A variant peptide of buffalo colostrum beta-lactoglobulin inhibits angiotensin I-converting enzyme activity

beta-lactoglobulin is a rich source of bioactive peptides. The LC-MS separated tryptic peptides of buffalo colostrum beta-lactoglobulin (BLG-col) were computed based on MS-MS fragmentation for de novo sequencing. Among the selected peptides (P1-P8), a variant was detected with methionine at position 74 instead of glutamate. The sequences of two peptides were identical to hypocholesterolemic peptides whereas the remaining peptides were in accordance with buffalo milk beta-lactoglobulin. Comparative sequence analysis of BLG-col to milk beta-lactoglobulin was carried out using CLUSTALW2 and a molecular model for BLG-col was constructed (PMDB ID-PM0076812). The synthesized variant pentapeptide (IIAMK, m/z-576 Da) was found to inhibit angiotensin I-converting enzyme (ACE) with an IC50 of 498 +/- 2 mu M, which was rationalized through docking simulations using Molgrow virtual docker. (C) 2012 Elsevier Masson SAS. All rights reserved.

Synthetic studies toward geranylated PPAP natural products oblongifolin A, oblongifolin D, and enervosanone

A concise approach of general utility toward mono- and di-geranylated PPAP frameworks employing `reconstructive aldol cyclization' as the key step is delineated. (C) 2012 Elsevier Ltd. All rights reserved.

Theoretical and in vitro studies of a C-terminal peptide from PGKC of Leishmania mexicana mexicana

Trypanosomatids cause deadly diseases in humans. Of the various biochemical pathways in trypanosomatids, glycolysis, has received special attention because of being sequestered in peroxisome like organelles critical for the survival of the parasites. This study focuses on phosphoglycerate kinase (PGK) from Leishmania spp. which, exists in two isoforms, the cytoplasmic PGKB and glycosomal PGKC differing in their biochemical properties. Computational analysis predicted the likelihood of a transmembrane helix only in the glycosomal isoform PGKC, of approximate length 20 residues in the 62-residue extension, ending at, arginine residues R471 and R472. From experimental studies using circular dichroism and NMR with deuterated sodium dodecyl sulfate, we find that the transmembrane helix spans residues 448 +/- 2 to 476 in Leishmania mexicana PGKC. The significance of this observation is discussed in the context of glycosomal transport and substrate tunneling. (C) 2012 Elsevier B.V. All rights reserved.

Cis-trans peptide variations in structurally similar proteins

The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino acid preferences and local structural changes associated with such variations. Nearly 34% of the Xaa-Proline cis bonds are not conserved in structural relatives; Proline also has a high tendency to get replaced by another amino acid in the trans conformer. At both positions bounding the peptide bond, Glycine has a higher tendency to lose the cis conformation. The cis conformation of more than 30% of beta turns of type VIb and IV are not found to be conserved in similar structures. A different view using Protein Block-based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes between cis and trans conformations are found to be associated with the evolution of new functions facilitated by local structural changes. This is most frequent in enzymes where new catalytic activity emerges with local changes in the active site. Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution.

Model synthetic studies toward jiadifenin and majucin type seco-prezizaane natural products via a stereo- and enantioselective approach

A concise stereo- and enantioselective approach to seco-prezizaane sesquiterpenoids, leading to the acquisition of two bicyclic fragments, is delineated. (c) 2012 Elsevier Ltd. All rights reserved.

A method for stabilizing the cis prolyl peptide bond: influence of an unusual n -> pi* interaction in 1,3-oxazine and 1,3-thiazine containing peptidomimetics

The cis/trans isomer ratios of the Xaa-Pyr (Pyr = pyrrolidine) 3 degrees amide bonds are significantly high (similar to 90% cis) in the novel peptidomimetics where Pyr contains 1,3-oxazine (Oxa) or 1,3-thiazine (Thi) at its 2 position. We find that an unusual n -> pi(i-1)* interaction, selectively stabilizes the cis conformer and the n X n repulsion destabilizes the trans conformer of these molecules. Both these electronic effects oppose the steric effects in the 3 degrees amide bond. The structural requirements for manifestation of these electronic effects are determined. (c) 2012 Elsevier Ltd. All rights reserved.

Interacting fermions in synthetic non-Abelian gauge fields

Generation and study of synthetic gauge fields has enhanced the possibility of using cold atom systems as quantum emulators of condensed matter Hamiltonians. In this article we describe the physics of interacting spin -1/2 fermions in synthetic non-Abelian gauge fields which induce a Rashba spin-orbit interaction on the motion of the fermions. We show that the fermion system can evolve to a Bose-Einstein condensate of a novel boson which we call rashbon. The rashbon-rashbon interaction is shown to be independent of the interaction between the constituent fermions. We also show that spin-orbit coupling can help enhancing superfluid transition temperature of weak superfluids to the order of Fermi temperature. A non-Abelian gauge field, when used in conjunction with another potential, can generate interesting Hamiltonians such as that of a magnetic monopole.

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Distinct Disulfide Isomers of mu-Conotoxins KIIIA and KIIIB Block Voltage-Gated Sodium Channels

In the preparation of synthetic conotoxins containing multiple disulfide bonds, oxidative folding can produce numerous permutations of disulfide bond connectivities. Establishing the native disulfide connectivities thus presents a significant challenge when the venom-derived peptide is not available, as is increasingly the case when conotoxins are identified from cDNA sequences. Here, we investigate the disulfide connectivity of mu-conotoxin KIIIA, which was predicted originally to have a C1-C9,C2-C15,C4-C16] disulfide pattern based on homology with closely related mu-conotoxins. The two major isomers of synthetic mu-KIIIA formed during oxidative folding were purified and their disulfide connectivities mapped by direct mass spectrometric collision-induced dissociation fragmentation of the disulfide-bonded polypeptides. Our results show that the major oxidative folding product adopts a C1-C15,C2-C9,C4-C16] disulfide connectivity, while the minor product adopts a C1-C16,C2-C9,C4-C15] connectivity. Both of these peptides were potent blockers of Na(v)1.2 (K-d values of 5 and 230 nM, respectively). The solution structure for mu-KIIIA based on nuclear magnetic resonance data was recalculated with the C1-C15,C2-C9,C4-C16] disulfide pattern; its structure was very similar to the mu-KIIIA structure calculated with the incorrect C1-C9,C2-C15,C4-C16] disulfide pattern, with an alpha-helix spanning residues 7-12. In addition, the major folding isomers of mu-KIIIB, an N-terminally extended isoform of mu-KIIIA, identified from its cDNA sequence, were isolated. These folding products had the same disulfide connectivities as mu-KIIIA, and both blocked Na(v)1.2 (K-d values of 470 and 26 nM, respectively). Our results establish that the preferred disulfide pattern of synthetic mu-KIIIA and mu-KIIIB folded in vitro is 1-5/2-4/3-6 but that other disulfide isomers are also potent sodium channel blockers. These findings raise questions about the disulfide pattern(s) of mu-KIIIA in the venom of Conus kinoshitai; indeed, the presence of multiple disulfide isomers in the venom could provide a means of further expanding the snail's repertoire of active peptides.

Metal-Ion Metathesis in Metal-Organic Frameworks: A Synthetic Route to New Metal-Organic Frameworks

A porous metalorganic framework, Mn(H3O)(Mn4Cl)(3)(hmtt)(8)] (POST-65), was prepared by the reaction of 5,5',10,10',15,15'-hexamethyltruxene-2,7,12-tricarboxylic acid (H(3)hmtt) with MnCl2 under solvothermal conditions. POST-65(Mn) was subjected to post-synthetic modification with Fe, Co, Ni, and Cu according to an ion-exchange method that resulted in the formation of three isomorphous frameworks, POST-65(Co/Ni/Cu), as well as a new framework, POST-65(Fe). The ion-exchanged samples could not be prepared by regular solvothermal reactions. The complete exchange of the metal ions and retention of the framework structure were verified by inductively coupled plasmaatomic emission spectrometry (ICP-AES), powder X-ray diffraction (PXRD), and BrunauerEmmettTeller (BET) surface-area analysis. Single-crystal X-ray diffractions studies revealed a single-crystal-to-single-crystal (SCSC)-transformation nature of the ion-exchange process. Hydrogen-sorption and magnetization measurements showed metal-specific properties of POST-65.

Inhibition of the Interaction Between NS3 Protease and HCV IRES With a Small Peptide: A Novel Therapeutic Strategy

Recently, we have demonstrated that the protease domain of NS3 alone can bind specifically to hepatitis C virus (HCV) internal ribosome entry site (IRES) near the initiator AUG, dislodges human La protein and inhibits translation in favor of viral RNA replication. Here, by using a computational approach, the contact points of the protease on the HCV IRES were putatively mapped. A 30-mer NS3 peptide was designed from the predicted RNA-binding region that retained RNA-binding ability and also inhibited IRES-mediated translation. This peptide was truncated to 15 mer and this also demonstrated ability to inhibit HCV RNA-directed translation as well as replication. More importantly, its activity was tested in an in vivo mouse model by encapsulating the peptide in Sendai virus virosomes followed by intravenous delivery. The study demonstrates for the first time that the HCV NS3-IRES RNA interaction can be selectively inhibited using a small peptide and reports a strategy to deliver the peptide into the liver.

Digestive ripening: a synthetic method par excellence for core-shell, alloy, and composite nanostructured materials

The solvated metal atom dispersion (SMAD) method has been used for the synthesis of colloids of metal nanoparticles. It is a top-down approach involving condensation of metal atoms in low temperature solvent matrices in a SMAD reactor maintained at 77 K. Warming of the matrix results in a slurry of metal atoms that interact with one another to form particles that grow in size. The organic solvent solvates the particles and acts as a weak capping agent to halt/slow down the growth process to a certain extent. This as-prepared colloid consists of metal nanoparticles that are quite polydisperse. In a process termed as digestive ripening, addition of a capping agent to the as-prepared colloid which is polydisperse renders it highly monodisperse either under ambient or thermal conditions. In this, as yet not well-understood process, smaller particles grow and the larger ones diminish in size until the system attains uniformity in size and a dynamic equilibrium is established. Using the SMAD method in combination with digestive ripening process, highly monodisperse metal, core-shell, alloy, and composite nanoparticles have been synthesized. This article is a review of our contributions together with some literature reports on this methodology to realize various nanostructured materials.

Molecular Design of Synthetic Benzimidazoles for the Switchover of the Duplex to G-quadruplex DNA Recognition

Benzimidazole derivatives are well known for their antibacterial, antiviral, anticonvulsant, antihistaminic, anthelmintic and antidepressant activities. Benzimidazole's unique base-selective DNA recognition property has been studied widely. However, most of the early benzimidazole systems have been targeted towards the binding of duplex DNA. Here we have shown the evolution and progress of the design and synthesis of new benzimidazole systems towards selective recognition of the double-stranded DNA first. Then in order to achieve selective recognition of the G-quadruplex DNA and utilize their potential as future anti-cancer drug candidates, we have demonstrated their selective cytotoxicity towards the cancer cells and potent telomerase inhibition ability.

A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus

Due to limited available therapeutic options, developing new lead compounds against hepatitis C virus is an urgent need. Human La protein stimulates hepatitis C virus translation through interaction with the hepatitis C viral RNA. A cyclic peptide mimicking the beta-turn of the human La protein that interacts with the viral RNA was synthesized. It inhibits hepatitis C viral RNA translation significantly better than the corresponding linear peptide at longer post-treatment times. The cyclic peptide also inhibited replication as measured by replicon RNA levels using real time RT-PCR. The cyclic peptide emerges as a promising lead compound against hepatitis C.

Designed three-stranded beta-sheet in an alpha/beta hybrid peptide

The incorporation of beta-amino acid residues into the antiparallel beta-strand segments of a multi-stranded beta-sheet peptide is demonstrated for a 19-residue peptide, Boc-LV(beta)FV(D)PGL(beta)FVVL(D)PGLVL(beta)FVV-OMe (BBH19). Two centrally positioned (D)Pro-Gly segments facilitate formation of a stable three-stranded beta-sheet, in which beta-phenylalanine ((beta)Phe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR-derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well-defined three-stranded beta-sheet structure in solution. Cross-strand interactions between (beta)Phe3/(beta)Phe17 and (beta)Phe3/Val15 residues define orientations of these side-chains. The observation of close contact distances between the side-chains on the N- and C-terminal strands of the three-stranded beta-sheet provides strong support for the designed structure. Evidence is presented for multiple side-chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three-stranded beta-sheet structures, which in turn influences the conformational interconversion between type I' and type II' beta-turns at the two (D)Pro-Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc-LV(beta)FV(D)PGL(beta)FVV-OMe (BBH10), which has been previously characterized as a type I' beta-turn nucleated hairpin, is shown to favour a type II' beta-turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.