Single chain variable fragment antibodies selected by phage display against the sporozoite surface antigen S16 of Cryptosporidium parvum

Two human single chain variable fragment (scFv) libraries were used to select clones that bound to the surface glycoprotein S16 of Cryptosporidium parvum. Panning of the Tomlinson libraries I and J resulted in the isolation of nine distinct clones. Of the four clones which had full-length scFv, three contained stop codons. The remaining five clones were truncated, with four missing the heavy chain, and one missing most of the light chain. The full-length clones exhibited better binding to native C. parvum proteins and recombinant S16 than the truncated clones, with the exception of one truncated clone. None of the selected clones cross-reacted with Giardia lamblia, Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus or another immunogenic target of C. parvum, P23. Clones expressed as the soluble scFv-gIIIp construct were able to detect C. parvum native proteins and sporozoites. Panning from naïve libraries was an useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.     

Development and characterization of simple sequence repeats for flowering dogwood (Cornus florida L.)

Abundant, codominant simple sequence repeats (SSRs) markers can be used for constructing genetic linkage maps and in marker-assisted breeding programs. Enrichment methods for SSR motifs were optimized with the ultimate aim of developing numerous loci in flowering dogwood (C. florida L.) genome. Small insert libraries using four motifs (GT, CT, TGG, and AAC) were constructed with C. florida ‘Cherokee Brave’ deoxyribonucleic acid (DNA). Colony polymerase chain reaction (PCR) of 2,208 selected clones with three primers we reported previously indicated that 47% or 1,034 of the clones harbored one of the four targeted SSR motifs. Sequencing the putative positive clones confirmed that nearly 99% (1,021 of 1,034) of them contained the desired motifs. Of the 871 unique SSR loci, 617 were dinucleotide repeats (70.8%), and 254 were trinucleotide or longer repeats (29.2%). In total, 379 SSR loci had perfect structure, 237 had interrupted, and 255 had compound structure. Primer pairs were designed from 351 unique sequences. The ability of the 351 SSR primer pairs to amplify specific loci was evaluated with genomic DNA of ‘Appalachian Spring’ and ‘Cherokee Brave’. Of these primers, 311 successfully amplified product(s) with ‘Cherokee Brave’ DNA, 21 produced weak or faint products, and 19 did not amplify any products. Additionally, 218 of the 311 primers pairs revealed polymorphisms between the two cultivars, and 20 out of 218 primers detected an average of 13.7 alleles from 38 selected Cornus species and hybrids. These SSR loci constitute a valuable resource of ideal markers for both genetic linkage mapping and gene tagging of flowering dogwood. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Computational protein design

The field of computational protein design is reaching its adolescence. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. Further developments of scoring functions, sampling strategies, and optimization methods will expand the range of applicability of computational protein design to larger and more varied systems, with greater incidence of success. Developments in this field are beginning to have significant impact on biotechnology and chemical biology.     

Smart peptide libraries are accessible via enzymatic modifications

The minireview summarizes the recent preparation of thefollowing unusually modified combinatorial peptide collectionsuseful for diagnostics and screening in drug finding. Tissuetransglutaminase catalyzes cross couplings with transamidationbetween Gln and Lys peptide chains resulting in libraries withisopeptide bonds. The enzyme is involved in the triggering ofautoantigenic B- and T-cell epitopes of coeliac disease. Themicrobial enzyme EpiD involved in lantibiotic biosynthesiscatalyzes oxidative decarboxylation of C-terminal cysteineresidues in peptide libraries transforming peptidyl-cysteinesto peptide (2-mercaptovinyl)amides. Novel backbone modifiedpeptide libraries are prepared using oxazole and thiazolebuilding blocks carrying amino acid side chains. These aminoacids have been found in many biologically active naturalproducts from marine and microbial organisms such as microcinB17. Dityrosine and isodityrosine linked peptide dimerlibraries are accessible by oxidative phenol coupling usinghorseradish peroxidase. Such structural elements are found forexample in the polycyclic glycopeptide antibiotics of thevancomycin type. Microstructured layers of linear and cyclicpeptide libraries are generated on transducer surfaces forcellular assays, sensor developments and even chiralrecognition. Examples include a light-directed andmicrostructured electrochemical polymerization of phenollabelled peptides.     

9th Annual Symposium on Advances in Separation Science and Mass Spectrometry

Evaluation of: Di Girolamo F, Boschetti E, Chung MC, Guadagni F, Righetti PG. ‘Proteomineering’ or not? The debate on biomarker discovery in sera continues. J. Proteomics 74(5), 589–594 (2011).

The combinatorial peptide ligand library in association with mass spectrometry can greatly enhance the dynamic range of the analysis of low- and very low-abundance proteins constituting the vast majority of species in any sample. When compared with untreated samples, the increment in detection of low-abundance species appears to be at least fourfold. Recently, the combinatorial peptide ligand library has been challenged; however, it has been clearly demonstrated in the evaluated paper that the protocols for elution of the captured polypeptides make the difference. Therefore, the solid-phase ligand library made of hexapeptides remains a promising and unique tool for biomarker discovery.     

Mapping epitopes of neutralizing monoclonal antibodies using phage random peptide libraries

Identification of protective determinants from microbial proteins is a necessary step in the rational design of subunit vaccines. We have previously used a synthetic peptide scan (Pepscan) assay to map a panel of eight neutralizing monoclonal antibodies (mAb; designated as C1.1 to C1.8) to a common motif sequence from Chlamydia trachomatis. In the present study, five of the eight mAbs were used to screen phage random peptide libraries. mAbs C1.1 and C1.3 selected a motif sequence of G-L-X-N-D from a pIII-based phage random peptide library and a motif sequence of G-X-X-N-D from a pVIII-based random peptide library while mAbs C1.6 to C1.8 failed to select recognizable motifs from either of the phage libraries. However, C1.6 to C1.8 bound to the same motif sequence displayed on phage when the appropriate conformational constraints were imposed onto the motif sequence. Thus the specificity of the mAbs identified on Pepscan assays correlates with the mAbs’ dependence on local epitope constraints displayed on the phage surface. Received 12 August 1996/ Accepted in revised form 03 November 1996     

Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.

Methodology is described here for the efficient parallel synthesis and cyclization of linear peptide libraries using intramolecular S-alkylation chemistry in combination with Multipin solid phase peptide synthesis (Multipin SPPS). The effective use of this methodology was demonstrated with the synthesis of a 72-member combinatorial library of cyclic thioether peptide derivatives of the conserved four-residue structural motif DD/EXK found in the active sites of the five crystallographically defined orthodox type II restriction endonucleases, EcoRV, EcoRI, PvuII, BamHI and BglI.     

Identification of monoclonal antibody defined epitopes on human leukocyte antigens utilizing phage display peptide libraries

Summary Utilizing phage display peptide libraries, we have identified and mapped the antigenic determinants recognized by mouse monoclonal antibodies (mAb) on two sets of immunologically important molecules, HLA class I and class II antigens. Anti-HLA class I mAb TP25.99 recognizes a conformational and a linear determinant on distinct regions of the HLA class I α3 domain. Anti-HLA class I mAb HO-4 recognizes a conformational determinant on the α2 domain of HLA-A2 and A28 allospecificities. Anti-HLA-DR1,-DR4,-DR6,-DR8,-DR9 mAb SM/549 recognizes a conformational determinant on the β chain of HLA class II antigens. These results indicate the versatility of phage display peptide libraries to characterize antigenic determinants recognized by anti-HLA mAb.