1.
The Thorny Way to the Mechanism of Ribosomal Peptide-Bond Formation.
Source
Department, AG Ribosomen, Abteilung Vingron, Max-Planck-Insitut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin (Germany).
Abstract
Per aspera ad astra: Kinetic isotope effects have indicated a new and comprehensive picture of the central ribosomal enzymatic activity, peptide-bond formation. To this end, isotopes were incorporated in the positions highlighted in red.
Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
- PMID:
- 22213275
- [PubMed - as supplied by publisher]
Local Unfolding of Cu, Zn Superoxide Dismutase Monomer Determines the Morphology of Fibrillar Aggregates.
Source
Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Abstract
Aggregation of Cu, Zn superoxide dismutase (SOD1) is often found in amyotrophic lateral sclerosis patients. The fibrillar aggregates formed by wild type and various disease-associated mutants have recently been found to have distinct cores and morphologies. Previous computational and experimental studies of wild-type SOD1 suggest that the apo-monomer, highly aggregation prone, displays substantial local unfolding dynamics. The residual folded structure of locally unfolded apoSOD1 corresponds to peptide segments forming the aggregation core as identified by a combination of proteolysis and mass spectroscopy. Therefore, we hypothesize that the destabilization of apoSOD1 caused by various mutations leads to distinct local unfolding dynamics. The partially unfolded structure, exposing the hydrophobic core and backbone hydrogen bond donors and acceptors, is prone to aggregate. The peptide segments in the residual folded structures form the "building block" for aggregation, which in turn determines the morphology of the aggregates. To test this hypothesis, we apply a multiscale simulation approach to study the aggregation of three typical SOD1 variants: wild type, G37R, and I149T. Each of these SOD1 variants has distinct peptide segments forming the core structure and features different aggregate morphologies. We perform atomistic molecular dynamics simulations to study the conformational dynamics of apoSOD1 monomer and coarse-grained molecular dynamics simulations to study the aggregation of partially unfolded SOD1 monomers. Our computational studies of monomer local unfolding and the aggregation of different SOD1 variants are consistent with experiments, supporting the hypothesis of the formation of aggregation "building blocks" via apo-monomer local unfolding as the mechanism of SOD1 fibrillar aggregation.
Copyright © 2011 Elsevier Ltd. All rights reserved.
The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations.
Source
School of Medical and Molecular Biosciences, Sydney, New South Wales, Australia.
Abstract
Malaria caused by several species of Plasmodium is major parasitic disease of humans, causing 1-3 million deaths worldwide annually. The widespread resistance of the human parasite to current drug therapies is of major concern making the identification of new drug targets urgent. While the parasite grows and multiplies inside the host erythrocyte it degrades the host cell hemoglobin and utilizes the released amino acids to synthesize its own proteins. The P. falciparum malarial M1 alanyl-aminopeptidase (PfA-M1) is an enzyme involved in the terminal stages of hemoglobin digestion and the generation of an amino acid pool within the parasite. The enzyme has been validated as a potential drug target since inhibitors of the enzyme block parasite growth in vitro and in vivo. In order to gain further understanding of this enzyme, molecular dynamics simulations using data from a recent crystal structure of PfA-M1 were performed. The results elucidate the pentahedral coordination of the catalytic Zn in these metallo-proteases and provide new insights into the roles of this cation and important active site residues in ligand binding and in the hydrolysis of thepeptide bond. Based on the data, we propose a two-step catalytic mechanism, in which the conformation of the active site is altered between the Michaelis complex and the transition state. In addition, the simulations identify global changes in the protein in which conformational transitions in the catalytic domain are transmitted at the opening of the N-terminal 8 Å-long channel and at the opening of the 30 Å-long C-terminal internal chamber that facilitates entry ofpeptides to the active site and exit of released amino acids. The possible implications of these global changes with regard to enzyme function are discussed.
Circular micro-proteins and mechanisms of cyclization.
Source
Department of Biochemistry, La Trobe University, Melbourne, Victoria 3086, Australia. m.anderson@latrobe.edu.au.
Abstract
Transpeptidation reactions result in the formation of new peptide bonds and this can occur between two separatepeptides or within the one peptide. These reactions are catalyzed by enzymes and when the N- and C-terminus of the one peptide are joined it results in the formation of cyclic proteins. Cyclization via head-to-tail linkage of the termini of apeptide chain occurs in only a small percentage of proteins but gives the resultant cyclic proteins exceptional stability. The mechanisms are not well understood and this review documents what is known of the events that lead to cyclization. Gene encoded cyclic proteins are found in both prokaryotic and eukaryotic species. The prokaryotic circular proteins include the bacteriocins and pilins. The eukaryotic circular proteins in mammals include the θ-defensins and retrocyclins. Small cyclic proteins are also found in fungi and a large range of cyclic proteins are expressed in cyanobacteria. Three types of cyclic proteins have been found in plants, the small cyclic proteins of 5-12 amino acids, the cyclic proteins from sunflower which are made up of 12-14 amino acids, and the larger group known as cyclotides which contain 28-37 amino acids. Three classes of enzymes are able to catalyse transpeptidation reactions, these include the cysteine, serine and threonine proteases. However only cysteine and serine proteases have been documented to cyclize proteins. The cyclotides from Oldenlandia affinis, the plant in which cyclotides were first discovered, are processed by an asparaginyl endopeptidase which is a cysteine protease. These proteases cleave an amide bond and form an acyl enzyme intermediate before nucleophilic attack of the amine group of the N-terminal residue to form a peptide bond, resulting in a cyclic peptide.
Rethinking amide bond synthesis.
Source
Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland.
Abstract
One of the most important reactions in organic chemistry--amide bond formation--is often overlooked as a contemporary challenge because of the widespread occurrence of amides in modern pharmaceuticals and biologically active compounds. But existing methods are reaching their inherent limits, and concerns about their waste and expense are becoming sharper. Novel chemical approaches to amide formation are therefore being developed. Here we review and summarize a new generation of amide-forming reactions that may contribute to solving these problems. We also consider their potential application to current synthetic challenges, including the development of catalytic amide formation, the synthesis of therapeutic peptides and the preparation of modified peptides and proteins.
An Exit Cavity Was Crucial to the Polymerase Activity of the Early Ribosome.
Source
1 Department of Biology and Biochemistry, University of Houston , Houston, Texas, USA .
Abstract
Abstract The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptidebond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di- or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World. Key Words: Ribosome-RNA World-Prebiotic synthesis-Chirality-Ribosomal RNA. Astrobiology 12, xxx-xxx.
The Early Life of a Peptide Cation-Radical. Ground and Excited-State Trajectories of Electron-Based Peptide Dissociations During the First 330 Femtoseconds.
Source
Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, USA.
Abstract
We report a new approach to investigating the mechanisms of fast peptide cation-radical dissociations based on an analysis of time-resolved reaction progress by Ehrenfest dynamics, as applied to an Ala-Arg cation-radical model system. Calculations of stationary points on the ground electronic state that were carried out with effective CCSD(T)/6-311++G(3df,2p) could not explain the experimental branching ratios for loss of a hydrogen atom, ammonia, and N-C(α)bond dissociation in (AR + 2H)(+[Symbol: see text]). The Ehrenfest dynamics results indicate that the ground and low-lying excited electronic states of (AR + 2H)(+[Symbol: see text]) follow different reaction courses in the first 330 femtoseconds after electron attachment. The ground (X) state undergoes competing loss of N-terminal ammonia and isomerization to an aminoketyl radical intermediate that depend on the vibrational energy of the charge-reduced ion. The A and B excited states involve electron capture in the Arg guanidine and carboxyl groups and are non-reactive on the short time scale. The C state is dissociative and progresses to a fast loss of an H atom from the Arg guanidine group. Analogous results were obtained by using the B3LYP and CAM-B3LYP density functionals for the excited state dynamics and including the universal M06-2X functional for ground electronic state calculations. The results of this Ehrenfest dynamics study indicate that reaction pathway branching into the various dissociation channels occurs in the early stages of electron attachment and is primarily determined by the electronic states being accessed. This represents a new paradigm for the discussion of peptide dissociations in electron based methods of mass spectrometry.
Microbial degradation of physiologically active peptides by strain B-9.
Source
Department of Pharmacology, Aichi Medical University, Nagakute, Aichi, 480-1195, Japan, fumio@ipc-tokai.or.jp.
Abstract
The reaction of some physiologically active peptides with bacterial strain B-9 has been investigated. Bradykinin, β-endorphin, and [Leu(5)]enkephalin were quickly degraded, with half-lives of <5 min. Somatostatin, substance P, and angiotensin I were degraded relatively smoothly, with half-lives of 10 min to 1 h, whereas oxytocin and insulin were slowly degraded, with half-lives of 1 and 4 days, respectively. Vasopressin was barely degraded, with a half-life of >7 days. Linearized vasopressin, prepared by the reductive cleavage of the disulfide bond followed by alkylation with iodoacetamide, was degraded significantly faster than intact vasopressin, with a half-life of 2.5 h. A loop formed by disulfide bond formation was regarded as one of the degradation-resistant factors. Hydrolysis of the peptides in this study took place through cleavage of various peptide bonds, and the strain B-9 may bear similarities to the neutral endopeptidase in terms of its broad selectivity.
Baupain, a plant cysteine proteinase that hinders thrombin-induced human platelet aggregation.
Source
Universidade Federal de São Paulo Departamento de Bioquímica Rua Três de Maio 100, 04044-020 São Paulo, SP, Brazil. olivaml.bioq@epm.br.
Abstract
Bauninia forficata is trivially known as cow paw, and popularly used in Brazil for treatment of diabetes mellitus. Denominated baupain a cysteine proteinase was purified from B. forficata leaves. In this study, we investigated the baupain effect on aggregation of isolated human platelets in vitro and the results show that baupain hinders thrombin - but not ADP- and collagen- induced platelet aggregation. With synthetic quenched-fluorescent peptides, the kinetics of the cleavage site of human proteinase-activated receptor 1 / 2 / 3 and 4 [PAR-1 / 2 / 3 and 4] by baupain was determined. In conclusion, similar to bromelain and papain, baupain hinders human platelets aggregation, probably through an unspecific cleavage in the Phe-Leu bond of PAR1.
- PMID:
- 22185503
- [PubMed - as supplied by publisher]
Multifunctional PEGylated 2C5-immunoliposomes containing pH-sensitive bonds and TAT peptide for enhanced tumor cell internalization and cytotoxicity.
Abstract
pH-sensitive PEGylated (with PEG-PE) long-circulating liposomes (HSPC:cholesterol and Doxil®), modified with cell-penetrating TAT peptide (TATp) moieties and cancer-specific mAb 2C5 were prepared. A degradable pH-sensitive hydrazone bond between a long shielding PEG chains and PE (PEG(2k)-Hz-PE) was introduced. TATp was conjugated with a short PEG(1k)-PE spacer and mAb 2C5 was attached to a long PEG chain (2C5-PEG(3.4k)-PE). The "shielding" effect of TATp by long PEG chains was investigated using three liposomal models. At normal pH, surface TATp moieties are "hidden" by the long PEG chains. Upon the exposure to lowered pH, this multifunctional carrier exposes TATp moieties after the degradation of the hydrazone bond and removal of the long PEG chains. Enhanced cellular uptake of the TATp-containing immunoliposomes was observed in vitro after pre-treatment at lowered pH (using flow cytometry and fluorescence microscopy techniques). The presence of mAb 2C5 on the liposome surface further enhanced the interaction between the carrier and tumor cells but not normal cells. Furthermore, multifunctional immuno-Doxil® preparation showed increased cellular cytotoxicity of B16-F10, HeLa and MCF-7 cells when pre-incubated at lower pH, indicating TATp exposure and activity. In conclusion, a multifunctional immunoliposomal nanocarrier containing a pH-sensitive PEG-PE component, TATp, and the cancer cell-specific mAb 2C5 promotes enhanced cytotoxicity and carrier internalization by cancer cells and demonstrates the potential for intracellular drug delivery after exposure to lowered pH environment, typical of solid tumors.
Copyright © 2011. Published by Elsevier B.V.
Solid-phase synthesis of functionalized bis-peptides.
Source
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Abstract
We demonstrate the first solid-phase synthesis of highly functionalized bis-peptides. Bis-peptides are ladder oligomers composed of stereochemically pure, cyclic bis-amino acids joined by substituted diketopiperazine linkages. They have a shape-programmable backbone that is controlled by controlling the stereochemistry and sequence of the monomers within each oligomer. Functionalized bis-peptides are assembled using a new amide bond forming reaction (acyl-transfer coupling) that we have previously developed and a novel activation strategy that allows the sequential formation of penta- and hexa-substituted diketopiperazines from extremely hindered N-alkyl-alpha,alpha-disubstituted amino acids. We present mechanistic evidence that acyl-transfer coupling is competitive with direct acylation in the formation of hindered amide bonds. We also detail the synthesis of four functionalized bis-peptides, and that by combining bis-peptides with amino acids through diketopiperazine linkages, bis-peptides can mimic the display of residues i, i+4, i+7 of an alpha-helical peptide.
- PMID:
- 22180905
- [PubMed - in process]
Computational Study of the Covalent Bonding of Microcystins to Cysteine Residues - A Reaction Involved in the Inhibition of the PPP Family of Protein Phosphatases.
Source
CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal Departmento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
Abstract
Microcystins are cyclic peptides produced by Cyanobacteria that are hepatotoxic to mammals. The toxicity mechanism involves the potent inhibition of protein phosphatases, as the toxins bind the catalytic subunits of five enzymes of the PPP family of serine/threonine-specific phosphatases: Ppp1 (aka PP1), Ppp2 (aka PP2A), Ppp4, Ppp5 and Ppp6. The interaction with the proteins includes the formation of a covalent bond with a cysteine residue. Although this reaction seems to be accessory for the inhibition of PPP enzymes, it has been suggested to play an important part in the biological role of microcystins, and is furthermore involved in their non-enzymatic conjugation to glutathione. In this study, the molecular interaction of microcystins with their targeted PPP catalytic subunits is reviewed, including the relevance of the covalent bond for overall inhibition. The chemical reaction that leads to the formation of the covalentbond was evaluated in silico, both thermodynamically and kinetically, using quantum mechanical-based methods. As a result, it was confirmed to be a Michael-type addition, with simultaneous abstraction of the thiol hydrogen by a water molecule, transfer of hydrogen from the water to the microcystin's α,β-unsaturated carbonyl group, and addition of the sulfur to the β-carbon of the microcystin's moiety. The calculated kinetics is in agreement with previous experimental results, which had indicated the reaction to occur in a second step after a fast noncovalent interaction that inhibited the enzymes per se.
Journal compilation © 2011 Federation of European Biochemical Societies.
Partial Blocking of Mouse DSPP Processing by Substitution of Gly(451)-Asp(452) Bond Suggests the Presence of Secondary Cleavage Site(s).
Source
Department of Biomedical Sciences, Baylor College of Dentistry, Texas A&M Health Science Center , Dallas, Texas 75246.
Abstract
Abstract Dentin sialophosphoprotein (DSPP) in the extracellular matrix of dentin is cleaved into dentin sialoprotein (DSP) and dentin phosphoprotein (DPP), which originate from the NH(2)-terminal and COOH-terminal regions of DSPP, respectively. In the proteolytic processing of mouse DSPP, the peptide bond at Gly(451)-Asp(452) has been shown to be cleaved by bone morphogenetic protein 1 (BMP1)/Tolloid-like metalloproteinases. In the present study, we generated transgenic mice expressing a mutant DSPP in which Asp(452) was substituted by Ala(452). Protein chemistry analyses of extracts from the long bone of these transgenic mice showed that the D452A substitution partially blocked DSPP processing in vivo. When the full-length form of mutant DSPP (designated "D452A-DSPP") isolated from the transgenic mice was treated with BMP1 in vitro, a portion of the D452A-DSPP was cleaved, suggesting the presence of secondarypeptide bond(s) that can be broken by BMP1. To identify the potential secondary DSPP cleavage site(s), site-directed mutagenesis was performed to generate nine DNA constructs expressing DSPP bearing substitutions at potential scission sites. These different types of mutant DSPP made in eukaryotic cell lines were treated with BMP1 and the digestion products were assessed by Western immunoblotting. All of the mutant DSPP molecular species were partially cleaved by BMP1, giving rise to a protein band on SDS-PAGE similar to that of normal DSP. Taken together, we concluded that in addition to the peptide bond Gly(451)-Asp(452), there must be a cryptic cleavage site or sites close to Asp(452) in the mouse DSPP that can be cleaved by BMP1.
Novel structures of self-associating stapled peptides.
Source
New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027. sbhattacharya@nysbc.org.
Abstract
Hydrocarbon stapling of peptides is a powerful technique to transform linear peptides into cell-permeable helical structures that can bind to specific biological targets. In this study, we have used high resolution solution NMR techniques complemented by Dynamic Light Scattering to characterize extensively a family of hydrocarbon stapledpeptides with known inhibitory activity against HIV-1 capsid assembly to evaluate the various factors that modulate activity. The helical peptides share a common binding motif but differ in charge, the length and position of the staple. An important outcome of the study was to show the peptides share a propensity to self-associate into organized polymeric structures mediated predominantly by hydrophobic interactions between the olefinic chain and the aromatic side-chains from the peptide. We have also investigated in detail the structural significance of the length and position of the staple, and of olefinic bond isomerization in stabilizing the helical conformation of the peptides as potential factors driving polymerization. This study presents the numerous challenges of designing biologically active stapled peptides and the conclusions have broad implications for optimizing a promising new class of compounds in drug discovery. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011.
Copyright © 2011 Wiley Periodicals, Inc.
Glycine insertion at protease cleavage site of SNAP25 resists cleavage but enhances affinity for botulinum neurotoxin serotype A.
Source
Department of Microbiology, University of Illinois at Urbana-Champaign.
Abstract
The light chain of botulinum neurotoxin A (BoNT/A-LC) is a Zn-dependent protease that specifically cleaves SNAP25 of the SNARE complex, thereby impairing vesicle fusion and neurotransmitter release at neuromuscular junctions. The C-terminus of SNAP25 (residues 141-206) retains full activity for BoNT/A-LC-catalyzed cleavage at P1-P1' (Gln197-Arg198). Using the structure of a complex between the C-terminus of SNAP25 and BoNT/A-LC as a model to design SNAP25-derived pseudosubstrate inhibitors (SNAPIs) that prevent presentation of the scissile bond to the active site, we introduced multiple His residues to replace Ala-Asn-Gln-Arg (residues 195-198) at the substrate cleavage site, with the intent to identify possible side-chain interactions with the active site Zn. We also introduced multiple Gly residues between the P1-P1' residues to explore the spatial tolerance within the active-site cleft. Using a FRET substrate YsCsY, we compared a series of SNAPIs for inhibition of BoNT/A-LC. Among the SNAPIs tested, several known cleavage-resistant, single-point mutants of SNAP25 were poor inhibitors, with most of the mutants losing binding affinity. Replacement with His at the active site did not improve inhibition over wildtype substrate. In contrast, Gly-insertion mutants were not only resistant to cleavage, but also surprisingly showed enhanced affinity for BoNT/A-LC. Two of the Gly-insertion mutants exhibited 10-fold lower IC(50) values than the wildtype 66-mer SNAP25 peptide. Our findings illustrate a scenario, where the induced fit between enzyme and bound pseudosubstrate fails to produce the strain and distortion required for catalysis to proceed.
Copyright © 2011 The Protein Society.
A Pseudo MS(3) Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search.
Source
Applied Biotechnology Branch, Air Force Research Laboratory, Dayton, OH, 45433, USA, jianzhongc@yahoo.com.
Abstract
It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs.
Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system.
Source
Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China.
Abstract
The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.
Copyright © 2011 Wiley Periodicals, Inc.
Peptidyl-tRNA hydrolase screening combined with molecular docking reveals the antibiotic potential of Syzygium johnsonii bark extract.
Source
Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
Abstract
With the rapid rise of antibiotic resistance in pathogenic bacteria, the need for new antibacterial agents is overwhelming. Herein we report the limited screening of tropical plant extracts for inhibitory activity against the essential enzyme peptidyl-tRNA hydrolase (Pth). Initial screening was conducted through an electrophoretic mobility assay and Northern blot detection. The ability of Pth to cleave the peptide-tRNA ester bond was assessed. The ethanol bark extract of Syzygium johnsonii showed strong inhibitory potential. Molecular docking studies point to Syzygium polyphenolics as the potential source of inhibition. This work is the forerunner of activity-directed isolation, purification, and structure elucidation of the inhibitory components from Syzygium johnsonii extracts and studies of compound interaction with Pth.
- PMID:
- 22164773
- [PubMed - in process]
Tissue engineering based on electrochemical desorption of an RGD-containing oligopeptide.
Source
Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan.
Abstract
This paper describes a non-invasive approach for efficient detachment of cells adhered to a gold substrate via a specific oligopeptide. Detachment is effected by an electrical stimulus. The oligopeptide contains cysteine, which spontaneously forms a gold-thiolate bond on a gold surface. This chemical adsorption reaches > 95% equilibrium within 10 min after immersion of a gold-coated substrate in a solution containing the peptide. The peptide is reversibly desorbed from the surface within 5 min of application of a negative electrical potential. By taking advantage of this simple adsorption and desorption mechanism, cells can be grown on an oligopeptide-functionalized gold surface and can be efficiently detached as single cells or cell sheets by application of a negative electrical potential. This approach was also applied to the surface of gold-coated microrods. Capillary-like microchannels were formed in collagen gel by transferring endothelial cells to the internal surfaces of the microchannels. During subsequent perfusion culture, the enveloped endothelial cells migrated into the collagen gel and formed luminal structures, which sprouted from the microchannels. This technique has the potential to provide a fundamental tool for the engineering of thick cell sheets as well as vascularized tissues and organs. Copyright © 2011 John Wiley & Sons, Ltd.
Copyright © 2011 John Wiley & Sons, Ltd.
Formation of y + 10 and y + 11 Ions in the Collision-Induced Dissociation ofPeptide Ions.
Source
Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, 100 Bureau Drive, MS8320, Gaithersburg, MD, 20899, USA, lisa.kilpatrick@nist.gov.
Abstract
Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to y(n-1) + 10 and y(n-1) + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO - H(2)O] and [+ CO - NH(3)], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H(2)O or NH(3). MS(3) spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The y(n-1) + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The y(n-1) + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the y(n-1) + 10 ions decrease with increasing peptide length. These data for y(n-1) + 10 and y(n-1) + 11 ion formation may be used to improve peptideidentification from tandem mass spectra.
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