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1.
Summary. A concise preparation of N
α-Fmoc-N
ɛ-(Boc, methyl)-lysine and its application in the synthesis of site-specifically lysine monomethylated peptide is described.
N
α-Fmoc-N
ɛ-(Boc, methyl)-lysine is obtained, via consecutive reductive benzylation and reductive methylation in a one-pot reaction,
followed by debenzylation through catalytic hydrogenolysis and Boc protection in another one-pot reaction. A peptide containing
monomethylated lysine is successfully synthesized by incorporating N
α-Fmoc-N
ɛ-(Boc, methyl)-lysine as a building block via solid-phase peptide synthesis. 相似文献
2.
Predicting secretory protein signal sequence cleavage sites by fusing the marks of global alignments
Summary. A newly synthesized secretory protein in cells bears a special sequence, called signal peptide or sequence, which plays the
role of “address tag” in guiding the protein to wherever it is needed. Such a unique function of signal sequences has stimulated
novel strategies for drug design or reprogramming cells for gene therapy. To realize these new ideas and plans, however, it
is important to develop an automated method for fast and accurately identifying the signal sequences or their cleavage sites.
In this paper, a new method is developed for predicting the signal sequence of a query secretory protein by fusing the results
from a series of global alignments through a voting system. The very high success rates thus obtained suggest that the novel
approach is very promising, and that the new method may become a useful vehicle in identifying signal sequence, or at least
serve as a complementary tool to the existing algorithms of this field. 相似文献
3.
Polimeno L Mittelman A Gennero L Ponzetto A Lucchese G Stufano A Kusalik A Kanduc D 《Amino acids》2008,34(3):479-484
Summary. Our labs are focused on identifying amino acid sequences having the ability to react specifically with the functional binding
site of a complementary antibody. Our epitopic definition is based on the analysis of the similarity level of antigenic amino
acid sequences to the host proteome. Here, the similarity profile to the human proteome of an HCV E1 immunodominant epitope,
i.e. the HCV E1315–328HRMAWDMMMNWSPT sequence, led to i) characterizing the immunoreactive HCV E1 315–328 region as a sequence endowed with a low
level of similarity to human proteins; ii) defining 2 contiguous immunodominant linear determinants respectively located at
the NH2 and COOH terminus of the conserved viral antigenic sequence. This study supports the hypothesis that low sequence similarity
to the host’s proteome modulates the pool of epitopic amino acid sequences in a viral antigen, and appears of potential value
in defining immunogenic viral peptide sequences to be used in immunotherapeutic approaches for HCV treatment.
Authors’ address: D. Kanduc, Department of Biochemistry and Molecular Biology, University of Bari, Via Orabona 4, Bari 70125,
Italy 相似文献
4.
5.
Using string kernel to predict signal peptide cleavage site based on subsite coupling model 总被引:2,自引:0,他引:2
Summary. Owing to the importance of signal peptides for studying the molecular mechanisms of genetic diseases, reprogramming cells
for gene therapy, and finding new drugs for healing a specific defect, it is in great demand to develop a fast and accurate
method to identify the signal peptides. Introduction of the so-called {−3,−1, +1} coupling model (Chou, K. C.: Protein Engineering, 2001, 14–2, 75–79) has made it possible to take into account the coupling effect among some key subsites and hence can significantly
enhance the prediction quality of peptide cleavage site. Based on the subsite coupling model, a kind of string kernels for
protein sequence is introduced. Integrating the biologically relevant prior knowledge, the constructed string kernels can
thus be used by any kernel-based method. A Support vector machines (SVM) is thus built to predict the cleavage site of signal
peptides from the protein sequences. The current approach is compared with the classical weight matrix method. At small false
positive ratios, our method outperforms the classical weight matrix method, indicating the current approach may at least serve
as a powerful complemental tool to other existing methods for predicting the signal peptide cleavage site.
The software that generated the results reported in this paper is available upon requirement, and will appear at http://www.pami.sjtu.edu.cn/wm.
An erratum to this article is available at . 相似文献
6.
Summary. The purpose of the present study was to determine whether the regulation of brain protein synthesis was mediated through changes
in the plasma concentrations of insulin and growth hormone (GH), and whether the concentrations of amino acids in the brain
and plasma regulate the brain protein synthesis when the quantity and quality of dietary protein is manipulated. Two experiments
were done on three groups of aged rats given diets containing 20% casein, 5% casein or 0% casein (Experiment 1), and 20% casein,
20% gluten, or 20% gelatin (Experiment 2) for 1 d (only one 5-h period) after all rats were fed the 20% casein diet for 10
d (only 5-h feeding per day). The aggregation of brain ribosomes, the concentration in plasma GH, and the branched chain amino
acids in the plasma and cerebral cortex declined with a decrease of quantity and quality of dietary protein. The concentration
of plasma insulin did not differ among groups. The results suggest that the ingestion of a higher quantity and quality of
dietary protein increases the concentrations of GH and several amino acids in aged rats, and that the concentrations of GH
and amino acids are at least partly related to the mechanism by which the dietary protein affects brain protein synthesis
in aged rats. 相似文献
7.
Summary. The five regioisomeric bromotryptophans (BrTrps) play an important role in the life of sponges and lower marine invertebrates.
These bromo-amino acids, which are formed by post-translational modifications, are not found in nature in their free state,
but rather are involved in more complex structures. Any of the BrTrps can be part of a peptide, a cyclic peptide, an indole
alkaloid, an ergot alkaloid, a macrocycle and others. The present review covers the synthesis, physical and spectroscopic
properties of the five BrTrps. It also describes the many exiting pharmacological and biological activities played by the
BrTrps and by various secondary metabolites containing brominated tryptophan moieties. Of special interest are cyclic peptides
containing the 2-BrTrp unit, which were isolated from marine sponges e.g. konbamide, orbiculamide A, the various keramamides,
jaspamide eusynstyelamide and more. Important families of non-cyclic peptides containing the 6-BrTrp, include the styelins,
the conotoxins, the cathelicidins and several constrained macrocyclic peptides. Many marine secondary BrTrp-containing, non-peptidic
metabolites also display a remarkable spectrum of bioactivities, which can be harnessed for therapeutic and other purposes.
Examples are: barettin, bromotryptanthrin, tetraacetyl clionamide, cyclocinamide A, clavicipitic acid, various brominated
β-carbolines. In this review we have presented the various synthetic routes leading to the preparation of the five BrTrps
and many of its derivatives. Also, we have introduced the reader to many synthetic routes leading to BrTrp-containing non-peptidic
natural products. Although the functional role of the various compounds in the human body is only poorly understood, its effects
were extensively studied. Almost all of these compounds exhibit important therapeutic properties e.g. antifungal, antimicrobial,
antihelmintic, insecticidal ichthyotoxic and anticancer activity. In the present review attempts have been made to provide
synopsis, synthesis and symbiosis of chemical and biological actions, which may provide future guidance and facilitate further
research in this area. 相似文献
8.
Brandsch M 《Amino acids》2006,31(2):119-136
Summary. Membrane transport of L-proline has received considerable attention in basic and pharmaceutical research recently. Of the
most recently cloned members of the solute carrier family, two are “proline transporters”. The amino acid transporter PAT1,
expressed in intestine, kidney, brain and other organs, mediates the uptake of proline and derivatives in a pH gradient-dependent
manner. The Na+-dependent proline transporter SIT1, cloned in 2005, exhibits the properties of the long-sought classical IMINO system. Proline-containing
peptides are of interest for several reasons. Many biologically important peptide sequences contain highly conserved proline
residues. Xaa-Pro peptides are very often resistant to enzymatic hydrolysis and display, in contrast to Pro-Xaa peptides,
a high affinity to the H+/peptide cotransporter PEPT1 which is expressed in intestinal, renal, lung and biliary duct epithelial cells. Furthermore,
several orally available drugs are recognized by PEPT1 as Xaa-Pro analogues due to their sterical resemblance to small peptides. 相似文献
9.
Krishnakumar I. M. Mathew Beena 《International journal of peptide research and therapeutics》2000,7(6):317-323
Summary The synthetic usefulness of the protocol using NMP/DMSO and DIEA for the synthesis of difficult sequence peptides on amphiphilic
and flexible 1,4-butanediol dimethacrylate-crosslinked polystyrene (BDDMA-PS) support was demonstrated by synthesizing [DAla17] analogue of gonadotropin releasing hormone precursor protein fragment (14–36) [hGnRH (14–36)] using Boc chemistry. The swelling
capacity of the peptidyl resin was followed as a measure of the aggregation of pendant peptide chains on the support. The
progress of chain assembly was monitored by quantitative ninhydrin test and amino acid analysis. The purity of the peptide
was checked by reverse phase HPLC and characterized by amino acid analysis and electrospray ionisation mass spectrometry (ESI-MS). 相似文献
10.
Role of osmoregulation in the actions of taurine 总被引:7,自引:0,他引:7
Summary. Taurine regulates an unusual number of biological phenomena, including heart rhythm, contractile function, blood pressure,
platelet aggregation, neuronal excitability, body temperature, learning, motor behavior, food consumption, eye sight, sperm
motility, cell proliferation and viability, energy metabolism and bile acid synthesis. Many of these actions are associated
with alterations in either ion transport or protein phosphorylation. Although the effects on ion transport have been attributed
to changes in membrane structure, they could be equally affected by a change in the activity of the affected transporters.
Three common ways of altering transporter activity is enhanced expression, changes in the phosphorylation status of the protein
and cytoskeletal changes. Interestingly, all three events are altered by osmotic stress. Since taurine is a key organic osmolyte
in most cells, the possibility that the effects of taurine on ion transport could be related to its osmoregulatory activity
was considered. This was accomplished by comparing the effects of taurine, cell swelling and cell shrinkage on the activities
of key ion channels and ion transporters. The review also compares the phosphorylation cascades initiated by osmotic stress
with some of the phosphorylation events triggered by taurine depletion or treatment. The data reveal that certain actions
of taurine are probably caused by the activation of osmotic-linked signaling pathways. Nonetheless, some of the actions of
taurine are unique and appear to be correlated with its membrane modulating and phosphorylation regulating activities.
Received January 25, 2000/Accepted January 31, 2000 相似文献
11.
Leila Malik A. Pernille Tofteng Søren L. Pedersen Kasper K. Sørensen Knud J. Jensen 《Journal of peptide science》2010,16(9):506-512
Precise microwave heating has emerged as a valuable method to aid solid‐phase peptide synthesis (SPPS). New methods and reliable protocols, as well as their embodiment in automated instruments, are required to fully use this potential. Here we describe a new automated robotic instrument for SPPS with microwave heating, report protocols for its reliable use and report the application to the synthesis of long sequences, including the β‐amyloid 1‐42 peptide. The instrument is built around a valve‐free robot originally developed for parallel peptide synthesis, where the robotic arm transports reagents instead of pumping reagents via valves. This is the first example of an ‘X‐Y’ robotic microwave‐assisted synthesizer developed for the assembly of long peptides. Although the instrument maintains its capability for parallel synthesis at room temperature, in this paper, we focus on sequential peptide synthesis with microwave heating. With this valve‐free instrument and the protocols developed for its use, fast and efficient syntheses of long and difficult peptide sequences were achieved. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
12.
Peptaibiomics: an advanced, rapid and selective analysis of peptaibiotics/peptaibols by SPE/LC-ES-MS
Summary. “Proteomics” and “peptidomics” are used as technical terms to define the analysis and study of all proteins and peptides expressed
in an organism or tissue. In analogy we propose the name peptaibiomics for the analysis of a group of fungal peptide antibiotics (peptaibiotics) containing the characteristic amino acid Aib (α-aminoisobutyric
acid). In analogy to the peptidome the complete expression of peptaibiotics by fungal multienzyme complexes should be named
the peptaibiome.
Peptaibiotics are defined as peptides containing Aib and exerting a variety of bioactivities. They comprise the sub-groups
of N-acetylated peptaibols, characterized also by a C-terminal amide-linked 2-amino alcohol, and lipopeptaibols having in place of an acetyl group a lipophilic fatty acid acyl
group. Furthermore, lipoaminopeptides are also known with long-chain fatty acid on the N-termini, a lipoamino acid in position three and a strongly basic secondary or tertiary amine form a subgroup of mixed forms
which could not be integrated in one of these three previously mentioned groups.
Here we present a specific and rapid screening method on the peptaibiome applicable directly onto filamentous fungi cultured
in a single Petri dish. The method comprises solid-phase extraction (SPE) of peptaibiotics followed by on-line reversed-phase
HPLC coupled to an ion trap electrospray tandem mass spectrometer (ES-MS). The presence of these peptides is indicated by
characteristic mass differences of Δm = 85.1 Da representing Aib-residues which can be observed in the b-series of acylium fragment ions resulting from ES-MS. Partial sequences can be deduced from the data and compared with structures
compiled in electronic peptaibol data bases. The judgement is possible whether or not structures are novel, already known
or related to known structures. Suitability of the method is demonstrated with the analysis of strains of Trichoderma and its teleomorph Hypocrea. New sequences of peptaibiotics are presented and those being related to established 10- to 18-residue peptaibols trichovirin,
trichogin and trichotoxin, which have been described in the literature. 相似文献
13.
E. Yu. Aleshina N. V. Pyndyk A. A. Moisa M. A. Sanzhakov O. N. Kharybin E. N. Nikolaev E. F. Kolesanova 《Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry》2008,2(3):288-292
The peptide RHDSGY, a fragment of the human β-amyloid Zn-binding site, and its isomers RH(D-Asp)SGY and RH(β-Asp)SGY have been obtained as amides by means of solid-phase synthesis and analyzed by HPLC and various mass spectrometric methods. The problem of low yield of the RHDSGY peptide and its isomers attributed to 9-fluorenylmethoxycarbonyl (Fmoc)-amino acids and/or formation of such side-products as RH(β-Asp)SGY (or RHDSGY during synthesis of RH(β-Asp)SGY) and RH(Asp-imide) SGY was solved via selection of individual reagents for removal of Fmoc groups from α-amino groups of the growing peptide chain. 相似文献
14.
Summary. The capability of ficin, a cystine protease, to form peptide bonds was investigated using several types of N-Boc-amino acid phenyl and naphthyl esters as acyl donor components. Enzyme-catalyzed peptide synthesis was carried out under
optimized reaction conditions of pH, acyl acceptor concentration and selection of the best yield organic solvent. It used
a condensation of N-Boc-Ala-OpGu and Ala-pNA as a model reaction. The products were obtained in 72–96% yield using 10 different substrates, within a few minutes of
reaction time.
Authors’ address: Prof. Haruo Sekizaki, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu,
Hokkaido 061-0293, Japan 相似文献
15.
Peeters NM Chapron A Giritch A Grandjean O Lancelin D Lhomme T Vivrel A Small I 《Journal of molecular evolution》2000,50(5):413-423
Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments
and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these
putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently
dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate
cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred
from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial).
These case histories are the best examples to date of capture of organellar aminoacyl-tRNA synthetases by the cytosolic protein
synthesis machinery.
Received: 8 October 1999 / Accepted: 23 January 2000 相似文献
16.
Using cellular automata images and pseudo amino acid composition to predict protein subcellular location 总被引:6,自引:0,他引:6
Summary. The avalanche of newly found protein sequences in the post-genomic era has motivated and challenged us to develop an automated
method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge
thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish
such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly
variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246–255), the approach of cellular automata image is introduced to cope with this problem. Many important features,
which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images.
One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target
aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively. 相似文献
17.
Summary. Transmembrane (TM) proteins represent about 20–30% of the protein sequences in higher eukaryotes, playing important roles
across a range of cellular functions. Moreover, knowledge about topology of these proteins often provides crucial hints toward
their function. Due to the difficulties in experimental structure determinations of TM protein, theoretical prediction methods
are highly preferred in identifying the topology of newly found ones according to their primary sequences, useful in both
basic research and drug discovery. In this paper, based on the concept of pseudo amino acid composition (PseAA) that can incorporate
sequence-order information of a protein sequence so as to remarkably enhance the power of discrete models (Chou, K. C., Proteins:
Structure, Function, and Genetics, 2001, 43: 246–255), cellular automata and Lempel-Ziv complexity are introduced to predict
the TM regions of integral membrane proteins including both α-helical and β-barrel membrane proteins, validated by jackknife
test. The result thus obtained is quite promising, which indicates that the current approach might be a quite potential high
throughput tool in the post-genomic era. The source code and dataset are available for academic users at liml@scu.edu.cn.
Authors’ address: Menglong Li, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China 相似文献
18.
A previously unidentified extension of an open reading frame from the genomic DNA of Japonica rice (Oryza sativa L.) encoding oryzacystatin-I (OC-I; access. M29259, protein ID AAA33912.1) has been identified as a 5′ gene segment coding for the OC-I signal peptide. The signal peptide appears to direct a pre-protein (SPOC-I; Accession No. AF164378) to the endoplasmic reticulum,
where it is processed into the mature form of OC-I. The start codon of SPOC-I begins 114 bp upstream from that previously published for OC-I. A putative proteolytic site, which may yield a mature OC-I approximately 12 residues larger than previously described, has
been identified within SPOC-I between Ala-26 and Glu-27. The signal peptide sequence was amplified by polymerase chain reaction
using genomic DNA from O. sativa seedlings and ligated to the 5′ end of the truncated OC-I gene at the endogenous SalI site. Partially purified protein extracts from Escherichia coli expressing SPOC-I reacted with polyclonal antibodies raised against OC-I and revealed a protein of the expected molecular weight (15,355 Da).
In-vitro translation of SPOC-I in the presence of microsomal membranes yielded a processed product approximately 2.7 kDa smaller than the pre-protein. Nicotiana tabacum L. cv. Xanthi plants independently transformed with the SPOC-I gene processed SPOC-I and accumulated the mature form of OC-I (approximately 12.6 kDa), which co-migrated with natural, mature
OC-I extracted from rice seed when separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Received: 29 July 1999 / Accepted: 25 August 1999 相似文献
19.
Summary. The accumulation of oxidized proteins is known to be linked to some severe neurodegenerative diseases like Alzheimer’s, Parkinson’s
and Huntington’s disease. Furthermore, the aging process is also accompanied by an ongoing aggregation of misfolded and damaged
proteins. Therefore, mammalian cells have developed potent degradation systems, which selectively degrade damaged and misfolded
proteins. The proteasomal system is largely responsible for the removal of oxidatively damaged proteins form the cellular
environment. Not only cytosolic proteins are prone to oxidative stress, also nuclear proteins are readily oxidized. The nuclear
proteasomal system is responsible for the degradation of these proteins. This review is focused on the specific degradation
of oxidized nuclear proteins, the role of the proteasome in this process and the regulation of the nuclear proteasomal system
under oxidative conditions. 相似文献
20.
Summary. Due to the obvious advantages of long-acting peptide and protein drugs, strategies to prolong plasma half life time of such
compounds are highly on demand. Short plasma half life times are commonly due to fast renal clearance as well as to enzymatic
degradation occurring during systemic circulation. Modifications of the peptide/protein can lead to prolonged plasma half
life times. By shortening the overall amino acid amount of somatostatin and replacing l-analogue amino acids with d-amino acids, plasma half life time of the derivate octreotide was 1.5 hours in comparison to only few minutes of somatostatin.
A PEG2,40 K conjugate of INF-α-2b exhibited a 330-fold prolonged plasma half life time compared to the native protein. It was the aim
of this review to provide an overview of possible strategies to prolong plasma half life time such as modification of N- and
C-terminus or PEGylation as well as methods to evaluate the effectiveness of drug modifications. Furthermore, fundamental
data about most important proteolytic enzymes of human blood, liver and kidney as well as their cleavage specificity and inhibitors
for them are provided in order to predict enzymatic cleavage of peptide and protein drugs during systemic circulation. 相似文献