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Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 17, Number 3, 2010
Contents
Regular Papers
Annotation of Non-Synonymous Single Polymorphisms
in Human Liver Proteome by Mass Spectrometry Pp.
277-286
M. Chen, B. Yang, W. Ying, F. He and X. Qian
[Abstract] [Purchase
Article] [PMID:
19508201 PubMed - indexed for MEDLINE]
Improve the Prediction of RNA-Binding Residues Using Structural
Neighbours Pp. 287-296
Q. Li, Z. Cao and H. Liu
[Abstract] [Purchase
Article] [PMID:
19508202 PubMed - indexed for MEDLINE]
Characterization of a New Defensin from Cowpea (Vigna
unguiculata (L.) Walp.) Pp. 297-304
L. Padovan, L. Segat, A. Tossi, T. Calsa Jr., A.K. Ederson,
L. Brandao, R.L. Guimarães, V. Pandolfi, M.C. Pestana-Calsa,
L.C. Belarmino, A.M. Benko-Iseppon and S. Crovella
[Abstract] [Purchase
Article] [Supplementary
Material] [PMID:
20236084 PubMed - indexed for MEDLINE]
Bryothamnion seaforthii Lectin Relaxes Vascular Smooth
Muscle: Involvement of Endothelium and NO Synthase
Pp. 305-310
R.F. Lima, D.N. Criddle, P.M.G. Soares, S.P. Ribeiro,
B.S. Cavada, K.S. Nascimento, A.H. Sampaio and A.M.S.
Assreuy
[Abstract] [Purchase
Article] [PMID:
20236085 PubMed - indexed for MEDLINE]
Isolation and Partial Characterization of a Novel Lipid Transfer
Protein (LTP) and Antifungal Activity of Peptides from Chilli
Pepper Seeds Pp. 311-318
L.P. Cruz, S.F.F.F. Ribeiro, A.O. Carvalho, I.M. Vasconcelos,
R. Rodrigues, M.D. Cunha and V.M. Gomes
[Abstract] [Purchase
Article] [PMID:
19508213 PubMed - indexed for MEDLINE]
Analyses of the Proteomes of the Leaf, Hypocotyl, and Root
of Young Soybean Seedlings Pp. 319-331
A. Afroz, A. Hashiguchi, M.R. Khan and S. Komatsu
[Abstract] [Purchase
Article] [PMID:
19508212 PubMed - indexed for MEDLINE]
3D Pharmacophore Based Virtual Screening of A2A
Adenosine Receptor Antagonists Pp. 332-339
J. Wei, W. Qu, Y. Ye and Q. Gao
[Abstract] [Purchase
Article] [PMID:
20236086 PubMed - indexed for MEDLINE]
Evaluation of Aflatoxin B1–Acetylcholinesterase
Dissociation Kinetic Using the Amperometric Biosensor Technology:
Prospect for Toxicity Mechanism Pp. 340-342
M. Pohanka, K. Musilek and K. Kuca
[Abstract] [Purchase
Article] [PMID:
19508188 PubMed - indexed for MEDLINE]
Solution Structure of a Photo-Switchable Insect Kinin Thioxo-Analog
Pp. 343-346
Z. Cong, Y. Huang, L. Yang, D. Ye and S. Dong
[Abstract] [Purchase
Article] [PMID:
19508199 PubMed - indexed for MEDLINE]
L-Valine
and L-Proline -
Solid-State IR-LD Spectroscopic Study Pp. 347-350
A.G. Chapkanov and S.Y. Zareva
[Abstract] [Purchase
Article] [PMID:
20236087 PubMed - indexed for MEDLINE]
Mutagenesis Studies of Human Cystathionine β-Synthase:
Residues Important for Heme Binding and Substrate Interactions
Pp. 351-355
S.-i. Ozaki, C. Sakaguchi, A. Nakahara and M.
Yoshiya
[Abstract] [Purchase
Article] [PMID:
19594435 PubMed - indexed for MEDLINE]
A Novel Approach to Predict Protein-Protein Interactions
Related to Alzheimer’s Disease Based on Complex Network
Pp. 356-366
J. Yang and X.-F. Jiang
[Abstract] [Purchase
Article] [PMID:
19508211 PubMed - indexed for MEDLINE]
Molecular Dynamics of Some Pentapeptides Having a
Strong Tendency to Helical Conformation Pp. 367-380
Z.-R. Huang, T.-Y. Zhu, T.-T. Wang, X.-N. Wang
and J. Yang
[Abstract] [Purchase
Article] [PMID:
19508214 PubMed - indexed for MEDLINE]
Stationary Phase Expression, Purification, and Characterization
of XorKI, a Restriction Endonuclease from Xanthomonas
oryzae pv. oryzae Pp. 381-385
W.Y. Kang and Y.K. Chae
[Abstract] [Purchase
Article] [PMID:
19594434 PubMed - indexed for MEDLINE]
Immunization with Peptide-Protein Conjugates: Impact on Benchmarking
B-Cell Epitope Prediction for Vaccine Design Pp.
386-398
S.E.C. Caoili
[Abstract] [Purchase
Article] [PMID:
19594433 PubMed - indexed for MEDLINE]
Interactions of Ginkgolides A and B with a Recombinant
Human Prion Protein Pp. 399-404
D. Georgieva, L. Redecke, M. von Bergen, N. Genov and
C. Betzel
[Abstract] [Purchase
Article] [PMID:
19958278 PubMed - indexed for MEDLINE]
Synthesis of N-Succinyl-L,
L-Diaminopimelic Acid Mimetics Via Selective
Protection Pp. 405-409
V. Vanek, J. Pícha, M. Budešínský,
M. Šanda, J. Jirácek, R.C. Holz and J.
Hlavácek
[Abstract] [Purchase
Article] [PMID:
19958280 PubMed - indexed for MEDLINE]
Abstracts
[Back to top] [Purchase
Article] [PMID:
19508201 PubMed - indexed for MEDLINE]
Annotation of Non-Synonymous Single Polymorphisms
in Human Liver Proteome by Mass Spectrometry
M. Chen, B. Yang, W. Ying, F. He and X. Qian
A novel strategy to annotate nsSNP-peptides in human
liver proteome based on LC-ESI-MS/MS and peptide database
search was proposed. Totally 115 nsSNP-peptides in human liver
proteins were annotated using our method. Among them, 42 peptides
were found to be amino acid mutation, 73 peptides were wild
type, 5 peptides were interpreted with both mutation and wild
type. The function of nsSNP-peptide was predicted using SIFT
algorithm, and 2 nsSNPs were predicted to be damaged for protein
function. The results here show that the strategy is very
effective for annotation of nsSNP at peptide level.
[Back to top]
[Purchase
Article] [PMID:
19508202 PubMed - indexed for MEDLINE]
Improve the Prediction of RNA-Binding Residues Using Structural
Neighbours
Q. Li, Z. Cao and H. Liu
The interactions between RNA-binding proteins (RBPs) with
RNA play key roles in managing some of the cell's basic functions.
The identification and prediction of RNA binding sites is
important for understanding the RNA-binding mechanism. Computational
approaches are being developed to predict RNA-binding residues
based on the sequence- or structure-derived features. To achieve
higher prediction accuracy, improvements on current prediction
methods are necessary. We identified that the structural neighbors
of RNA-binding and non-RNA-binding residues have different
amino acid compositions. Combining this structure-derived
feature with evolutionary (PSSM) and other structural information
(secondary structure and solvent accessibility) significantly
improves the predictions over existing methods. Using a multiple
linear regression approach and 6-fold cross validation, our
best model can achieve an overall correct rate of 87.8% and
MCC of 0.47, with a specificity of 93.4%, correctly predict
52.4% of the RNA-binding residues for a dataset containing
107 non-homologous RNA-binding proteins. Compared with existing
methods, including the amino acid compositions of structure
neighbors lead to clearly improvement. A web server was developed
for predicting RNA binding residues in a protein sequence
(or structure), which is available at http://jeele.go.3322.org/RNA/.
[Back to top]
[Purchase
Article] [PMID:
20236084 PubMed - indexed for MEDLINE]
Characterization of a New Defensin from Cowpea (Vigna
unguiculata (L.) Walp.)
L. Padovan, L. Segat, A. Tossi, T. Calsa Jr., A.K. Ederson,
L. Brandao, R.L. Guimarães, V. Pandolfi, M.C. Pestana-Calsa,
L.C. Belarmino, A.M. Benko-Iseppon and S. Crovella
[Supplementary
Material]
Using Phaseoleae defensins available in databases, a putative
defensin gene was isolated in cowpea (Vigna unguiculata
(L.) Walp.) and cloned from genomic cowpea DNA. The putative
mature defensin sequence displays the characteristic defensins
residues arrangement, secondary and tertiary structures were
predicted and splicing analysis was performed. Using RT-PCR,
defensin expression and differences in response to biotic
stimuli between infected and non infected plants were tested.
[Back to top]
[Purchase
Article] [PMID:
20236085 PubMed - indexed for MEDLINE]
Bryothamnion seaforthii Lectin Relaxes Vascular Smooth
Muscle: Involvement of Endothelium and NO Synthase
R.F. Lima, D.N. Criddle, P.M.G. Soares, S.P. Ribeiro,
B.S. Cavada, K.S. Nascimento, A.H. Sampaio and A.M.S.
Assreuy
Bryothamnion seaforthii lectin (BSL) induced
reversible concentration-related relaxation of endothelized
aorta, maximal at 30μg/ml
(IC50= 4.8 ± 0.6μg/ml).
This effect was inhibited by L-NAME and reversed by mucin,
probably via interaction with a specific lectin-binding site
on the endothelium activating nitric oxide synthase.
[Back to top]
[Purchase
Article] [PMID:
19508213 PubMed - indexed for MEDLINE]
Isolation and Partial Characterization of a Novel Lipid Transfer
Protein (LTP) and Antifungal Activity of Peptides from Chilli
Pepper Seeds
L.P. Cruz, S.F.F.F. Ribeiro, A.O. Carvalho, I.M. Vasconcelos,
R. Rodrigues, M.D. Cunha and V.M. Gomes
The aims of this study were to isolate and characterize
peptides present in chilli pepper seeds and evaluate their
antifungal activities. An isolated peptide closer to 9 kDa
showed high sequence homology to the antimicrobial peptide
lipid transfer protein. The peptide fraction containing the
LTP inhibited the growth of the fungi, Fusarium oxysporum,
Colletotrium lindemunthianum, the yeasts, Saccharomyces
cerevisiae, Pichia membranifaciens, Candida tropicalis, Candida
albicans, inhibited glucose-stimulated acidification
of the medium by yeast cells of S. cerevisiae and
caused several morphological changes in P. membranifaciens.
[Back to top]
[Purchase
Article] [PMID:
19508212 PubMed - indexed for MEDLINE]
Analyses of the Proteomes of the Leaf, Hypocotyl, and Root
of Young Soybean Seedlings
A. Afroz, A. Hashiguchi, M.R. Khan and S. Komatsu
The functions of organs in young soybean seedling were determined
by means of proteomic analysis. Extracts from leaves, hypocotyls,
and roots were separated by two-dimensional polyacrylamide
gel electrophoresis, and the proteins were identified by mass
spectrometry and protein sequencing. The identified proteins
were categorized into various groups according to their function.
The leaf was abundant in proteins associated with energy production
(50.0%), the hypocotyl was rich in defense proteins (31.8%),
and the root contained defense-related proteins (16.7%) and
destination and storage proteins (26.7%). Stem 31-kDa glycoprotein,
20 kDa chaperonin, 50S ribosomal protein, and trypsin inhibitor
were common to all three tissues. The sequence information
obtained from the soybean proteome should be helpful in predicting
the functions of unknown proteins.
[Back to top]
[Purchase
Article] [PMID:
20236086 PubMed - indexed for MEDLINE]
3D Pharmacophore Based Virtual Screening of A2A
Adenosine Receptor Antagonists
J. Wei, W. Qu, Y. Ye and Q. Gao
A2A
adenosine receptor (A2AAR)
antagonists are considered to be useful in cancer immunotherapy
and vaccines and as potential drugs for the treatment of Parkinson’s
disease. To better understand the chemical features responsible
for the recognition mechanism and the receptor-ligand interaction,
we performed the molecular docking study using selective A2AAR
antagonists and combined with a pharmacophore based virtual
library screening. The putative binding mode for the antagonists
served as the templates for pharmacophore modeling and a virtually
generated library have been screened for novel A2AAR
antagonist development.
[Back to top]
[Purchase Article]
[PMID: 19508188 PubMed - indexed for MEDLINE]
Evaluation of Aflatoxin B1– Acetylcholinesterase
Dissociation Kinetic Using the Amperometric Biosensor Technology:
Prospect for Toxicity Mechanism
M. Pohanka, K. Musilek and K. Kuca
Aflatoxins are group of secondary metabolites from
moulds. The main toxic effect of alfatoxins on body is based
on metabolic activation on cytochrome P450 system. Recently,
some studies appointed at anticholinergic properties of aflatoxins
and inhibition of acetylcholinesterases (AChE) was described.
Inhibition is reversible; however, some questions arose. Is
the interaction firmly enough to prevent distribution of aflatoxins
in body? Could be AChE considered as a scavenger of aflatoxins?
Amperometric biosensor with immobilized acetylcholinesterase
was used for evaluation of aflatoxin B1 (AFB1) – AChE
complex spontaneous dissociation, where AFB1 acts as an inhibitor.
Displacement of solution with substrate and AFB1 by the intact
one enabled estimation of dissociation kinetics. The dissociation
rate constant kdis
was found 0.0047 ± 0.0005 s-1.
The half time (t1/2)
of complex dissociation was 146 s. The achieved data appoint
at fact that AChE could allow to distribute aflatoxins in
body instead acting as a scavenger. Analytical impact of study
is discussed, too.
[Back to top]
[Purchase
Article] [PMID:
19508199 PubMed - indexed for MEDLINE]
Solution Structure of a Photo-Switchable Insect Kinin Thioxo-Analog
Z. Cong, Y. Huang, L. Yang, D. Ye and S. Dong
The photo-switchable insect kinin thioxo-analog Phe1-Tyr2-Ψ[CS-N]-Pro3-Trp4-Gly5-NH2
(Ψ[CS-N]2-Kinin)
can change from ground state to photo-stationary state by
following a pulse of UV irradiation and its bioactivity increases
simultaneously. To investigate the conformation-activity relationship,
the solution structure of its ground state was determined
by two-dimensional NMR spectroscopy. In contrast, the photo-stationary
state could not be determined because of its relatively fast
thermal reisomerization. The molecular dynamics-calculated
structures based on NMR constraints demonstrate that the trans
Pro conformer is the predominant conformation for the ground
state in aqueous solution, which was also confirmed by the
very weak signal of the cis Pro conformer in the
spectroscopy. The aromatic side chains of residues 2 and 4
form an electrostatic interaction rather than 1 and 4. The
results explain the low bioactivity before UV irradiation,
and indicate the importance of the 1-4 electrostatic interaction
for the activity of insect kinins.
[Back to top]
[Purchase
Article] [PMID:
20236087 PubMed - indexed for MEDLINE]
L-Valine
and L-Proline -
Solid-State IR-LD Spectroscopic Study
A.G. Chapkanov and S.Y. Zareva
Spectral investigation including IR-characteristic
bands assignment of the amino acids zwitterions L-Valine
( L-Val)
and L-Proline
( L-Pro)
was carried out by linear-dichroic infrared (IR-LD) spectroscopy
of oriented solid sample as a nematic liquid crystal suspension.
The obtained experimental IR-LD results (transition moment
directions) were compared with known crystal X-ray data for
molecules orientation in the unit cells of the studied compounds,
confirming the applicability of the used spectral method for
structural determination. The influence of the protonation
on the IR-spectroscopic patterns of the both amino acids is
discussed.
[Back to top]
[Purchase
Article] [PMID:
19594435 PubMed - indexed for MEDLINE]
Mutagenesis Studies of Human Cystathionine β-Synthase:
Residues Important for Heme Binding and Substrate Interactions
S.-i. Ozaki, C. Sakaguchi, A. Nakahara and M.
Yoshiya
Human cystathionine β-synthase
(CBS) is a pyridoxal 5’-phosphate (PLP) dependent hemoprotein,
which catalyzes the condensation of serine and homocysteine.
Our mutagenesis studies suggest that Arg-266 is important
to sense structural changes in heme-binding site, and that
Gln-222 as well as Tyr-223 are involved in interactions with
substrates.
[Back to top]
[Purchase
Article] [PMID:
19508211 PubMed - indexed for MEDLINE]
A Novel Approach to Predict Protein-Protein Interactions
Related to Alzheimer’s Disease Based on Complex Network
J. Yang and X.-F. Jiang
A protein domain interaction prediction program was complied
using C++ to predict whether
a query protein could interact with other hub proteins. It
is indicated that the proteins interacting with AATF (Apoptosis-Antagonizing
Transcription Factor) possess a common conservative
pattern: I-x(0,1)-E-x(2)-[A/E/N/T]-x-[E/K]. Our method is
attempted to integrate the characteristics of protein interaction
network with the simplest building blocks-conservative patterns.
[Back to top]
[Purchase
Article] [PMID:
19508214 PubMed - indexed for MEDLINE]
Molecular Dynamics of Some Pentapeptides Having a
Strong Tendency to Helical Conformation
Z.-R. Huang, T.-Y. Zhu, T.-T. Wang, X.-N. Wang
and J. Yang
Some pentapeptides with higher alpha-helical tendency
possess typical sequence pattern, such as “+ –
+ + – – +”, “+ – – + –
– +”, “+ – + – – –
+”, and “– + + – – – +”
(“+” = D,N,E,Q,K,R,T,C, or H; “–”
= L,I,V, or A), especially symmetrical motifs (a pair of reverse
sequences beside palindromic segments), such as ALALA, QQAQE/EQAQQ,
and REALE/ELAER, hint that the nascent peptide can fold a
certain conformation in a two-way folding fashion.
[Back to top]
[Purchase
Article] [PMID:
19594434 PubMed - indexed for MEDLINE]
Stationary Phase Expression, Purification, and Characterization
of XorKI, a Restriction Endonuclease from Xanthomonas
oryzae pv. oryzae
W.Y. Kang and Y.K. Chae
An endonuclease from Xanthomonas oryzae pathovar
oryzae KACC 10331, XorKI, was heterologously produced
in Escherichia coli by applying the stationary state
induction method. The yield was 5.4 mg of XorKI per liter
of LB medium. XorKI existed in multiple oligomeric forms as
evidenced by gel filtration chromatography. The specific activity
of purified XorKI was 323000 units per mg.
[Back to top]
[Purchase
Article] [PMID:
19594433 PubMed - indexed for MEDLINE]
Immunization with Peptide-Protein Conjugates: Impact on Benchmarking
B-Cell Epitope Prediction for Vaccine Design
S.E.C. Caoili
Benchmarking B-cell epitope prediction for vaccine design
is meaningful if based on empirical reference data pertaining
to cross-reactivities of antipeptide antibodies with native
protein antigens; yet it is complicated by such data acquired
using antibodies raised against peptide-protein conjugates,
as peptide-protein conjugation can differentially suppress
antibody responses to peptide epitopes.
[Back to top]
[Purchase
Article] [PMID:
19958278 PubMed - indexed for MEDLINE]
Interactions of Ginkgolides A and B with a Recombinant
Human Prion Protein
D. Georgieva, L. Redecke, M. von Bergen, N. Genov and
C. Betzel
In the presence of ginkgolides A and B a recombinant
human prion protein (90-231) is more susceptible to proteolysis,
which is characteristic for the non-infective form of prion
proteins and more thermostable than in the absence of ginkgolides.
Probably, ginkgolides exert a neuroprotective effect through
a rearrangement of the prion structure.
[Back to top]
[Purchase
Article] [PMID:
19958280 PubMed - indexed for MEDLINE]
Synthesis of N-Succinyl-L
, L-Diaminopimelic Acid Mimetics
Via Selective Protection
V. Vanek, J. Pícha, M. Budešínský,
M. Šanda, J. Jirácek, R.C. Holz and J.
Hlavácek
The search for potential inhibitors that target so far
unexplored bacterial enzyme mono-N-succinyl-L,L-diaminopimelic
acid desuccinylase (DapE) has stimulated a development of
methodology for quick and efficient preparation of mono-N-acylated
2,6-diaminopimelic acid (DAP) derivatives bearing the different
carboxyl groups or lipophilic moieties on their amino group.
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