Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.
Abstract: Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.
Abstract: This study aims to demonstrate the quantification of
peptides based on isotope dilution surface enhanced Raman
scattering (IDSERS). SERS spectra of phenylalanine (Phe), leucine
(Leu) and two peptide sequences TGQIFK (T13) and
YSFLQNPQTSLCFSESIPTPSNR (T6) as part of the 22-kDa
human growth hormone (hGH) were obtained on Ag-nanoparticle
covered substrates. On the basis of the dominant Phe and Leu
vibrational modes, precise partial least squares (PLS) prediction
models were built enabling the determination of unknown T13 and
T6 concentrations. Detection of hGH in its physiological
concentration in order to investigate the possibility of protein
quantification has been achieved.
Abstract: Biologically active peptides are of particular interest
in food science and human nutrition because they have been shown to play several physiological roles. In vitro gastrointestinal digestion of lentil and whey proteins in this study produced high angiotensin-I converting enzyme inhibitory activity with 75.5±1.9 and 91.4±2.3%
inhibition, respectively. High ACE inhibitory activity was observed in lentil after 5 days of germination (84.3±1.2%). Fractionation by
reverse phase chromatography gave inhibitory activities as high as
86.3±2.0 for lentil, 94.8±1.8% for whey and 93.7±1.7% at 5th day of germination. Further purification by HPLC resulted in several
inhibitory peptides with IC50 values ranging from 0.064 to 0.164
mg/ml. These results demonstrate that lentil proteins are a good
source of peptides with ACE inhibitory activity that can be released by germination or gastrointestinal digestion. Despite the lower bioactivity in comparison with whey proteins, incorporation of lentil proteins in functional food formulations and natural drugs look promising.