-locking strategy and of the covalent bond between the agent and Bfl-1.

Engineering uranyl-chelating peptides from NikR for electrochemical peptide-based sensing applications

We have, for the first time, designed three uranyl-chelating peptides by modeling after the uranyl binding pocket found in a mutated Ni(II)-dependent transcriptional repressor (NikR). All three thiolated and methylene blue (MB)-modified peptides, NikR-5, NikR-11, and NikR-15, contain the five core amino acids responsible for target recognition, but the two longer peptides have either one or two additional glycine residues in between the five amino acids. These three peptide probes were then used in the fabrication of electrochemical peptide-based (E-PB) uranyl ion (U(VI)) sensors, with the goal of elucidating the effects of the added glycine residues and probe flexibility on target recognition. The sensing mechanism is similar to other “signal-off” E-PB sensors, in which binding of the target rigidifies the probe, resulting in a decrease in the redox signal from the tethered MB label. Although all three sensors responded to U(VI), the NikR-15 sensor's behavior was irreproducible and thus precluded from the rest of the study. The NikR-11 sensor showed the largest response to U(VI), whereas the NikR-5 sensor showed higher specificity for U(VI). The limit of detection was 50 nM for both sensors, which is well below the U.S. Environmental Protection Agency maximum contaminant level for uranium. Both sensors were further tested and proven functional in a 50% synthetic aquifer sample. Overall, the NikR-11 sensor, fabricated with the 11-amino acid probe, is deemed the optimal design. Incorporating glycine residues is a strategic way to lengthen the peptide slightly to improve target binding. This simple yet versatile approach to recreating binding pockets on electrode surfaces can potentially be employed in the design of other E-PB and surface-based metal ion sensors.

Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that optimizes the peptide cargo of major histocompatibility class I (MHC-I) molecules and regulates adaptive immunity. It has unusual substrate selectivity for length and sequence, resulting in poorly understood effects on the cellular immunopeptidome. To understand substrate selection by ERAP1, we solved 2 crystal structures of the enzyme with bound transition-state pseudopeptide analogs at 1.68 Å and 1.72 Å. Both peptides have their N terminus bound at the active site and extend away along a large internal cavity, interacting with shallow pockets that can influence selectivity. The longer peptide is disordered through the central region of the cavity and has its C terminus bound in an allosteric pocket of domain IV that features a carboxypeptidase-like structural motif. These structures, along with enzymatic and computational analyses, explain how ERAP1 can select peptides based on length while retaining the broad sequence-specificity necessary for its biological function.

Influence of the production technology on kefir characteristics: Evaluation of microbiological aspects and profiling of phosphopeptides by LC-ESI-QTOF-MS/MS.

The influence of production technology, namely, temperature, pH and 2-step fermentation (back-slopping approach), on the microbiological characteristics and on the phosphopeptide profile of kefir obtained with kefir grains was investigated. The growth of yeasts, lactic acid bacteria (LAB) and acetic acetic bacteria (AAB) in both grains and kefir was affected by the incubation temperature and by the use of back-slopping. In particular, at 25°C the microbiota of kefir grains was mainly composed by LAB and yeasts, while at 18°C yeasts represented the dominant group in kefir. Back-slopping at 25°C determined a significant increase of AAB. A comprehensive characterization of potentially bioactive peptides, including caseino-phosphopeptides (CPPs), was performed, for the first time, in kefir obtained with kefir grains, using preliminary enrichment on hydroxyapatite followed by dephosphorylation and analysis by Liquid Chromatography-ElectroSpray Ionization-Quadrupole-Time of Flight-tandem mass spectrometry (LC-ESI-QTOF-MS/MS). As a result, seventy-three phosphopeptides, mostly arising from caseins (79% β-casein, 8% αs1-casein and 9% αs2-casein) and all including from three to five serine residues in their sequences, were identified. Seventy-one of them showed the typical motif "SerP-SerP-SerP-Glu-Glu", which is crucial for the ability of caseins to bind to minerals. Several peptides were observed, for the first time, from the 1-40 region of β-casein. As for the effect of production technology, phosphopeptide profiles of kefirs obtained at 25°C and 18°C were very similar, whereas kefir produced under acidic conditions showed a predominance of smaller peptides, suggesting a higher level of proteolysis. Conversely, kefir obtained through back-slopping at 25°C contained longer peptides, thus indicating a lower proteolytic activity and a poor reproducibility in the kefir phosphopeptide profile occurring when grains are reused.

Dual-Mode Electrochemical Assay of Prostate-Specific Antigen Based on Antifouling Peptides Functionalized with Electrochemical Probes and Internal References.

Sensitive and selective detection of target analytes in complex biological samples is currently a major challenge. Herein we constructed a dual-mode antifouling electrochemical sensing platform for the detection of prostate-specific antigen (PSA) based on two kinds of antifouling peptides functionalized with a graphene oxide-Fe3O4-thionine (GO-Fe3O4-Thi) probe and internal reference ferrocene (Fc), respectively. The longer peptide (Pep1) modified with the GO-Fe3O4-Thi probe was designed to contain a peptide sequence (HSSKLQK) capable of being recognized and cut by PSA. The GO-Fe3O4-Thi probe functions not only as a peroxidase mimick (GO-Fe3O4) but also works as an electrochemical probe due to the presence of thionine (Thi). The concentration of PSA can be measured through both the increase of differential pulse voltammetry (DPV) signal change of Thi and the decrease of chronoamperometry (CA) signal of the reduction of H2O2 electrocatalyzed by GO-Fe3O4. The shorter peptide (Pep2) was tagged with Fc, whose DPV signal remained constant and was independent of the presence of PSA, and it was used as an internal reference to ensure the reliability and accuracy of the measurement. The dual-mode PSA sensor exhibits a wide linear range from 5 pg/mL to 10 ng/mL, with low detection limits of 0.76 and 0.42 pg/mL through DPV and CA modes, respectively. More importantly, owing to the antifouling capability of the designed peptides, the biosensor performances remained operable even in human serum, indicating feasibility of the electrochemical biosensor for practical PSA quantification in complex samples.

A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site.

This paper presents the results of research on determining the optimal length of a peptide chain to effectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with different sequences were selected. Molecular modelling results of ligand docking with selected peptides were correlated with experimental results. The use of low-molecular synthetic peptides, instead of the whole protein, enabled the construction OBPPs-based biosensors. This work aims at developing a biomimetic piezoelectric OBPPs sensor for selective detection of octanal. Moreover, the research is concerned with the ligand binding affinity depending on different peptides’ chain lengths. The authors believe that the chain length can have a substantial influence on the type and effectiveness of peptide–ligand interaction. A confirmation of in silico investigation results is the correlation with the experimental results, which shows that the highest affinity to octanal is exhibited by the longest peptide (OBPP4 – KLLFDSLTDLKKKMSEC-NH2). We hypothesized that the binding of long chain aldehydes to the peptide, mimicking the binding site of HarmOBP7, induced a conformational change in the peptide deposited on a selected transducer. The constructed OBPP4-based biosensors were able to selectively bind octanal in the gas phase. It was also shown that the sensors were characterized by high selectivity with respect to octanal, as well as to acetaldehyde and benzaldehyde. The results indicate that the OBPP4 peptide, mimicking the binding domain in the Odorant Binding Protein, can provide new opportunities for the development of biomimicking materials in the field of odor biosensors.

A phase I study of the safety and immunogenicity of a multi-peptide personalized genomic vaccine in the adjuvant treatment of solid tumors and hematological malignancies.

e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic variations that occur during carcinogenesis and can be characterized via genetic sequencing and used to identify MTAs. We developed a platform for a fully-personalized MTA-based vaccine in the adjuvant treatment of solid and hematological malignancies. Methods: This is a single-arm, open label, proof-of-concept phase I study designed to test the safety and immunogenicity of Personalized Genomic Vaccine 001 (PGV001) that targets up to 10 predicted personal tumor neoantigens based on patient’s HLA profile (ClinicalTrials.gov: NCT02721043). Results: Patients who completed vaccination with PGV001_002 (head and neck squamous cell cancer) received 10 doses of vaccine comprising 10 long peptides (LP) combined with poly-ICLC (toll-like receptor-3 agonist) intradermally. Vaccine-induced T-cell responses were determined at weeks 0 and 27 (before and after treatment, respectively), ex vivo by interferon (IFN)-g enzyme-linked immunospot assay and after expansion by intracellular cytokine staining. Overlapping 15-mer peptides (OLPs) spanning the entirety of each LP and 9-10-mer peptides corresponding to each predicted class I epitope (Min) were pooled. Ex vivo responses to these peptide pools were undetectable at week 0 but were evident at week 27 against 2 OLPs out of 10 (20%) and in 5 Min out of 10 (50%). After in vitro expansion, neoantigen-specific CD4+ and CD8+ T-cell responses were found in 5 out of 10 pooled peptides (50%). 7 out of 10 (70%) epitopes elicited polyfunctional T-cell responses (secretion of INF-g, TNF-a, and/or IL-2) from either CD4+ or CD8+ T cells. Conclusions: The PGV001 vaccine in our first patient showed both safety and immunogenicity, eliciting CD4+ and CD8+ responses to the vaccine peptides. As we enroll additional patients in this clinical trial, and perform deeper phenotyping of their tumor-reactive T cells, we will learn the determinants necessary for the successful generation of MTA-based vaccines, while informing future immunotherapeutic approaches and rational combinations. Clinical trial information: NCT02721043.

Optimizing PLG nanoparticle-peptide delivery platforms for transplantation tolerance using an allogeneic skin transplant model

A robust regimen for inducing allogeneic transplantation tolerance involves pre-emptive recipient treatment with donor splenocytes (SP) rendered apoptotic by 1-ethyl-3-(3′-dimethylaminopropyl)-carbodiimide(ECDI) treatment. However, such a regimen is limited by availability of donor cells, cost of cell procurement, and regulatory hurdles associated with cell-based therapies. Nanoparticles (NP) delivering donor antigens are a promising alternative for promoting transplantation tolerance. Here, we used a B6.C-H-2bm12(bm12) to C57BL/6(B6) skin transplant model involving a defined major histocompatibility antigen mismatch to investigate design parameters of poly(lactide-co-glycolide) (PLG) NPs delivering peptides containing the donor antigen for optimizing skin allograft survival. We showed that an epitope-containing short peptide (P1) was more effective than a longer peptide (P2) at providing graft protection. Importantly, the NP and P1 complex (NP-ECDI-P1) resulted in a significant expansion of graft-infiltrating Tregs. Interestingly, in comparison to donor ECDI-SP that provided indefinite graft protection, NP-ECDI-P1 targeted different splenic phagocytes and skin allografts in these recipients harbored significantly more graft-infiltrating CD8+IFN-γ+ cells. Collectively, the current study provides initial engineering parameters for a cell-free and biocompatible NP-peptide platform for transplant immunoregulation. Moreover, it also provides guidance to future NP engineering endeavors to recapitulate the effects of donor ECDI-SP as a goal for maximizing tolerance efficacy of NP formulations.

Plasmid DNA Delivery Using Cell-Penetrating Peptide Foldamers Composed of Arg-Arg-Aib Repeating Sequences.

Arginine (Arg)-rich cell-penetrating peptides (CPPs) are promising tools for plasmid DNA (pDNA) delivery. α-Aminoisobutyric acid (Aib) is known to stabilize peptide helical secondary structures and has been used as a building block for foldamers. In the current study, we prepared Aib CPP foldamers, (Arg-Arg-Aib)n (n = 1-6) and examined their pDNA transfection abilities. Transfection efficiencies of peptide/pDNA complexes are dependent on peptide chain length, with longer peptides (n ≥ 4) exhibiting better transfection abilities than an Arg nonapeptide. Furthermore, Aib CPP foldamers achieve prolonged transfection abilities compared with commercially available transfection reagents, which is probably because of the high resistance of the peptides to enzymatic degradation, thereby protecting the encapsulated pDNA for a long period. The obtained results demonstrated promising features of Aib CPP foldamers as pDNA delivery carriers.

Separation and identification of peptides in hydrolysed protein extracts from edible macroalgae by HPLC-ESI-QTOF/MS

Macroalgae contain significant amounts of high-quality proteins which, because of their structural diversity, contain a range of yet undiscovered peptides within their primary structures. In this work, an analytical methodology was developed for the separation and identification of peptides present in protein hydrolysates from three different edible macroalgae used for human consumption (Saccharina latissima (brown macroalga), Codium spp. (green macroalga), and Mastocarpus stellatus (red macroalga)). The extraction of aqueous and alkaline soluble proteins was carried out followed by their precipitation with HCl or acetone. The protein extracts obtained were submitted to enzymatic digestion with alcalase and subsequently analyzed by reversed-phase high-performance liquid chromatography-quadrupole-time-of flight mass spectrometry (RP-HPLC-QTOF/MS) and de novo sequencing tool to separate and identify different short chain peptides. Thirty-seven peptides were identified in the hydrolysed protein extracts from the three macroalgae, five of them being common in brown and red macroalgae. After checking against BIOPEP database, several sequenced peptides were found within longer peptides with potential antibacterial activity. Any of the identified peptides had previously been identified in macroalgae.

Structures and activities of widely conserved small prokaryotic aminopeptidases‐P clarify classification of M24B peptidases

M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases.

Rapid and low-cost multiplex synthesis of chemokine analogs

Peptides represent a promising source of new medicines, but improved technologies are needed to facilitate discovery and optimization campaigns. In particular, longer peptides with multiple disulfide bridges are challenging to produce, and producing large numbers of structurally related variants is dissuasively costly and time-consuming. The principal cost and time drivers are the multiple column chromatography purification steps that are used during the multistep chemical synthesis procedure, which involves both ligation and oxidative refolding steps. In this study, we developed a method for multiplex parallel synthesis of complex peptide analogs in which the structurally variant region of the molecule is produced as a small peptide on a 384-well synthesizer with subsequent ligation to the longer, structurally invariant region and oxidative refolding carried out in-well without any column purification steps. To test the method, we used a panel of 96 analogs of the chemokine RANTES (regulated on activation normal T cell expressed and secreted)/CCL5 (69 residues, two disulfide bridges), which had been synthesized using standard approaches and characterized pharmacologically in an earlier study. Although, as expected, the multiplex method generated chemokine analogs of lower purity than those produced in the original study, it was nonetheless possible to closely match the pharmacological attributes (anti-HIV potency, capacity to elicit G protein signaling, and capacity to elicit intracellular receptor sequestration) of each chemokine analog to reference data from the earlier study. This rapid, low-cost approach has the potential to support discovery and optimization campaigns based on analogs of other chemokines as well as those of other complex peptide and small protein targets of a similar size.