Protein and Peptide Letters - Volume 19, Issue 12, 2012

In this work the efficient and simple method of improvement specificity and solubility of low molecular weight proteinase substrates is described. The series of fluorescent substrates of selected proteolytic enzymes (neutrophil elastase, cathepsin G and proteinase 3 along with human airway trypsin like protease) were synthesized and modified by selective pegylation by the attachment of 2-(2-(2-aminoethoxy)ethoxy)acetic acid. Modification of the C-terminal carboxyl group resulted in the decrease in the specificity constants (kcat/KM) for all obtained analogues. The covalent attachment of PEG to N-terminal amino group has the opposite effect, as the increase in specificity constant was observed for all studied compounds. This outcome was pronounced the most for proteinase 3 substrate PEG-ABZ-Tyr-Tyr-Abu-ANB-NH2, whose catalytic constant (kcat) increased over three fold. The introduction of PEG moieties at both C- and N-terminal yielded the substrates with lower specificity constants. For substrate (ABZ-Arg-Gln-Asp-Arg-ANB-NH2) the influence of the PEG chain length on its kinetic parameters was investigated. Elongation of the PEG chain at N-terminal of this peptide decreased the specificity constant. In addition to the effect of pegylation on the kinetic parameters of the studied substrates, the introduced modifications significantly improved their solubility in buffer solutions applied for enzymatic investigations.

A new synthetic pathway is described to prepare asymmetrically protected 2,7-diaminosuberic acid. This strategy exploits (acyloxy)alkoxy promoiety as protecting group and RCM reaction using second generation Grubbs catalyst and provides the trans isomer of (2R,7R)-7-(((9H-fluoren-9-yl)methoxy)carbonylamino)-2-(tert-butoxycarbonylamino)-8- methoxy-8-oxooct-4-enoic acid, which was in turn reduced to obtain (2R,7R)-7-(((9H-fluoren-9-yl)methoxy)carbonylamino)- 2-(tert-butoxycarbonylamino)-8-methoxy-8-oxooctanoic acid.

How to correctly and efficiently map small molecule to its possible metabolic pathway is a meaningful topic to metabonomics research. In this work, a novel approach to address this problem was introduced to encode physicochemical properties of small molecules. Based on this encoding method, a two stage feature selection method called mRMR-FFSAdaBoost was adopted to map small molecules to their corresponding metabolic pathways possible. As a result, the accuracies of 10-folds cross-validation test and independent set test for predicting the metabolic pathways of small molecules reached 83.88% and 85.23%, respectively. An online server for predicting metabolic pathways of unknown small molecules as described in this paper is accessible at http://chemdata.shu.edu.cn:8080/PathwayPrediction/.

Based on the structure of Octreotide (SMS 201-995) some modified at positions 5 with Dap (diaminopropanoic acid), Dab (diaminobutanoic acid) and Orn new C-amide analogs were synthesized. The Thr6 was replaced by unnatural amino acids Tle (t-leucine). The cytotoxic effects of the novel compounds were tested in vitro against a panel of human tumor cell lines. All investigated compounds exhibited different concentration-dependent antiproliferative effects against the HT-29, MDA-MB-231, HepG2 and HeLa cell lines after 24 h treatment. The compound 2 (D-Phe-c(Cys-Phe-D-Trp- Dap-Tle-Cys)-Thr-NH2) had antiproliferative effects on MDA-MB-231 cells with the IC50 0.03 mM. The HeLa and HepG-2 cells were most sensitive towards tested compounds at various concentrations. Results demonstrated that the peptide analogs 3 (D-Phe-c(Cys-Phe-D-Trp-Lys-Tle-Cys)-Thr-NH2), 4 (D-Phe-c(Cys-Phe-D-Trp-Orn-Tle-Cys)-Thr-NH2) and 5 (RC-102) exert the most pronounced inhibition of the cell vitality up to 77% at higher concentrations and were not toxic to the normal Lep-3 cells.

ClpX is a general stress protein which belongs to the heat shock protein, Clp/Hsp100 family of molecular chaperones. ClpX, in association with ClpP degrades proteins in an ATP dependent manner. Some members of the Clp family have been shown to be involved in the pathogenesis of many bacteria. The Helicobacter pylori genome demonstrates the presence of ClpX along with ClpA, ClpB and ClpP, the other members of the caseinolytic protease family. H. pylori ClpX is a 386 amino acid long protein. In this study, we have over-expressed H. pylori ClpX in E. coli, purified the recombinant protein to homogeneity and functionally characterized it. The recombinant H. pylori ClpX showed an inherent ATPase activity and prevented the heat induced aggregation of a model protein in vitro. The chaperonic activity of H. pylori ClpX was dependent on ATP hydrolysis and involved hydrophobic interaction with the substrate protein. Biophysical studies reveal the secondary structure tolerance of ClpX at various temperatures and in the presence of guanidine hydrochloride. The study demonstrates that H. pylori ClpX manifests chaperonic activity in the absence of any adaptor protein.

Colon cancer is one of the most common malignances. In vitro and in vivo study show that retinoic acids inhibit a wide variety of cancer cells but the molecular mechanism of their anti-tumor effects are not yet fully understood. Alltrans retinoic acid (ATRA), an isomer of retinoic acid, can inhibit the proliferation of HCT-15 human colon cancer cell line. A proteomic analysis was performed using HCT-15 treated with ATRA to further elucidate the retinoic acid signaling pathway and its anti-tumor effect mechanism. MTT results showed that the growth of HCT-15 cells were significantly inhibited by ATRA. The alkaline phosphatase activity assay showed that ATRA failed to induce the differentiation of HCT-15. The DNA ladder detection showed that ATRA induced apoptosis in HCT-15. Two-dimensional gel electrophoresis coupled with MALDI-TOF/TOF mass spectrometry identified 13 differentially expressed proteins in HCT-15 cells after all-trans retinoic acid treatment. Among the identified differentially expressed proteins, there were four scaffold proteins (YWHAE, SFN, YWHAB, and YWHAZ), two ubiquitin modification related proteins (ISG-15 and UBE2N), two translational initiation factors (EIF1AX and EIF3K), two cytoskeleton related proteins (EZRI and CNN3), two proteinmodification related proteins (TXNDC17 and PIMT), and one enzyme related to phospholipid metabolism (PSP). Both EZRI and UBE2N were rendered to western-blot validation and the results were consistent with the two-dimension electrophoresis analysis. In this study, the differentially expressed proteins in HCT-15 treated by ATRA were identified, which will assist the further elucidation of the anti-tumor mechanism of retinoic acids.

Cysteine peptidases are the best characterized peptidases among those involved with storage protein mobilization during seed germination. In the present work we show two major groups of cysteine peptidase activities, one of higher (55 to 97 kDa) and other with lower (15 to 20 kDa) molecular masses which are temporally activated after 24 and 48 HAI, respectively, in germinating cowpeas. The former group is found both in protein bodies and in cytoplasmic fraction, while the latter is mostly present outside protein bodies. A third cysteine peptidase activity of ∼37 kDa was specifically active at quiescent cotyledons and at 12 and 60 hours after imbibition (HAI). Main peptidase activities of albumin fractions were synchronizedly detected with radicle emergence at 36 HAI. Major vicilin mobilization was more pronounced from 60 HAI onwards and steadily increased until 144 HAI, when low levels of the smallest vicilin subunit were present. Cysteine peptidases were susceptible to iodoacetamide, E-64, iodoacetic acid, pCMB and β-mercaptoethanol, except for the ∼37 kDa peptidase, which was not affected by any of the inhibitors. By a two-dimensional native/SDS-PAGE combination it was observed an apparent linear arrangement of protein breakdown products as well as of peptidase activity spots. The finding may indicate a complex set of sequential proteolytic events where peptidases induce or activate new peptidases, which may act upon different aggregates or zymogens, and these hydrolysis products appear in a line of constant decreasing Rf x Mr ratio.

A novel antifungal peptide with 36 amino acids was identified by functional screening of a marine metagenomic library. The peptide did not show similarity with any existing antimicrobial peptide sequences in the databank. The108 bp ORF designated as mmgp1 was cloned and expressed in Escherichia coli BL21 (DE3) using pET expression system. Mass spectrometry analysis of the purified recombinant peptide revealed a molecular mass of 5026.9 Da. The purified recombinant peptide inhibited the growth of Candida albicans and Aspergillus niger. The peptide was predicted to adopt α- helical conformation with an extended coil containing a ligand binding site for N-acetyl-D-glucosamine. The α- helicity of the peptide was demonstrated by circular dichroism spectroscopy in the presence of chitin or membrane mimicking solvent, trifluoroethanol. The chitin binding property of the peptide was also confirmed by fast performance liquid chromatography.

Relative importance of the intrinsic properties of the polypeptide chain vis-a-vis the environmental influences, in driving the folding of a protein, has been a subject of extensive debate and investigation. Folding/misfolding lead to self association in many systems, which have biological functional significance. We compare here, the NMR derived equilibrium folding transitions driven under different environmental conditions in the GTPase Effector Domain of dynamin, which self-associates into megadalton size species. We conclude that though hierarchy of folding and association of GED is substantially influenced by the solvents, these properties, to a good extent are also driven by intrinsic properties of the polypeptide chain, and the regions that form secondary structures, the types of secondary structures formed in those regions, and finally the regions that participate in the self-association are the same, indicating near neighbor interactions would have a telling effect on the final outcome of the folding process. These observations would open a new reliable frontier for elucidating the multiple folding trajectories and consequent self-association, by simulations in vacuum, for this protein.

Bcl-xL protein belongs to BCL-2 family which has either pro- or anti-apoptotic activities owing to their importance in the regulation of apoptosis, tumor genesis and cellular responses to anti-cancer therapy. Bcl-xL permeabilize the outer mitochondrial membrane of cells and inhibit these processes. Protein–inhibitor interactions play an important role in regulating the expression of Bcl-xL protein. Here, we report the docking studies that resulted in the identification of new inhibitors distinct from the previously reported inhibitor against this protein. The results have been validated using Sybyl surflux docking. New potent inhibitors from docking analysis are pentacyclic triterpenoid derivative (2S,4aR,6aR, 6bS,8aS,10R,12R,12aS,12bR,14bR,E)-10,12-dihydroxy-2,4a,14b-trimethyl-9-((((R)-3,4,5-trihydroxy-6-methyl-2H-pyran- 2-yl)oxy)methylene)-1,2,3,4,4a,5,6,6a,6b,8a,9,10,11,12,12a,12b,13,14b-octadecahydropicene-2-car-boxylic acid and 4- alkyl-4-methoxypiperidine derivative 8h (where R= 4-Cl-Ph) that promotes the release of pro-apoptotic proteins from the mitochondria which is a key event in cell death signaling. The compounds form stable complex with protein exhibiting highest binding affinity and Gibbs free energy. Pentacyclic triterpenoid derivatives compound-201 and piperidine derivative compound-39 are potent inhibitors with Ki value of 172.62nM and 175.24 nM high affinity and inhibitory potency. Salt bridge, pi-pi and hydrogen bonding interactions predominantly contribute towards the stability of the complexes. These compounds can further be exploited for their potential to enhance apoptosis. We have established the correlation between the experimental Ki value with our computational inhibition constant. The quantitative predictions in this study provide a scope for further experimental testing giving structural insights into the design and development of novel anticancer drugs.

Defensins are considered to play an important role in the innate immune system of virtually all life forms, from insects and plants to amphibians and mammals. They are classified into alpha, beta and theta-defensins. Fast and accurate computational prediction of defensin and defensin types will help in annotating unidentified defensin novel peptides. Identified defensins, owing to their small length and potent antimicrobial activity can be used effectively for development of new clinically applicable antibiotics. Thus predicting the defensin candidates will aid in accurate identification of novel peptide drugs. Support vector machines prediction model accuracy was 99% for defensin and defensin types. The results indicate that it is most accurate and efficient prediction method for defensin peptides. User friendly defensin web server is provided at www.defensinpred.cdac.in for the benefit of scientific community.

Previously we constructed a fusion protein based on GLP-1 and globular adiponectin but unfortunately its yield was low because it was mainly expressed as inclusion bodies. Herein to optimize the soluble expression of this fusion protein we tried several fusion tag systems. Fusion tags, including GST-, Trx- and MBP-tag, greatly improved the soluble expression of the fusion protein. However, these tag-fusion proteins were aggregation-prone as judged by Native PAGE and gel filtration chromatography, and this aggregation reduced the specificity of enterokinase-mediated enzyme cleavage which was essential to remove the fusion tags. To improve the specificity of protein cleavage, we employed on-column cleavage for downstream purification. Finally using optimized expression followed by on-column cleavage, we obtained the product fusion protein with a yield of 1.2 mg per g wet bacterial cells which was 8-fold higher than before. This method improved the yield and simplified the process, and as a convenient method it can also be used for the preparation of other aggregation-prone proteins.

Heme oxygenase-1 (HO-1) is an antioxidant, antiapoptotic and cytoprotective enzyme, catalysing the degradation of heme to carbon monoxide, biliverdin and ferrous iron. Recent studies indicated that expression of HO-1 is under the control of proapoptotic transcription factor p53 and antioxidant transcription factor Nrf2. Whether each of these transcription factors act independently or there is a cooperation between them in inducing HO-1 expression remains to be elucidated. In this study, we examined the expression of HO-1 in B16F10 melanoma and 4T1 breast cancer cells after cell exposure to proteasome inhibitors. We found that HO-1 protein level is increased by about 70% in p53-wt B16F10 cells in response to proteasome inhibitor MG132 after 6 h. Likewise, a 6.8 fold increase in HO-1 level was observed after cell exposure to the highly specific proteasome inhibitor bortezomib after 6 h of treatment in B16F10 cells. Whereas no induction of HO-1 was observed in p53-null 4T1 cells after treatment with bortezomib for 6 h. Next, we aligned HO-1 untranslated region with a consensus p53-responsive element. This bioinformatic analysis identified a p53-responsive element within the untranslated region of HO-1. Then, we examined HO-1 expression after a prolonged exposure to bortezomib in both B16F10 and 4T1 cell. These analyses similarly indicated that HO-1 is strongly induced in B16F10 cells in a dosedependent; contrary to our expectations, a strong induction of HO-1 is also observed in 4T1 cells. Therefore, it is concluded that HO-1 expression is under the control of p53 during early time points of proteasomal inhibition. However, during prolonged incubation with proteasome inhibitors, HO-1 expression can be induced in a p53-independent manner, suggesting participation of other protein(s) with longer half-lives.

The cornea is physiologically avascular. Following a corneal injury, wound healing often proceeds without neovascularization (NV); however, corneal NV may be induced during wound healing in certain inflammatory, infectious, degenerative, and traumatic states. Such states disrupt the physiologic balance between pro-angiogenic and antiangiogenic mediators, favoring angiogenesis. Contributors to such states are matrix metalloproteinases (MMPs), which are key factors in both extracellular matrix remodeling and angiogenesis. Similarly, vascular endothelial growth factor A (VEGF-A) and basic fibroblast growth factor (bFGF) exert pro-angiogenic effects. Here, we elaborate on the facilitative role of MMPs—specifically Membrane Type 1 MMP (MT1-MMP, MMP14)—in corneal NV. Additionally, we provide new insight into the signaling relating to MT1-MMP, Ras, and ERK in the bFGF-induced VEGF-A expression pathways within the corneal fibroblasts.