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Protein & Peptide Letters
ISSN: 0929-8665
Protein & Peptide Letters
Volume 13, Number 10, 2006
Contents
Regular Papers
Two-Dimensional Gel Electrophoresis Based Technologies
for Potential Biomarkers Identification in Amniotic Fluid:
A Simple Model Pp. 959-963
P.-A. Queloz, D. Crettaz, L. Thadikkaran, V. Sapin and
J.-D. Tissot
[Abstract]
Support Vector Machine for Discrimination of
Thermophilic and Mesophilic Proteins Based on Amino Acid Composition
Pp. 965-970
G. Zhang and B. Fang
[Abstract]
Prediction of Mutations in H5N1 Hemagglutinins from
Influenza A Virus Pp. 971-976
G. Wu and S. Yan
[Abstract]
A Role for the Strained Phenylalanine Ring Rotation
Induced by Substrate Binding to Cytochrome CYP102A1
Pp. 977-980
D.C. Haines
[Abstract]
Methodological Improvements on Extraction of Nuclear
Proteins and Its Preliminary Analysis During the Maize (Zea
mays L.) Endosperm Development Pp. 981-984
B.S. Ferreira, A.T. Branco, M.A. de Oliveira, M.G. Pereira
and G.A. de Souza Filho
[Abstract]
Improved Performance in Protein Secondary Structure
Prediction by Combining Multiple Predictions Pp.
985-991
D.-S. Huang and X. Huang
[Abstract]
Roles of Nitric Oxide Synthase inhibitor on Antinociceptive
Effects of μ-Opioid
Agonist in Mice Pp. 993-997
L.-X. Chen, Y.-M. Qi, R. Wang, X. Duan, Y.-F. Gao and
D.-J. Yang
[Abstract]
Inferring Protein-Protein Interacting Sites Using
Residue Conservation and Evolutionary Information
Pp. 999-1005
B. Wang, H.S. Wong and D.-S. Huang
[Abstract]
Conformational Features of the Dippu-AST 8 Neuropeptide
from the Cockroach Diploptera punctata Pp.
1007-1015
I.N. Alieva, L.I. Velieva, M.A. Musayev and N.M. Gojayev
[Abstract]
Immunoreceptor Transmembrane Peptides and Their Effect
on Natural Killer (NK) Cell Cytotoxicity Pp. 1017-1024
H. Vandebona, M. Ali, M. Amon, V. Bender and N. Manolios
[Abstract]
Antiviral Properties of Combination Peptides of HIV-1
Rev NLS and NES Pp. 1025-1027
N. Kobayashi, T. Sato and T. Yoshida
[Abstract]
Cloning and Characterization of a cDNA Encoding a
Cowpea Seed Defensin and Analysis of Its Expression
Pp. 1029-1036
A.O. Carvalho, G.A.S. Filho, B.S. Ferreira, A.T. Branco,
A.L. Okorokova-Façanha and V.M. Gomes
[Abstract]
Endomorphins Restored the Endothelium-Dependent Relaxation
of the Rabbit Aorta Rings Exposed to High D-Glucose Condition
Via NO-cGMP Pathway Pp. 1037-1044
J. Liu, W.-M. Wu, J.-J. Che, J. Zhang and R. Wang
[Abstract]
Expression of the Canavalia brasiliensis
Lectin (ConBr) in Tobacco Plants Pp. 1045-1049
C.P.S. Carvalho, T.O. Correia, S.M.S. Ribeiro, I.C. Silva,
J.T.A. Oliveira and T.B. Grangeiro
[Abstract]
Crystallization Report
Protein Preparation, Crystallization and Preliminary
X-Ray Crystallographic Studies of Smu.1392c from Streptococcus
mutans Pp. 1051-1052
Z.-Q. Gao, H.-F. Hou, Y.-H. Liang, L.-F. Li, X.-D. Su
and Y.-H. Dong
[Abstract]
Abstracts
[Back to top]
Two-Dimensional Gel Electrophoresis Based Technologies for
Potential Biomarkers Identification in Amniotic Fluid: A Simple
Model
P.-A. Queloz, D. Crettaz, L. Thadikkaran, V. Sapin and
J.-D. Tissot
To assess the efficiency of two-dimensional fluorescence
difference gel electrophoresis (2D-DIGE) and of two-dimensional
electrophoresis and ammoniacal silver staining (2D-E), different
amounts of soybean trypsin inhibitor and horse myoglobin were
added to amniotic fluid. In this model, a minimum of 5 to
10 ng of “artificial” biomarkers was detected.
[Back to top]
Support Vector Machine for Discrimination of
Thermophilic and Mesophilic Proteins Based on Amino Acid Composition
G. Zhang and B. Fang
The identification of the thermostability from the amino acid
sequence information would be helpful in computational screening
for thermostable proteins. We have developed a method to discriminate
thermophilic and mesophilic proteins based on support vector
machines. Using self-consistency validation, 5-fold cross-validation
and independent testing procedure with other datasets, this
module achieved overall accuracy of 94.2%, 90.5% and 92.4%,
respectively. The performance of this SVM-based module was
better than the classifiers built using alternative machine
learning and statistical algorithms including artificial neural
networks, Bayesian statistics, and decision trees, when evaluated
using these three validation methods. The influence of protein
size on prediction accuracy was also addressed.
[Back to top]
Prediction of Mutations in H5N1 Hemagglutinins from
Influenza A Virus
G. Wu and S. Yan
In this study, we determine the mutation relation among 333
H5N1 hemagglutinins of influenza A viruses according to their
amino acid and RNA codon sequences. Then, we calculate seven
probabilistic numbers, which have been developed by us since
1999, for each amino acid in these hemagglutinins. With the
seven numeric numbers as independents and the probability
of occurrence of mutation at each hemagglutinin position as
dependent, we use the logistic regression to model 967 missense
point mutations from 333 hemagglutinins to get the population
estimates. Thereafter, we predict the future mutation positions
in H5N1 hemagglutinin. Finally, we use the translation probabilities
between RNA codons and mutated amino acids to predict the
would-be-mutated amino acids in H5N1 hemagglutinin.
[Back to top]
A Role for the Strained Phenylalanine Ring Rotation
Induced by Substrate Binding to Cytochrome CYP102A1
D.C. Haines
X-ray crystal structures of CYP102A1 (P450BM-3) have shown
that PHE87 rotates upon substrate binding and is in contact
with the heme cofactor. Analysis of substrate binding data
combined with DFT calculations suggest that the ring is rotated
into an unfavorable interaction with the heme and this could
drive active site rearrangement.
[Back to top]
Methodological Improvements on Extraction of Nuclear
Proteins and Its Preliminary Analysis During the Maize (Zea
mays L.) Endosperm Development
B.S. Ferreira, A.T. Branco, M.A. de Oliveira, M.G. Pereira
and G.A. de Souza Filho
A procedure to obtain endosperm protein extracts was standardized.
After confirming the enrichment with nuclear proteins by immunodetection,
the protein profiles of extracts from different seed development
stages were compared by SDS-PAGE that showed the existence
of several differentially expressed proteins.
[Back to top]
Improved Performance in Protein Secondary Structure
Prediction by Combining Multiple Predictions
D.-S. Huang and X. Huang
In this paper1 we present a novel framework for
protein secondary structure prediction. In this prediction
framework, firstly we propose a novel parameterized semi-probability
profile, which combines single sequence with evolutionary
information effectively. Secondly, different semi-probability
profiles are respectively applied as network input to predict
protein secondary structure. Then a comparison among these
different predictions is discussed in this article. Finally,
naïve Bayes approaches are used to combine these predictions
in order to obtain a better prediction performance than individual
prediction. The experimental results show that our proposed
framework can indeed improve the prediction accuracy.
[Back to top]
Roles of Nitric Oxide Synthase inhibitor on Antinociceptive
Effects of μ-Opioid
Agonist in Mice
L.-X. Chen, Y.-M. Qi, R. Wang, X. Duan, Y.-F. Gao and
D.-J. Yang
In the present study, it was found that intraperitoneal (i.p.)
pre-injection of NG-nitro-L-arginine methyl ester
(L-NAME) significantly influenced the endomorphin-1 (EM-1)
and endomorphin-2 (EM-2) induced antinociception. These effects
could be inhibited or reversed by L-Arg or naloxone. Our results
suggest that the modulatory effect of NO system on the mu-receptor
evoked analgesia is different between the two mu receptor
subtypes.
[Back to top]
Inferring Protein-Protein Interacting Sites Using
Residue Conservation and Evolutionary Information
B. Wang, H.S. Wong and D.-S. Huang
This paper proposes a novel method using protein residue conservation
and evolution information, i.e., spatial sequence profile,
sequence information entropy and evolution rate, to infer
protein binding sites. Some predictors based on support vector
machines (SVMs) algorithm are constructed to predict the role
of surface residues in protein-protein interface. By combining
protein residue characters, the prediction performance can
be improved obviously. We then made use of the predicted labels
of neighbor residues to improve the performance of the predictors.
The efficiency and the effectiveness of our proposed approach
are verified by its better prediction performance based on
a non-redundant data set of heterodimers.
[Back to top]
Conformational Features of the Dippu-AST 8 Neuropeptide
from the Cockroach Diploptera punctata
I.N. Alieva, L.I. Velieva, M.A. Musayev and N.M. Gojayev
Spatial structure and conformational properties of the Dippu-AST
8 (allatostatin III) neuropeptide have been investigated by
the molecular mechanics method. The conformational energy
and geometrical parameters corresponding to the low-energy
states of the molecule are obtained. A single backbone conformation
with a very restricted set of Ser 3, Phe 4 and Leu 9 amino
acids positions is observed for Dippu-AST 8 neuropeptide.
[Back to top]
Immunoreceptor Transmembrane Peptides and Their Effect
on Natural Killer (NK) Cell Cytotoxicity
H. Vandebona, M. Ali, M. Amon, V. Bender and N. Manolios
Short peptides derived from the transmembrane sequence of
NK activating receptors and associated molecules were tested
in vitro for inhibition of NK cell cytotoxicity using
a standard 51Cr release assay in the absence or
presence of peptides. NKL23 cell line was used as the NK effector
and the target was the NKL23 sensitive 721.221 cell line.
NKp46, NKp30, NKG2D and CD3-ζ
peptides inhibited NK activity at higher concentration
(100 μM)
compared to controls by 6-13% (p<0.05). Modification of
one non-effective peptide (NKP44) significantly enhanced inhibition
by 30%, 17% and 11% at 100 μM,
50μM
and 10μM
respectively compared to controls. A T-cell antigen receptor-alpha
chain transmembrane sequence derived peptide (CP) significantly
inhibited NKL cell activation by 20-30% (p<0.05) at 50
μM
and 100 μM
concentrations compared to the control. The structural similarities
between these immuno-receptors, and in particular the need
for transmembrane electrostatic interactions for receptor
function, provides the basis for current and future targeted
therapeutic strategies.
[Back to top]
Antiviral Properties of Combination Peptides of HIV-1
Rev NLS and NES
N. Kobayashi, T. Sato and T. Yoshida
Nuclear translocation signal has been identified as a mediator
of protein shuttling between nuclear and cytoplasm. Here we
report that the combination of peptides from nuclear localization
signal (NLS) and nuclear export signal (NES) of HIV-1 Rev
have an antiviral activity against the Herpes virus of turkey
and Marek's disease virus serotype 1.
[Back to top]
Cloning and Characterization of a cDNA Encoding a
Cowpea Seed Defensin and Analysis of Its Expression
A.O. Carvalho, G.A.S. Filho, B.S. Ferreira, A.T. Branco,
A.L. Okorokova-Façanha and V.M. Gomes
We have previously isolated a cowpea seed defensin with potent
antifungal activity. Here we report the cloning of its cDNA
obtained from RT-PCR. The sequence of the deduced protein
VUDEF exhibited homology to plant defensins. Northern
analysis revealed that VUDEF mRNA is accumulated
during cowpea seed development and its level increases in
seedling tissues after exposure to fungal pathogen and cold.
[Back to top]
Endomorphins Restored the Endothelium-Dependent Relaxation
of the Rabbit Aorta Rings Exposed to High D-Glucose Condition
Via NO-cGMP Pathway
J. Liu, W.-M. Wu, J.-J. Che, J. Zhang and R. Wang
Rings of rabbit aorta that were both incubated in a high concentration
of D-glucose and contracted submaximally by phenylephrine
showed significantly decreased endothelium-dependent relaxations
induced by acetylcholine. The cGMP production of aorta rings
was also reduced. Treatment with endomorphins (1-1000 nmol/L)
restored acetylcholine-induced relaxations of aorta rings
incubated in high glucose concentrations and increased the
cGMP synthesis. Moreover, this effect of endomorphins on endothelium
was antagonized by naloxone, and the increase in the production
of cGMP was also blocked.
[Back to top]
Expression of the Canavalia brasiliensis
Lectin (ConBr) in Tobacco Plants
C.P.S. Carvalho, T.O. Correia, S.M.S. Ribeiro, I.C. Silva,
J.T.A. Oliveira and T.B. Grangeiro
Tobacco plants were transformed with gene constructs encoding
prepro-ConBr (Canavalia brasiliensis lectin). Transgenic
plants confirmed by PCR expressed the recombinant protein
as revealed by Western blot. However, the apparent molecular
mass of the recombinant polypeptide (ca. 34 kDa) was higher
than the native lectin (about 30 kDa), showing that further
proteolytic processing of pro-ConBr was not detected.
[Back to top]
Protein Preparation, Crystallization
and Preliminary X-Ray Crystallographic Studies of Smu.1392c
from Streptococcus mutans
Z.-Q. Gao, H.-F. Hou, Y.-H. Liang, L.-F. Li, X.-D. Su
and Y.-H. Dong
Smu.1392c is a protein with 158 residues of uncharacterized
function. Bioinformatics studies predict it is a putative
acetyltransferase. In order to identify its exact function
via structural studies, Smu.1392c gene was amplified from
Streptococcus mutans genomic DNA and cloned into
expression vector PET28a. Smu.1392c was crystallized and diffracted
to a resolution of 3 Å in-house. The crystal belongs
to R32 space group, with unit cell parameters a=b=229.10,
c=63.49 Å. There are 2 or 3 molecules in the asymmetric
unit.
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