Asymmetry of calmodulin revealed by peptide binding

The binding of amphiphilic peptides to calmodulin has been studied using fluorescence energy transfer techniques. Calmodulin has no tryptophan residues but possesses two tyrosines (at positions 99 and 138) in the C-terminal half of the protein. The peptides have a single tryptophan which serves as energy acceptor for the protein tyrosine fluorescence. For the binding of mastoparan or peptide Baa17, with a tryptophan at position 3, the observed quenching of the tyrosine fluorescence of over a factor of 2 corresponds to an average tyrosine-trytophan distance of less than 14 Å. These results indicate that the peptides binds preferentially with the tryptophan in the C-terminal half of the protein.     

Effects of transition metal ion coordination on the collision-induced dissociation of polyalanines

Transition metal-polyalanine complexes were analyzed in a high-capacity quadrupole ion trap after electrospray ionization. Polyalanines have no polar amino acid side chains to coordinate metal ions, thus allowing the effects metal ion interaction with the peptide backbone to be explored. Positive mode mass spectra produced from peptides mixed with salts of the first row transition metals Cr(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(I), and Cu(II) yield singly and doubly charged metallated ions. These precursor ions undergo collision-induced dissociation (CID) to give almost exclusively metallated N-terminal product ions whose types and relative abundances depend on the identity of the transition metal. For example, Cr(III)-cationized peptides yield CID spectra that are complex and have several neutral losses, whereas Fe(III)-cationized peptides dissociate to give intense non-metallated products. The addition of Cu(II) shows the most promise for sequencing. Spectra obtained from the CID of singly and doubly charged Cu-heptaalanine ions, [M + Cu - H](+) and [M + Cu](2+) , are complimentary and together provide cleavage at every residue and no neutral losses. (This contrasts with [M + H](+) of heptaalanine, where CID does not provide backbone ions to sequence the first three residues.) Transition metal cationization produces abundant metallated a-ions by CID, unlike protonated peptides that produce primarily b- and y-ions. The prominence of metallated a-ions is interesting because they do not always form from b-ions. Tandem mass spectrometry on metallated (Met = metal) a- and b-ions indicate that [b(n) + Met - H](2+) lose CO to form [a(n) + Met - H](2+), mimicking protonated structures. In contrast, [a(n) + Met - H](2+) eliminate an amino acid residue to form [a(n-1) + Met - H](2+), which may be useful in sequencing.     

Determination of ricin by nano liquid chromatography/mass spectrometry after extraction using lactose-immobilized monolithic silica spin column

Ricin is a glycosylated proteinous toxin that is registered as toxic substance by Chemical Weapons convention. Current detection methods can result in false negatives and/or positives, and their criteria are not based on the identification of the protein amino acid sequences. In this study, lactose-immobilized monolithic silica extraction followed by tryptic digestion and liquid chromatography/mass spectrometry (LC/MS) was developed as a method for rapid and accurate determination of ricin. Lactose, which was immobilized on monolithic silica, was used as a capture ligand for ricin extraction from the sample solution, and the silica was supported in a disk-packed spin column. Recovery of ricin was more than 40%. After extraction, the extract was digested with trypsin and analyzed by LC/MS. The accurate masses of molecular ions and MS/MS spectra of the separated peptide peaks were measured by Fourier transform-MS and linear iontrap-MS, respectively. Six peptides, which were derived from the ricin A-(m/z 537.8, 448.8 and 586.8) and B-chains (m/z 701.3, 647.8 and 616.8), were chosen as marker peptides for the identification of ricin. Among these marker peptides, two peptides were ricin-specific. This method was applied to the determination of ricin from crude samples. The monolithic silica extraction removed most contaminant peaks from the total ion chromatogram of the sample, and the six marker peptides were clearly detected by LC/MS. It takes about 5 h for detection and identification of more than 8 ng/ml of ricin through the whole handling, and this procedure will be able to deal with the terrorism using chemical weapon.     

9-Fluorenylmethoxycarbonyl-based solid-phase synthesis of peptide α-thioesters

Peptide thioesters play a key role in convergent protein synthesis strategies such as native chemical ligation, traceless Staudinger ligation, and Ag(+) -mediated thioester ligation. The Boc-based solid-phase synthesis provides a very reliable access to peptide thioesters. However, the acid lability of many peptide modifications and the requirements of most parallel peptide synthesizers call for the milder Fmoc-based solid-phase synthesis. The Fmoc-based synthesis of peptide thioesters is more cumbersome and typically proceeds with lower yields than the synthesis of peptide acids and peptide amides. The success of native chemical ligation and related technologies has sparked intensive research effort devoted to the development of new methods. The recent progress in this rapidly expanding field is reviewed.     

5‐(Pyren‐1‐yl)uracil as a Base‐Discriminating Fluorescent Nucleobase in Pyrrolidinyl Peptide Nucleic Acids

A pyrene‐labeled uridine (U^Py) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2‐aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U^Py base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T_m) experiments. The fluorescence of the U^Py‐containing single‐stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7–41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U^Py and dA, making the U^Py‐modified acpcPNA useful as a hybridization‐responsive fluorescence probe for DNA‐sequence determination.     

Use of phage display methods to identify heptapeptide sequences for use as affinity purification 'tags' with novel chelating ligands in immobilized metal ion affinity chromatography

This study describes the screening of a peptide phage display library for amino acid sequences that bind with different affinities to a novel class of chelating ligands complexed with Ni2+ ions. These chelating ligands are based on the 1,4,7-triazacyclononane (TACN) structure and have been chosen to allow enhanced efficiency in protein capture and decreased propensity for metal ion leakage in the immobilized metal ion affinity chromatographic (IMAC) purification of recombinant proteins. Utilising high stringency screening conditions, various peptide sequences containing multiple histidine, tryptophan, and/or tyrosine residues were identified amongst the different phage peptide sequences isolated. The structures, and particularly the conserved locations of these key amino acid residues within the selected heptapeptides, form a basis to design specific peptide tags for use with these novel TACN ligands as a new mode of IMAC purification of recombinant proteins.     

Screening and Identification of Peptides that Bind Specifically to the X gene Promoter of Hepatitis B Virus Using a Combinatorial Peptide Library Approach

Hepatitis B virus (HBV) X protein (HBx) plays a key role in the development of hepatocellular carcinoma (HCC) in HBV carriers. A drug that can bind to the promoter region of HBV may shut down the expression of HBx and subsequently prevent the development of HCC in the HBV carrier. We have constructed a seven amino acid residue peptide library on a TentaGel resin using a combinatorial one‐bead one‐sequence peptide synthesis method. The fluorescently labeled eicosanucleotide (5′‐(6‐FAM) CTTTTGGGCT TTGCTGCCCC‐3′) of the HBx promoter region was used as a monitor to screen for peptides that have high binding affinity to the HBx promoter. Two heptapeptides, KAPLFSI and SRVRMTW, were identified, and synthesized. The binding affinities of the peptides to the HBx promoter oligonucleotide were determined using Surface Plasmon Resonance (SPR). The peptide KAPLFSI had a greater binding affinity constant (k_a) and equilibrium constant (K_D) than SRVRMTW. The k_a and K_D values with the full X‐promoter sequence were found to be 1.425 E+5 (1/Ms) and 1.186 E‐8 (M), respectively. The peptide may open a new route for tumor suppression in HBV carriers.     

Validation of a bioanalytical method for the quantification of a therapeutic peptide, ramoplanin, in human dried blood spots using LC-MS/MS

A method has been developed and validated for the quantification of ramoplanin, a 2554 Da peptide antibiotic, in human dried blood spots using high‐performance liquid chromatography with tandem mass spectrometric detection. The validation data meet FDA acceptance criteria for bioanalytical assays and cover the quantification of ramoplanin over the range 10–5000 ng/mL. The assay determines ramoplanin at the same lower limit of quantification as conventional liquid sample methods. Dried blood spot analysis provides an approach for quantification of peptide therapeutics and delivers significant benefits for sample collection and handling and also sample cleanup over conventional plasma and serum assays. Copyright © 2010 John Wiley & Sons, Ltd.     

A Supramolecular Hydrogel Inspired by Elastin

Self‐assembly prevails in nature and learning from nature will lead to biofunctional materials. Inspired by the protein of elastin, we reported in this study on a supramolecular hydrogel bearing the elastin repeating peptide of VPGAG. The visco‐elasticity property, morphology of the nanostructures, and aromatic stacking in the self‐assembled nanostructure were characterized by a rheometry, transmission electron microscope (TEM), and fluorescence microscope, respectively. The biocompatibility of the gelator was also proved by an MTT assay. Though the supramolecular hydrogel failed to exhibit a high elasticity like elastin, the thixotropic hydrogel might have potentials for the applications in fields of cell culture, controlled‐drug release, etc.