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Protein
& Peptide Letters
ISSN: 0929-8665
Protein &
Peptide Letters
Volume 17, Number 5, 2010
Contents
Regular Papers
Kinetics of Interaction of HLA-B2705 with Natural
Killer Cell Immunoglobulin-Like Receptor 3DS1 Pp.
547-554
H. Li, S.-L. Peng, Y. Cui, Q.-X. Fu, Y. Zhou, Q.-L. Wang,
L.-S. Zhan and S. Zhong
[Abstract] [Purchase
Article] [PMID:
19995342 PubMed - indexed for MEDLINE]
Histone Deacetylase 6 (HDAC6) Is an
Independent Deacetylase for α-Tubulin
Pp. 555-558
Z. Zhao, H. Xu and W. Gong
[Abstract] [Purchase
Article] [PMID:
19961433 PubMed - indexed for MEDLINE]
Prediction of G-Protein-Coupled Receptor
Classes in Low Homology Using Chou’s Pseudo Amino Acid
Composition with Approximate Entropy and Hydrophobicity Patterns
Pp. 559-567
Q. Gu,Y.-S. Ding and T.-L. Zhang
[Abstract] [Purchase
Article] [PMID:
19594431 PubMed - indexed for MEDLINE]
Production of Active MMP7 in E.
coli and Its Application for Metalloproteinase Inhibitors
Screening Pp. 568-572
H. Katsuno, R. Shirakawa, K. Miyazaki, Y. Ozeki and
H. Yasumitsu
[Abstract] [Purchase
Article] [PMID:
20156184 PubMed - indexed for MEDLINE]
IgE-Binding Epitope Analysis of Bla
g 5, the German Cockroach Allergen Pp. 573-577
K.-J. Jeong, K.Y. Jeong, C.-R. Kim and T.-S.
Yong
[Abstract] [Purchase
Article] [PMID:
20044919 PubMed - indexed for MEDLINE]
Evidence for Significantly Enhancing
Reduction of Azo Dyes in Escherichia coli by Expressed
Cytoplasmic Azoreductase (AzoA) of Enterococcus faecalis
Pp. 578-584
J. Feng, T.M. Heinze, H. Xu, C.E. Cerniglia and
H. Chen
[Abstract] [Purchase
Article] [PMID:
19663804 PubMed - indexed for MEDLINE]
Ribosome Display and Selection of Human
Anti-Placental Growth Factor scFv Derived from Ovarian Cancer
Patients Pp. 585-590
F. Li, P. Su, C. Lin, H. Li, J. Cheng and D.
Shi
[Abstract] [Purchase
Article] [PMID:
19645688 PubMed - indexed for MEDLINE]
A Multi-Scale Parameterization Approach
of Peptides for Quantitative Sequence-Activity Models
Pp. 591-598
W. Niu, Q. Xia and G. Liang
[Abstract] [Purchase
Article]
Predicting Enzyme Subclasses by Using
Support Vector Machine with Composite Vectors Pp.
599-604
R. Shi and X. Hu
[Abstract] [Purchase
Article] [PMID:
19645687 PubMed - indexed for MEDLINE]
Functional Characterization of the In
Vitro Folded Human Y1
Receptor in Lipid Environment Pp. 605-609
S. Schimmer, D. Lindner, P. Schmidt, A.G. Beck-Sickinger,
D. Huster and R. Rudolph
[Abstract] [Purchase
Article] [PMID:
19689227 PubMed - indexed for MEDLINE]
Efficient Growth Inhibition of Human
Osteosarcoma Cells Using a Peptide Derived from the MDM-2-Binding
Site of p53 Pp. 610-615
R. Ito, H. Kanno, A. Takahashi, R. Matsumoto, N. Kobayashi,
T. Yoshida and T. Saito
[Abstract] [Purchase
Article] [PMID:
20015022 PubMed - indexed for MEDLINE]
In Vitro Studies of the Activity
of Newly Sinthesized Nociceptin / Orphanin FQ Receptor Ligand
Analogues Pp. 616-620
L. Kasakov, M. Nashar, E. Naydenova, L. Vezenkov and
M. Vlaskovska
[Abstract] [Purchase
Article] [PMID:
19689226 PubMed - indexed for MEDLINE]
Binding of Reactive Brilliant Red to
Human Serum Albumin: Insights into the Molecular Toxicity
of Sulfonic Azo Dyes Pp. 621-629
W.-Y. Li, F.-F. Chen and S.-L. Wang
[Abstract] [Purchase
Article] [PMID:
20156186 PubMed - indexed for MEDLINE]
Codon Usage Biases in Alzheimer’s
Disease and Other Neurodegenerative Diseases Pp.
630-645
J. Yang, T.-Y. Zhu, Z.-X. Jiang, C. Cheng, Y.-L. Wang,
S. Zhang, X. F. Jiang, T.-T. Wang, L. Wang, W.-H. Xia, L.
Li, J.-J. Chen, J.-Y. Wang, W.-W. Wang, and W.-J.
Zheng
[Abstract] [Purchase
Article] [PMID:
20441557 PubMed - indexed for MEDLINE]
Molecular Modeling of Human Hepatocyte
PKA (cAMP Dependent Protein Kinase Type-II) and Its Structure
Analysis Pp. 646-659
J. Yang
[Abstract] [Purchase
Article] [PMID:
20441558 PubMed - indexed for MEDLINE]
Stabilization of Folding Intermediate
States from Alkaline Induced Unfolded State of Bovine Serum
Fetuin in Trifluoroethanol and Acetonitrile Pp. 660-666
B. Ahmad, Z. Islam, A. Varshney and R.H. Khan
[Abstract] [Purchase
Article] [PMID:
19995341 PubMed - indexed for MEDLINE]
Purification and Kinetics of Bovine
Kidney Cortex Glutathione Reductase Pp. 667-674
B. Tandogan and N.N. Ulusu
[Abstract] [Purchase
Article] [PMID:
19702563 PubMed - indexed for MEDLINE]
GOVis,
A Gene Ontology Visualization Tool Based on Multi-Dimensional
Values Pp. 675-680
Z. Ning and Z. Jiang
[Abstract] [Purchase
Article] [PMID:
19995339 PubMed - indexed for MEDLINE]
Abstracts
[Back to top] [Purchase
Article] [PMID:
19995342 PubMed - indexed for MEDLINE]
Kinetics of Interaction of HLA-B2705 with Natural
Killer Cell Immunoglobulin-Like Receptor 3DS1
H. Li, S.-L. Peng, Y. Cui, Q.-X. Fu, Y. Zhou, Q.-L. Wang,
L.-S. Zhan and S. Zhong
The recognition of human leukocyte antigen (HLA)
molecules by specific receptors is a crucial step in the regulation
of natural killer (NK) cell function. Killer cell immunoglobulin-like
receptor (KIR) 3DS1 is one of the activating receptors of
NK cell and is implicated in slowing disease progression in
HIV infection. KIR3DS1 play an important role in the outcome
of multiple diseases associated with viral infections. In
contrast to the inhibitory receptor, much less is known about
the ligands of KIR3DS1. In order to achieve a better understanding
of the biology of KIR3DS1 and its ligand systems, it is necessary
to identify the ligands of KIR3DS1. In this work, we utilized
recombinant HLA-B2705 molecules and DsbA-KIR3DS1 fusion protein
to monitor the interaction between HLA-B2705 complexes and
DsbA-KIR3DS1 using BIAcore 3000 SPR sensor and found that
the specific binding between KIR3DS1 and HLA-B2705 existed
and the affinity was 6.95×10-6
mol//L. So we concluded that HLA-B2705 is a possible ligand
of KIR3DS1.
[Back to top]
[Purchase Article] [PMID:
19961433 PubMed - indexed for MEDLINE]
Histone Deacetylase 6 (HDAC6) Is an
Independent Deacetylase for α-Tubulin
Z. Zhao, H. Xu and W. Gong
Histone deacetylase 6 (HDAC6) is a cytosolic
enzyme that catalyzes deacetylation of several proteins. Acetylated
tubulin has been recently identified as a physiological substrate
of HDAC6. However in previous reports, all in vitro
binding and enzymatic assays were accomplished with only partially
purified protein samples. Therefore, it still remained unclear
whether HDAC6 alone could interact with tubulin and catalyze
deacetylation. In this study, both binding and enzymatic assays
were conducted using recombinant-derived HDAC6 and purified
α/β
tubulin to eliminate possible contamination. The results
clearly demonstrated that interaction between HDAC6 and tubulin
is independent of other proteins. In addition, HDAC6 can independently
catalyze deacetylation of both tubulin dimer and microtubule
polymer.
[Back to top]
[Purchase Article] [PMID:
19594431 PubMed - indexed for MEDLINE]
Prediction of G-Protein-Coupled Receptor
Classes in Low Homology Using Chou’s Pseudo Amino Acid
Composition with Approximate Entropy and Hydrophobicity Patterns
Q. Gu,Y.-S. Ding and T.-L. Zhang
We use approximate entropy and hydrophobicity
patterns to predict G-protein-coupled receptors. Adaboost
classifier is adopted as the prediction engine. A low homology
dataset is used to validate the proposed method. Compared
with the results reported, the successful rate is encouraging.
The source code is written by Matlab.
[Back to top]
[Purchase Article] [PMID:
20156184 PubMed - indexed for MEDLINE]
Production of Active MMP7 in E.
coli and Its Application for Metalloproteinase Inhibitors
Screening
H. Katsuno, R. Shirakawa, K. Miyazaki, Y. Ozeki and
H. Yasumitsu
MMP-7 is the smallest metalloproteinase. Its
unregulated activities and existence in serum are recently
known to be tightly related with life-threatening disease
such as cardiac disease and several cancers. The protein production
is thought to be useful for its characterization and antibody
generation. Although many attempts at bacterial expressions
have been conducted, they were recovered as insoluble and
inactive protein. In this study, after soluble expression,
single-step purification and conversion to active protease,
it was applied for the screening secretory metalloproteinase
inhibitors in conditioned media of human cancer cells.
[Back to top]
[Purchase Article] [PMID:
20044919 PubMed - indexed for MEDLINE]
IgE-Binding Epitope Analysis of Bla
g 5, the German Cockroach Allergen
K.-J. Jeong, K.Y. Jeong, C.-R. Kim and T.-S.
Yong
Cockroach infestations have been linked with
allergic diseases such as asthma in humans. Bla g 5, sigma
class glutathione S-transferase (GST), is the major cockroach
allergen which has the highest IgE response value of all cockroach
allergens. Although several cockroach allergens have been
identified and cloned, information regarding their B ell and
T cell IgE-binding epitopes is limited.
In order to analyze the IgE binding epitopes of Bla g 5, full-length
and five peptide fragments (A, 1-100 amino acid residue; B,
91-201; Ba, 1-125; Bb, 1-150; Bc, 1-175) were expressed. Twelve
(37.5%) of 32 sera from cockroach-sensitized subjects showed
positive IgE reactivity to the recombinant Bla g 5 (rBla g
5). Six strong positive sera were selected for the epitope
study. Recombinant proteins not containing 176-201 amino acid
residues were unable to react to sera from cockroach sensitized
individuals, suggesting that this region contains the IgE-binding
epitope. Despite strong IgE reactivity to rBla g 5, the pooled
serum from 5 cockroach-sensitized patients did not show IgE
reactivity to all synthetic peptides consisting of 15 residues
covering 161-201 amino acids.
These results suggest the possibility that Bla g 5 may have
a conformational epitope in the C-terminal region. GST is
the important target for the development of vaccines and drugs
against allergic diseases because of high cross-reactivity
among insect species. This study will aid recombinant allergen
research for immunotherapy of cockroach allergens and other
insect allergens.
[Back to top]
[Purchase Article] [PMID:
19663804 PubMed - indexed for MEDLINE]
Evidence for Significantly Enhancing
Reduction of Azo Dyes in Escherichia coli by Expressed
Cytoplasmic Azoreductase (AzoA) of Enterococcus faecalis
J. Feng, T.M. Heinze, H. Xu, C.E. Cerniglia and
H. Chen
Although cytoplasmic azoreductases have been
purified and characterized from various bacteria, little evidence
demonstrating that these azoreductases are directly involved
in azo dye reduction in vivo is known. In order to
evaluate the contribution of the enzyme to azo dye reduction
in vivo, experiments were conducted to determine
the effect of a recombinant cytoplasmic azoreductase (AzoA)
from Enterococcus faecalis expressed in Escherichia
coli on the rate of metabolism of Methyl Red, Ponceau
BS and Orange II. The intact cells that contained IPTG induced
AzoA had a higher rate of dye reduction with increases of
2 (Methyl Red), 4 (Ponceau BS) and 2.6 (Orange II)-fold compared
to noninduced cells, respectively. Metabolites of Methyl Red
isolated from induced cultures were identified as N,N-dimethyl-p-phenylenediamine
and 2-aminobenzoic acid through liquid chromatography electrospray
ionization tandem mass spectrometry (LC/ESI-MS/MS) analyses.
In conclusion, our data demonstrate that AzoA from Ent.
faecalis is capable of increasing the reduction of azo
dyes in intact E. coli cells and that cytoplasmic
azoreductase is involved in bacterial dye degradation in
vivo.
[Back to top]
[Purchase Article] [PMID:
19645688 PubMed - indexed for MEDLINE]
Ribosome Display and Selection of Human
Anti-Placental Growth Factor scFv Derived from Ovarian Cancer
Patients
F. Li, P. Su, C. Lin, H. Li, J. Cheng and D.
Shi
Ribosome display is a powerful cell-free technology
to select a desired antibody together with its encoding mRNA.
In this study, a human single-chain variable fragment (scFv)
library was generated from the peripheral blood lymphocyte
RNA of 10 ovarian cancer patients and then panned against
bead-conjugated human PlGF, a protein that may contribute
to the growth and metastasis of ovarian cancer. A selected
scFv antibody was evaluated by Western blot and its affinity
constant to the PlGF was determined by noncompetitive enzyme
immunoassay. This study highlights the ribosomal display technology
for the selection of human antibody from patient-derived gene
pools.
[Back to top]
[Purchase Article] [PMID:
19995342 PubMed - indexed for MEDLINE]
A Multi-Scale Parameterization Approach
of Peptides for Quantitative Sequence-Activity Models
W. Niu, Q. Xia and G. Liang
A multi-scale parameterization approach, factor
analysis scales of generalized amino acid information combined
with auto cross covariance, was used to develop quantitative
sequence-activity models of peptides using support vector
machines. The results demonstrated that this approach could
well characterize sequence features of the peptides studied.
[Back to top]
[Purchase Article] [PMID:
19645687 PubMed - indexed for MEDLINE]
Predicting Enzyme Subclasses by Using
Support Vector Machine with Composite Vectors
R. Shi and X. Hu
Based on enzyme sequence, using composite vectors
with amino acid composition, low-frequency power spectral
density, increment of diversity by combining a different form
of pseudo amino acid composition to express the information
of sequence, a support vector machine (SVM) for predicting
enzyme subclasses is proposed. By the jackknife test, success
rates of our algorithm are higher than other methods.
[Back to top]
[Purchase Article] [PMID:
19689227 PubMed - indexed for MEDLINE]
Functional Characterization of the In
Vitro Folded Human Y1
Receptor in Lipid Environment
S. Schimmer, D. Lindner, P. Schmidt, A.G. Beck-Sickinger,
D. Huster and R. Rudolph
We describe the recombinant production of the
human Y1 receptor from inclusion
bodies of E. coli cultures. The in vitro
refolding was carried out in the presence of lipids from bovine
brain extracts. Y1 receptors
in brain lipids compete for cellular receptors in competitive
binding experiments.
[Back to top]
[Purchase Article] [PMID:
20015022 PubMed - indexed for MEDLINE]
Efficient Growth Inhibition of Human
Osteosarcoma Cells Using a Peptide Derived from the MDM-2-Binding
Site of p53
R. Ito, H. Kanno, A. Takahashi, R. Matsumoto, N. Kobayashi,
T. Yoshida and T. Saito
Protein transduction therapy is a promising
alternative to gene therapy, but has not previously been investigated
for osteosarcoma. We here demonstrate efficient growth inhibition
of human osteosarcoma cells using a p53 peptide. Our result
suggests that protein transduction therapy has significant
potential as a novel therapeutic approach for osteosarcoma.
[Back to top]
[Purchase Article] [PMID:
19689226 PubMed - indexed for MEDLINE]
In Vitro Studies of the Activity
of Newly Sinthesized Nociceptin / Orphanin FQ Receptor Ligand
Analogues
L. Kasakov, M. Nashar, E. Naydenova, L. Vezenkov and
M. Vlaskovska
Based on template hexapeptides Ac-Arg-Tyr-Tyr-Arg-Trp-Lys-NH2
and Ac-Arg-Tyr-Tyr-Arg-Ile-Lys-NH2
analogues and corresponding deacylated homologues were synthesized
substituting ornithine, diaminobutanoic (Dab) and diaminopropanoic
(Dap) acids for lysine at position 6. The aim was to investigate
the effect of the newly synthesized compounds on the neurogenic
contractions of isolated rat vas deferens. Ac-Arg-Tyr-Tyr-Arg-Trp-Lys-NH2
and its analogues manifested a strong inhibitory effect on
the neurogenic contractions without effect on the muscle tone,
which is characteristic effect of NOP receptor agonists. In
contrast, Ac-Arg-Tyr-Tyr-Arg-Ile-Lys-NH2
and its analogs manifested a strong inhibitory effect on the
muscle tone and negligible effect on the neurogenic contractions
which is characteristic effect of NOP receptor antagonists.
The most active were the peptides in which Dab or Dap is the
substitute. The study reveals that substitution of Lys with
shorter amino acids could increase agonist or antagonist activity
of the peptide.
[Back to top]
[Purchase Article] [PMID:
20156186 PubMed - indexed for MEDLINE]
Binding of Reactive Brilliant Red to
Human Serum Albumin: Insights into the Molecular Toxicity
of Sulfonic Azo Dyes
W.-Y. Li, F.-F. Chen and S.-L. Wang
The non-covalent interaction of reactive brilliant
red (RBR) as a representative of sulfonic azo compounds with
human serum albumin (HSA) was investigated by a combination
of UV-VIS spectrometry, fluorophotometry, circular dichroism
(CD) and isothermal titration calorimetry (ITC) technique.
The thermodynamic characterization of the interaction was
performed. The saturation binding numbers of RBR on peptide
chains were determined and the effects of electrolytes and
temperature were investigated. The ionic interaction induced
a combination of multiple non-covalent bonds including hydrogen
bonds, hydrophobic interactions and van der Waals force. A
three-step binding model of RBR was revealed. The binding
of RBR molecules might occur on the external surface of HSA
via electric interaction when the mole ratio of RBR to HSA
was less than 40 and RBR molecules entered the hydrophobic
intracavity of HSA when the ratio was more than 40. Moreover,
RBR binding resulted in a conformational change in the structure
of HSA or even the precipitation of HSA and inhibited its
function accordingly. The possible binding site and the conformational
transition of HSA were hypothesized and illustrated. This
work provides a new insight into non-covalent interaction
between a sulfonic azo compound and protein, which may be
further used to investigate the potential toxicity of azo
dyes.
[Back to top]
[Purchase Article] [PMID:
20441557 PubMed - indexed for MEDLINE]
Codon Usage Biases in Alzheimer’s
Disease and Other Neurodegenerative Diseases
J. Yang, T.-Y. Zhu, Z.-X. Jiang, C. Cheng, Y.-L. Wang,
S. Zhang, X. F. Jiang, T.-T. Wang, L. Wang, W.-H. Xia, L.
Li, J.-J. Chen, J.-Y. Wang, W.-W. Wang, and W.-J.
Zheng
Establishing codon usage biases are crucial
for understanding the etiology of central nervous system neurodegenerative
diseases (CNSNDD) especially Alzheimer’s disease (AD)
as well as genetic factors. G and C ending codons are strongly
biased in the coding sequences of these proteins as a result
of genomic GC composition constraints. On the other hand,
codons that identified as translationally optimal in the major
trend all end in C or G, suggesting translational selection
should also be taken into consideration additional to compositional
constraints. Furthermore, this investigation reveals that
three common codons, CGC (Arg), AGC (Ser), and GGC (Gly),
are also critical in affecting codon usage bias. They not
only can offer an insight into the codon usage bias of AD
and its mechanism, but also may help in the possible cures
for these diseases.
[Back to top]
[Purchase Article] [PMID:
20441558 PubMed - indexed for MEDLINE]
Molecular Modeling of Human Hepatocyte
PKA (cAMP Dependent Protein Kinase Type-II) and Its Structure
Analysis
J. Yang
Two binary complexes (KAP2-C subunit and cAMP-bound
KAP2) were built, to investigate molecular interaction. The
binding sites of KAP2 include the acidic sequence motif (Asp73-Glu87),
the inhibitor peptide/linker region (Arg93-Val118), and beta
barrel of cAMP-binding domains (CBD-A/B). The binding surface
on the C subunit anchoring KAP2 extends to the inhibitor binding
site at the active site cleft (Glu127-Glu230), Pro243-Ser252
helix and the phosphorylated activation loop (Arg194-Thr201)
of the large lobe besides some sites in the small lobe. KAP2
undergoes major conformational changes in comparison of the
two complexes above, especially the linker region and Met251
at Arg234-Phe252 helix as an inflexion point of the turnaround.
Additionally, the interaction between KAP2 and cAMP concentrates
on two catalytic motifs (FGELAL and PRAA) of phosphate binding
cassette regions and the cyclic-monophosphate and ribose of
cAMP. On the other hand, WAVE1 of BAD complex maybe interacts
with the D/D domain of KAP2 by each of three helical motifs
(Asn24-Lys46, Pro492-Val514, and Glu525-Glu547). This is helpful
for our research of molecular mechanism of PKA and further
analysis of BAD complex how to modulate glycolysis and apoptosis.
[Back to top]
[Purchase Article] [PMID:
19995341 PubMed - indexed for MEDLINE]
Stabilization of Folding Intermediate
States from Alkaline Induced Unfolded State of Bovine Serum
Fetuin in Trifluoroethanol and Acetonitrile
B. Ahmad, Z. Islam, A. Varshney and R.H. Khan
The conformation of bovine serum fetuin (BSF)
was examined over the pH 7.0-12.9 regions by circular dichroism,
intrinsic fluorescence and ANS binding. We observed that at
higher pH, BSF exists in alkaline unfolded state. Our results
provided evidence that correlates simultaneous formation of
secondary structure followed by accumulation of hydrophobic
clusters.
[Back to top]
[Purchase Article] [PMID:
19702563 PubMed - indexed for MEDLINE]
Purification and Kinetics of Bovine
Kidney Cortex Glutathione Reductase
B. Tandogan and N.N. Ulusu
Glutathione reductase was purified 34806-fold
with a final yield of 85 % from the bovine kidney cortex.
Some molecular and kinetic properties of purified enzyme are
investigated. Product inhibition studies showed that the enzyme
obeys ‘branched’ mechanism: KmNADPH
18 ± 3 μM
and KmGSSG 65 ± 5
μM
were determined.
[Back to top]
[Purchase Article] [PMID:
19995339 PubMed - indexed for MEDLINE]
GOVis,
A Gene Ontology Visualization Tool Based on Multi-Dimensional
Values
Z. Ning and Z. Jiang
Most of gene product similarity measurements concentrate on
the information content of Gene Ontology (GO) terms or use
a path-based similarity between GO terms, which may ignore
other important information contained in the structure of
the ontology. In our study, we integrate different GO similarity
measure approaches to analyze the functional relationship
of genes and gene products with a new triangle-based visualization
tool called GOVis. The purpose
of this tool is to demonstrate the effect of three important
information factors when measuring the similarity between
gene products. One advantage of this tool is that its important
ratio can be adjusted to meet different measuring requirements
according to the biological knowledge of each factor. The
experimental results demonstrate that GOVis
can display diagrams of the functional relationship for gene
products effectively.
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