In Silico Derivation of HLA-Specific Alloreactivity Potential from Whole Exome Sequencing of Stem Cell Transplant Donors and Recipients: Understanding the Quantitative Immuno-biology of Allogeneic Transplantation

Donor T cell mediated graft vs. host effects may result from the aggregate alloreactivity to minor histocompatibility antigens (mHA) presented by the HLA in each donor-recipient pair (DRP) undergoing stem cell transplantation (SCT). Whole exome sequencing has demonstrated extensive nucleotide sequence variation in HLA-matched DRP. Non-synonymous single nucleotide polymorphisms (nsSNPs) in the GVH direction (polymorphisms present in recipient and absent in donor) were identified in 4 HLA-matched related and 5 unrelated DRP. The nucleotide sequence flanking each SNP was obtained utilizing the ANNOVAR software package. All possible nonameric-peptides encoded by the non-synonymous SNP were then interrogated in-silico for their likelihood to be presented by the HLA class I molecules in individual DRP, using the Immune-Epitope Database (IEDB) SMM algorithm. The IEDB-SMM algorithm predicted a median 18,396 peptides/DRP which bound HLA with an IC50 of <500nM, and 2254 peptides/DRP with an IC50 of <50nM. Unrelated donors generally had higher numbers of peptides presented by the HLA. A similarly large library of presented peptides was identified when the data was interrogated using the Net MHCPan algorithm. These peptides were uniformly distributed in the various organ systems. The bioinformatic algorithm presented here demonstrates that there may be a high level of minor histocompatibility antigen variation in HLA-matched individuals, constituting an HLA-specific alloreactivity potential. These data provide a possible explanation for how relatively minor adjustments in GVHD prophylaxis yield relatively similar outcomes in HLA matched and mismatched SCT recipients.Comment: Abstract: 235, Words: 6422, Figures: 7, Tables: 3, Supplementary figures: 2, Supplementary tables:

Identification of hepta-histidine as a candidate drug for Huntington's disease by in silico-in vitro- in vivo-integrated screens of chemical libraries.

We identified drug seeds for treating Huntington's disease (HD) by combining in vitro single molecule fluorescence spectroscopy, in silico molecular docking simulations, and in vivo fly and mouse HD models to screen for inhibitors of abnormal interactions between mutant Htt and physiological Ku70, an essential DNA damage repair protein in neurons whose function is known to be impaired by mutant Htt. From 19,468 and 3,010,321 chemicals in actual and virtual libraries, fifty-six chemicals were selected from combined in vitro-in silico screens; six of these were further confirmed to have an in vivo effect on lifespan in a fly HD model, and two chemicals exerted an in vivo effect on the lifespan, body weight and motor function in a mouse HD model. Two oligopeptides, hepta-histidine (7H) and Angiotensin III, rescued the morphological abnormalities of primary neurons differentiated from iPS cells of human HD patients. For these selected drug seeds, we proposed a possible common structure. Unexpectedly, the selected chemicals enhanced rather than inhibited Htt aggregation, as indicated by dynamic light scattering analysis. Taken together, these integrated screens revealed a new pathway for the molecular targeted therapy of HD

The antigenic index: a novel algorithm for predicting antigenic determinants

In this paper, we introduce a computer algorithm which can be used to predict the topological features of a protein directly from its primary amino acid sequence. The computer program generates values for surface accessibility parameters and combines these values with those obtained for regional backbone flexibility and predicted secondary structure. The output of this algorithm, the antigenic index, is used to create a linear surface contour profile of the protein. Because most, if not all, antigenic sites are located within surface exposed regions of a protein, the program offers a reliable means of predicting potential antigenic determinants. We have tested the ability of this program to generate accurate surface contour profiles and predict antigenic sites from the linear amino acid sequences of well-characterized proteins and found a strong correlation between the predictions of the antigenic index and known structural and biological data

Identification of novel bioactive proteins and their produced oligopeptides from Torreya grandis nuts using proteomic based prediction

Torreya grandis nut is a chief functional food in China consumed for centuries. Besides its rich protein composition, increasing studies are now focusing on T. grandis functional proteins that have not yet identified. In this study, liquid chromatography coupled with mass spectrometry detection of smaller and major proteins, revealed that the major peptide was 36935.00 Da. Proteome sequencing annotated 142 proteins in total. Bioactive proteins such as defensin 4 was annotated and its anti-microbial function was verified. Finally, functional oligopeptides were predicted by searching sequences of digested peptides in databases. Ten group of oligopeptides were suggested to exhibit antioxidant, Angiotensin-converting enzyme inhibition, anti-inflammatory. The predicted antioxidant activity was experimentally validated. It is interesting that a peptide GYCVSDNN digested from defensin 4 showed antioxidant activity. This study reports novel functional peptides from T. grandis nuts that have not been isolated and/or included as functional ingredients in nutraceuticals and in food industry

Challenges in the quantitation of the naturally generated bioactive peptides in processed meats

[EN] Background: The final characteristics of processed meats depend on many factors but one of the most important is the intense proteolysis occurred in muscle proteins due to the action of endogenous enzymes in dry-cured ham, and also microbial peptidases in the case of dry-fermented meats, that not only affects taste and flavour but also the generation of bioactive peptides. Scope and approach: In this review main difficulties in the identification of bioactive peptides in processed meats have been described. This study highlights the novel strategies used during the last years to identify naturally generated peptides, and emphasises the need of robust quantitative methodologies for the adequate characterisation of their bioavailability. In fact, the most common and well established quantitation approaches using proteomics are not adapted for peptidomics analysis, so alternative strategies need to be considered. Key findings and conclusions: The progress in the identification and characterisation of the activity of natural bioactive peptides is highly dependent on modern instruments and bioinformatics tools as well as updated protein databases. In fact, the use of in silico approaches and proteomics can be complementary tools in the identification of peptides from meat protein sources as the empirical experimental design can be simplified by using bioinformatics for computer simulation in most of the steps. Finally, Multiple Reaction Monitoring mass spectrometry methodology previously used in the quantitation of therapeutic peptides and biomarkers arises as a powerful tool for absolute quantitation or semiquantitation of bioactive peptides.The research leading to these results received funding from the European Union 7th Framework Programme (FP7/2007-2013) under Grant Agreement 312090 (BACCHUS). This publication reflects only the author views and the Community is not liable for any use made of the information contained therein. Grant AGL2014-57367-R from MINECO and FEDER funds and the Juan de la Cierva postdoctoral contract to LM are acknowledged. The proteomic analysis was performed in the proteomics facility of SCSIE University of Valencia that belongs to ProteoRed, PRB2-ISCIII, (IPT13/0001 - ISCIII-SGEFI/FEDER).Mora Soler, L.; Gallego-Ibáñez, M.; Reig Riera, MM.; Toldrá Vilardell, F. (2017). Challenges in the quantitation of the naturally generated bioactive peptides in processed meats. Trends in Food Science & Technology. 69:306-314. https://doi.org/10.1016/j.tifs.2017.04.011S3063146

Programi i baze podataka o peptidima i proteolitičkim enzimima na internetu – kratak osvrt na 2007. i 2008. godinu

Bioinformatics methods have become one of the most important tools in peptide science. The number of available peptide databases is growing rapidly. The number of online programs able to process peptide sequences to extract information concerning their structure, physicochemical and biological properties is also increasing. Many of such programs were designed to manipulate protein sequences, but they have no built-in restrictions disabling their application to process oligopeptides containing less than 20 amino acid residues. Publications addressing these programs cannot be found in literature databases using the keyword \u27peptide\u27 or \u27peptides\u27, in connection with the term \u27bioinformatics\u27 or related terms, thus a reference source summarizing data from such publications seems necessary. This paper provides a brief review of bioactive peptide databases and sequence alignment programs enabling the search for peptide motifs, determination of physicochemical properties of amino acid residues, prediction of peptide structure, the occurrence of posttranslational glycosylation and immunogenicity, as well as the support of peptide design process. The review also includes databases and programs providing information about proteolytic enzymes. The databases and programs discussed in this paper were developed or updated between September 2007 and December 2008.Bioinformatičke metode postale su jedan od najvažnijih alata u području istraživanja peptida. Sve je veći broj dostupnih baza podataka o peptidima, a i „online” programa koji obradom aminokiselinskih sljedova daju informacije o strukturi peptida te njihovim fizikalno-kemijskim i biološkim svojstvima. Mnogi od tih programa dizajnirani su za obradu aminokiselinskih sljedova proteina, ali nemaju ugrađenu restrikciju njihove primjene na oligopeptide koji sadrže manje od 20 aminokiselinskih ostataka. Radovi o takvim programima ne mogu se pronaći u bazama publikacija uporabom ključnih riječi „peptid” ili „peptidi”, u kombinaciji s pojmom „bioinformatika” ili sličnim terminima. Stoga je važno sažeti rezultate objavljenih radova u jednom izvoru. U ovom je radu dan kratak pregled baza podataka o bioaktivnim peptidima i programima za analizu aminokiselinskoga slijeda koji omogućuju: pronalazak peptidnih motiva; određivanje fizikalno-kemijskih svojstava aminokiselinskih ostataka; predviđanje strukture peptida, pojave posttranslacijske glikozilacije i imunogenosti; te programsku podršku za dizajn peptida. Također su prikazani programi i baze podataka o proteolitičkim enzimima. Svi navedeni programi i baze razvijeni su i ažurirani od rujna 2007. do prosinca 2008

Characterization of Desmoglein-3 Epitope Region Peptides as Synthetic Antigens: Analysis of their in vitro T-cell Stimulating Efficacy, Cytotoxicity, Stability and their Conformational Features

Desmoglein-3 (Dsg3) adhesion protein is the main target of autoantibodies and autoreactive T cells in Pemphigus vulgaris (PV) autoimmune skin disorder. Several mapping studies of Dsg3 T cell epitope regions were performed, and based on those data, we designed and synthesized four peptide series corresponding to Dsg3 T cell epitope regions. Each peptide series consists of a 17mer full-length peptide (Dsg3/189–205, Dsg3/206–222, Dsg3/342–358, and Dsg3/761–777) and its N-terminally truncated derivatives, resulting in 15 peptides altogether. The peptides were prepared on solid phase and were chemically characterized. In order to establish a structure–activity relationship, the solution conformation of the synthetic peptides has been investigated using electronic circular dichroism spectroscopy. The in vitro T cell stimulating efficacy of the peptides has been determined on peripheral blood mononuclear cells isolated from whole blood of PV patients and also from healthy donors. After 20h of stimulation, the interferon (IFN)-γ content of the supernatants was measured by enzyme-linked immunosorbent assay. In the in vitro conditions, peptides were stable and non-cytotoxic. The in vitro IFN-γ production profile of healthy donors and PV patients, induced by peptides as synthetic antigens, was markedly different. The most unambiguous differences were observed after stimulation with 17mer peptide Dsg3/342–358, and three truncated derivatives from two other peptide series, namely, peptides Dsg3/192–205, Dsg3/763–777, and Dsg3/764–777. Comparative analysis of in vitro activity and the capability of oligopeptides to form ordered or unordered secondary structure showed that peptides bearing high solvent sensibility and backbone flexibility were themost capable to distinguish between healthy and PV donors

Spectroscopic Investigations of Oligopeptides from Aquatic Cyanobacteria: Characterisation of New Oligopeptides, Development of Microcystin Quantification Tools and Investigations into Microcystin Production

Cyanobacteria (blue-green algae) are a group of ancient prokaryotic organisms which have become synonymous with water quality deterioration. An array of compounds is produced by aquatic cyanobacteria, the largest group being the oligopeptides. A major class of cyanobacterial oligopeptides are the microcystins; cyclic heptapeptides which contain the unique amino acid Adda (3 amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid). Due to their ability to inhibit protein phosphatases 1 and 2A and as they are concentrated in the liver, microcystins can be highly toxic to animals. Anabaenopeptins are cyclic hexapeptides which contain a carbonyl-linked sidechain amino acid and a ring which is cyclised through the sidechain amine of the position two D-lysine. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI TOF MS) analysis of a cyanobacterial bloom sample from Lake Wiritoa (Manawatu, New Zealand) led to the identification of a new anabaenopeptin. The putative structure for anabaenopeptin 906 was constructed using tandem MS (MS/MS) data, in conjunction with the sequences of the known anabaenopeptins. A Microcystis species (CYN06) isolated from Lake Hakanoa (Huntly, New Zealand) was investigated as it produced a large number of microcystin congeners. Liquid chromatography-MS/MS analysis was used to identify seventeen known microcystin congeners and to characterise ten new variants. Two of the new microcystins, MC-FA and MC-WA, were structurally characterised using amino acid analysis and nuclear magnetic resonance (NMR) spectroscopy. The other new congeners included MC FAba, MC WAba, MC FL, MC-WL as well as [Asp³] analogues of MC FA, MC WA, and [Asp³] analogues of two known congeners; MC-RA and MC-RAba. A review of the number of microcystin congeners produced by reported cyanobacterial strains placed CYN06 in the upper ten percentile. However, CYN06 differed from the other strains as it showed relaxed substrate specificity at position two and four and simultaneously produced microcystin congeners which contained no arginine residues, one arginine residue and two arginine residues. Microcystis CYN06 also contained an unidentified microcystin with a mass of 1014.5 Da. Structural characterisation by NMR spectroscopy indicated that it was an analogue of MC-WA which contained N-formylkynurenine at position two. As N-formylkynurenine is a known oxidation product of tryptophan it was proposed that further unidentified microcystins from CYN06 contained two other oxidation products of tryptophan; kynurenine and oxindolyalanine. This is the first report of the presence of oxidised tryptophan residues in microcystins. Analysis of a cyanobacterial hydroterrestrial mat sample collected from Miers Valley in Eastern Antarctica indicated the presence of fourteen new oligopeptides. A combination of MS/MS and amino acid analysis was used to characterise eight new microcystins which each contained a position one glycine. A recently-developed thiol derivatisation technique indicated that the position seven amino acid in each of the microcystins was very likely dehydrobutyrine. Different combinations of variable modifications at positions two, four and five resulted in eight unique structures. These included four microcystins with Adda moieties which possessed an O-acetyl group (ADMAdda) instead of the conventional C9 methoxy. As well as being the first report of microcystins containing a position one glycine, this is the first report of ADMAdda-containing microcystins in the southern hemisphere. The putative structures of six new Antarctic linear peptides were determined through a combination of mass spectrometric techniques. The compounds contained an N terminus with the molecular formula C₉H₁₄NO₂ linked to isoleucine, two aromatic amino acids and an ester linked hydroxyphenyllactic acid. The hydroxyphenyllactic acid C terminus and the unidentified N terminus suggest that these new compounds are a novel class of cyanobacterial oligopeptide. Seven different sample preparation techniques for the quantitative analysis of microcystins by MALDI-TOF MS were assessed for signal reproducibility and sensitivity using a cost-effective internal standard (angiotensin I). The sensitivity of six of the preparations was acceptable, as was the reproducibility for two thin layer preparations performed on a polished steel target. Both thin layer preparations could be used with a MALDI-TOF mass spectrometer which automatically acquires data. The thin-layer-spot preparation could also be used in an automated sample preparation work-flow. Further investigation using this preparation demonstrated that linear quantification of three different microcystin congeners ([Dha⁷] MC-LR, MC-RR and MC-YR) was possible. Use of this MALDI sample preparation will allow large numbers of microcystin-containing samples to be analysed rapidly and at low cost. A batch culture experiment using Microcystis CYN06 exhibited a decreased abundance of arginine-containing microcystins as nitrate concentrations decreased. Linear regression of the relationship between log10 microcystin content and nitrate concentration revealed slopes which were dependent upon the number of arginine residues present in the compound. During this experiment the abundance of congeners with a single arginine residue at position two did not change (p > 0.05), whilst the abundance of the congeners with a position four arginine decreased significantly (p ≤ 0.001). This suggests that there could be an element of selectivity in regards to which arginine in the microcystin structure is modulated and could explain why congener modulation in response to nitrogen concentration has not been observed previously. Whilst it was not proven that nitrogen supply was the causative factor for the congener modulation, the results from this experiment warrant further study in this area. This research has significantly expanded our knowledge of oligopeptide diversity, improved an existing method of quantifying microcystins and shed new light on the regulation of the abundance of microcystin congeners. The identification of eighteen new microcystins is a 16% increase upon the 111 presently characterised. Also reported was the identification of nine oxidised analogues of tryptophan-containing microcystins from Microcystis CYN06. The presence of oxidised Trp residues in microcystins has not been reported previously and will allow researchers working with samples of Trp-containing microcystins to now assign the oxidised analogues. Seven new cyanobacterial oligopeptides were characterised during this study, six of which may belong to a novel class of linear peptides. A sample preparation designed for the quantification of microcystins by MALDI TOF MS gave comparative performance to the previously reported method but was compatible with automated high-throughput sample preparation and data acquisition. For the first time, a culturing experiment showed a relationship between the abundance of arginine-containing microcystins and nitrogen supply