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Protein
& Peptide Letters
ISSN: 0929-8665
Protein & Peptide Letters
Volume 16, Number 1, 2009
Contents
Regular Papers
Substrate Specificity of Rat DESC4, A Type
II Transmembrane Serine Protease Pp. 1-6
M. Behrens, F. Buck and W. Meyerhof
[Abstract] [Full text Article]
[PMID:
19149666 PubMed - indexed for MEDLINE]
Identification of a Biosurfactant Producing
Strain: Bacillus subtilis HOB2 Pp.
7-13
N.I.A. Haddad, J. Wang and B. Mu
[Abstract] [Full Text Article]
[PMID:
19149667 PubMed - indexed for MEDLINE]
Mechanisms of Prion Protein Aggregation
Pp. 14-26
S.N. Fontaine and D.R. Brown
[Abstract] [Full Text Article]
[PMID:
19149668 PubMed - indexed for MEDLINE]
Prediction of Protein Secondary Structure
Content by Using the Concept of Chou’s Pseudo Amino
Acid Composition and Support Vector Machine Pp.
27-31
C. Chen, L. Chen, X. Zou and P.
Cai
[Abstract] [Full Text Article]
[PMID:
19149669 PubMed - indexed for MEDLINE]
Hydroxyl Radical Mediates Oxidative Modification
of Caprine Alpha-2 Macroglobulin Pp. 32-35
S.A. Khan and F.H. Khan
[Abstract] [Full Text Article]
[PMID:
19149670 PubMed - indexed for MEDLINE]
Structural Bioinformatics of Vibrio
cholerae Aminopeptidase A (PepA) Monomer Pp.
36-45
G. Lutfullah, N. Azhar, F. Amin, Z. Khan,
M.K. Azim, K. Shouqat, S. Noor and R. Ali
[Abstract] [Full Text Article]
[PMID:
19149671 PubMed - indexed for MEDLINE]
The Inhibitory Effect of Propofol on
Bovine Lactoperoxidase Pp. 46-49
M. Sisecioglu, M. Çankaya, I.
Gülçin and H. Özdemir
[Abstract] [Full Text Article]
[PMID:
19149672 PubMed - indexed for MEDLINE]
Correlation Between Protein Sequence
Similarity and X-Ray Diffraction Quality in the Protein Data
Bank Pp. 50-55
H.-M. Lu, D.-C. Yin, Y.-J. Ye, H.-M. Luo,
L.-Q. Geng, H.-S. Li, W.-H. Guo and P. Shang
[Abstract] [Full Text Article]
[PMID:
19149673 PubMed - indexed for MEDLINE]
Tertiary Butanol Induced Amyloidogenesis
of Hen Egg White Lysozyme (HEWL) Is Facilitated by Aggregation-Prone
Alkali-Induced Molten Globule Like Conformational State
Pp. 56-60
M. Hameed, B. Ahmad, R.H. Khan, K.I. Andrabi
and K.M. Fazili
[Abstract] [Full Text Article]
[PMID:
19149674 PubMed - indexed for MEDLINE]
Structure Solution of Misfolded Conformations
Adopted by Intrinsically Disordered Alzheimer's Tau Protein
Pp. 61-64
J. Sevcik, R. Skrabana, E. Kontsekova and
M. Novak
[Abstract] [Full Text Article]
[PMID:
19149675 PubMed - indexed for MEDLINE]
Expression of HPV 58 Long and Short L1
Capsid Proteins in Primary Mouse Keratinocyte Cultures
Pp. 65-74
X. Wang, J. Liu, W.M. Zhao and K.-N.
Zhao
[Abstract] [Full Text Article]
[PMID:
19149676 PubMed - indexed for MEDLINE]
Molecular Cloning and Expression of Several
New Anopheles cracens Epsilon Class Glutathione Transferases
Pp. 75-81
J. Wongtrakul, J. Wongsantichon, A.
Vararattanavech, P. Leelapat, L.-a. Prapanthadara and
A.J. Ketterman
[Abstract] [Full Text Article]
[PMID:
19149677 PubMed - indexed for MEDLINE]
Pomegranin, An Antifungal Peptide from
Pomegranate Peels Pp. 82-85
G. Guo, H.X. Wang and T.B. Ng
[Abstract] [Full Text Article]
[PMID:
19149678 PubMed - indexed for MEDLINE]
Design, Synthesis and Docking Studies
of Hydroxyethylamine and Hydroxyethylsulfide BACE-1 Inhibitors
Pp. 86-90
L. Rizzi, N. Vaiana, F. Sagui, E. Genesio,
E. Pilli, V. Porcari and S. Romeo
[Abstract] [Full Text Article]
[PMID:
19149679 PubMed - indexed for MEDLINE]
Proteinase K-Resistant Aggregates of
Recombinant Prion Protein PrP-(23-98) Are Toxic to Cultured
Cells Pp. 91-96
N. Shiraishi, Y. Inai and Y. Ihara
[Abstract] [Full Text Article][PMID:
19149680 PubMed - indexed for MEDLINE]
Crystallization Reports
Crystallization and Preliminary X-Ray Crystallographic
Analysis of Human Plasma Platelet Activating Factor Acetylhydrolase
Pp. 97-100
U. Samanta, C. Wilder and B.J.
Bahnson
[Abstract] [Full Text Article]
[PMID:
19149681 PubMed - indexed for MEDLINE]
Crystallization and Preliminary Diffraction
Studies of Nudix Hydrolase YmfB from Escherichia coli
K-1 Pp. 101-104
M.-K. Hong, J.-K. Kim, Y.-J. Ahn and
L.-W. Kang
[Abstract] [Full Text Article]
[PMID:
19149682 PubMed - indexed for MEDLINE]
Abstracts
[Back to top]
[Full Text Article] [PMID:
19149666 PubMed - indexed for MEDLINE]
Substrate Specificity of Rat DESC4, A Type II Transmembrane
Serine Protease
M. Behrens, F. Buck and W. Meyerhof
Type II transmembrane serine proteases (TTSPs) are involved
in important physiological processes, such as pro-hormone
processing, cellular signaling, host immune defense, and cancer
development. The diversity of functions is reflected by the
multidomain architecture of these proteases, which are composed
of a variety of functional domains in addition to the catalytic
domain. Recently, we identified rat DESC4, a member of the
HAT/DESC1-like subfamily of TTSPs. Intriguingly, DESC4 gene
expression is confined to few tissues including gustatory
papillae. In the current publication we present the purification
of the catalytic domain of recombinant rat DESC4. Subsequently,
the catalytic domain was subjected to a refolding procedure.
During refolding we observed endogenous catalytic activity
leading to smaller fragments, which were analyzed by peptide
sequencing. The identified cleavage-sites are typical for
trypsin-like serine proteases. For further analyses a homology-based
model of the DESC4 catalytic domain was generated enabling
us to in-vestigate protease-substrate interaction in more
detail.
[Back to top]
[Full Text Article] [PMID:
19149667 PubMed - indexed for MEDLINE]
Identification of a Biosurfactant Producing Strain:
Bacillus subtilis HOB2
N.I.A. Haddad, J. Wang and B. Mu
A biosurfactant-producing strain was isolated from the
production water of an oil-field and was identified as Bacillus
subtilis HOB2 by 16S rRNA gene sequencing. The production
of biosurfactant by Bacillus subtilis HOB2 has been
investigated using different carbon and nitrogen sources,
under thermophilic and mesophilic conditions. The strain was
able to grow and to produce surfactant, reducing the surface
tension of medium to 27 mN/m on sucrose, and 28 mN/m on glucose
after 24 h of cultivation. The strain was able to produce
the maximum amount of biosurfactant when ammonium ions were
used as nitrogen source. The surface-active compound was stable
during exposure to elevate temperature (100°C),
high salinity (25% NaCl) and a wide range of pH values (5.0-11.0).
The biosurfactant was capable of forming a promising emulsification
index (E24= 68%)
with kerosene. The kinetic studies revealed that biosurfactant
production is a cell growth-associated process. Preliminary
chemical characterization revealed that the surfactant has
a lipopeptide composition similar to surfactin as confirmed
by TLC and IR analysis. Properties and characteristics of
the biosurfactant produced by Bacillus subtilis HOB2
suggesting potential commercial applications, such as enhanced
oil recovery, bioremediation of soil and marine environments,
and food industries.
[Back to top]
[Full Text Article]
[PMID:
19149668 PubMed - indexed for MEDLINE]
Mechanisms of Prion Protein Aggregation
S.N. Fontaine and D.R. Brown
The prion protein is a cell surface glycoprotein that
is converted to a protease resistant abnormal isoform during
the course of prion disease. The normal isoform of this protein
has been shown to be an antioxidant that aids the survival
of neurones. The abnormal isoform is associated with both
the transmissible agent of prion diseases and is also toxic.
Recent studies have shown that there are multiple end states
in terms of aggregation of the protein. Both soluble oligomers
and insoluble fibrils can form from the abnormal isoform.
Although fibrils are characteristic of the disease, the most
infectious prions are associated with oligomers. Neurotoxicity
can be associated with fibrils but mostly appears to be due
to small aggregates. For many years fibrils were believed
to be central to the disease process but currently evidence
supports the notion that fibrils represent a "bulk"
form of abnormal protein, which is largely inert, but carried
along a small active component. This review will examine what
is known about the mechanisms behind prion protein aggregation,
and the relevance of each form for the disease.
[Back to top]
[Full Text Article]
[PMID:
19149669 PubMed - indexed for MEDLINE]
Prediction of Protein Secondary Structure Content
by Using the Concept of Chou’s Pseudo Amino Acid Composition
and Support Vector Machine
C. Chen, L. Chen, X. Zou and P.
Cai
Protein secondary structure carries information about
local structural arrangements. Significant majority of successful
methods for predicting the secondary structure is based on
multiple sequence alignment. However, the multiple alignment
fails to achieve accurate results when a protein sequence
is characterized by low homology. To this end, we propose
a novel method for prediction of secondary structure content
through comprehensive sequence representation. The method
is featured by employing a support vector machine (SVM) regressing
system and adopting a different pseudo amino acid composition
(PseAAC), which can partially take into account the sequence-order
effects to represent protein samples. It was shown by both
the self-consistency test and the independent-dataset test
that the trained SVM has remarkable power in grasping the
relationship between the PseAAC and the content of protein
secondary structural elements, including α-helix,
310-helix, π-helix,
β-strand,
β-bridge,
turn, bend and the rest random coil. Results prior to or competitive
with the popular methods have been obtained, which indicate
that the present method may at least serve as an alternative
to the existing predictors in this area.
[Back to top]
[Full Text Article]
[PMID:
19149670 PubMed - indexed for MEDLINE]
Hydroxyl Radical Mediates Oxidative Modification
of Caprine Alpha-2 Macroglobulin
S.A. Khan and F.H. Khan
ROS, including .OH, is now recognized as the hallmark
of inflammation and damage to the anti-proteinase barrier
has been implicated in a number of pathophysiological conditions.
We have previously shown that O2.-
and H2O2/HOCl
are physiologically relevant inactivators of α2M,
a key anti-proteinase. Here, we show that .OH disrupted caprine
α2M
structure and antiproteolytic potential in vitro,
suggesting that its function could be compromised via oxidative
modification.
[Back to top]
[Full Text Article]
[PMID:
19149671 PubMed - indexed for MEDLINE]
Structural Bioinformatics of Vibrio cholerae
Aminopeptidase A (PepA) Monomer
G. Lutfullah, N. Azhar, F. Amin, Z. Khan,
M.K. Azim, K. Shouqat, S. Noor and R. Ali
Aminopeptidase A (PepA) is a metalloexopeptidase found
in Vibrio cholerae .It functions as a transcriptional
repressor in regulatory cascade that controls virulence gene
expression in V. cholerae. It is involved in protein
degradation and in the metabolism of biologically active peptides.
We proposed a 3D model of PepA based upon the crystal structure
of PepA from Escherichia coli (E. coli) with an intention
to evaluate the active site of the enzyme and to predict the
properties of this enzyme, study of its 3D structure will
help in understanding its role in DNA binding.
[Back to top]
[Full Text Article]
[PMID:
19149672 PubMed - indexed for MEDLINE]
The Inhibitory Effect of Propofol on Bovine Lactoperoxidase
M. Sisecioglu, M. Çankaya, I. Gülçin
and H. Özdemir
Propofol (2,6-diisopropylphenol) is a hypnotic intravenous
agent with in vivo antioxidant properties. This study
was undertaken to examine the in vitro effect of
propofol on lactoperoxidase (LPO; E.C. 1.11.1.7) obtained
from bovine milk. Lactoperoxidase was purified with three
purification steps: Amberlite CG-50 resin, CM-Sephadex C-50
ionexchange chromatography and Sephadex G-100 gel filtration
chromatography, respectively. Lactoperoxidase was purified
with a yield of 21.6%, a specific activity of 34 EU/mg proteins
and 14.7-fold purification. One enzyme unit is defined as
the oxidation of 1 μmol
ABTS per min under the assay condition (25°C,
pH: 6.0). To determine enzyme purity, sodium dodecyl sulphate-polyacrylamide
gel electrophoresis (SDS-PAGE) was performed and single band
was observed. The effect of propofol on lactoperoxidase were
determined using 2,2'-azino-bis (3-ethylbenzthiazoline-6 sulfonic
acid) diammonium salt (ABTS) as a chromogenic substrate. The
IC50 value of propofol was
found as 15.97 μM.
Also, Ki constant for propofol
was 3.72 μM
and propofol was found as competitive inhibitor.
[Back to top]
[Full Text Article]
[PMID:
19149673 PubMed - indexed for MEDLINE]
Correlation Between Protein Sequence Similarity and
X-Ray Diffraction Quality in the Protein Data Bank
H.-M. Lu, D.-C. Yin, Y.-J. Ye, H.-M. Luo,
L.-Q. Geng, H.-S. Li, W.-H. Guo and P. Shang
As the most widely utilized technique to determine the
3-dimensional structure of protein molecules, X-ray crystallography
can provide structure of the highest resolution among the
developed techniques. The resolution obtained via X-ray crystallography
is known to be influenced by many factors, such as the crystal
quality, diffraction techniques, and X-ray sources, etc.
In this paper, the authors found that the protein sequence
could also be one of the factors. We extracted information
of the resolution and the sequence of proteins from the Protein
Data Bank (PDB), classified the proteins into different clusters
according to the sequence similarity, and statistically analyzed
the relationship between the sequence similarity and the best
resolution obtained. The results showed that there was a pronounced
correlation between the sequence similarity and the obtained
resolution. These results indicate that protein structure
itself is one variable that may affect resolution when X-ray
crystallography is used.
[Back to top]
[Full Text Article]
[PMID:
19149674 PubMed - indexed for MEDLINE]
Tertiary Butanol Induced Amyloidogenesis of Hen Egg
White Lysozyme (HEWL) Is Facilitated by Aggregation-Prone
Alkali Induced Molten Globule Like Conformational State
M. Hameed, B. Ahmad, R.H. Khan, K.I. Andrabi
and K.M. Fazili
Proteins may form undesirable aggregates during the process
of folding. Increasing evidence suggests that amyloid fibrils
may arise from partially folded precursor molecules. We have
previously demonstrated that hen egg white lysozyme [HEWL]
exists as molten globule at pH 12.7. Here, we report that
lysozyme at pH 7.0 and 11.0 are nearly stable to the addition
of up to 45% t-butanol, but treatment of the alkali-induced
molten globule form of HEWL [AMGL] with 20% t-butanol caused
the formation of amyloid-like fibrils as evidenced by enhanced
Thioflavin T binding and DLS measurements.
[Back to top]
[Full Text Article]
[PMID:
19149675 PubMed - indexed for MEDLINE]
Structure Solution of Misfolded Conformations Adopted
by Intrinsically Disordered Alzheimer's Tau Protein
J. Sevcik, R. Skrabana, E. Kontsekova and
M. Novak
Until now it was impossible to obtain atomic structure
of intrinsically disordered protein (IDP) tau and/or its assembly
in Alzheimer’s paired helical filaments as neither of
them could have been prepared in the form amenable to X-ray
or NMR techniques. Using IDP tau property to attain regular
tertiary structure after binding events during self-assembly
or when complexed with its target we propose monoclonal antibodies
as surrogate tau protein binding partners to form complexes
and crystals for structure solution by X-ray technique.
[Back to top]
[Full Text Article]
[PMID:
19149676 PubMed - indexed for MEDLINE]
Expression of HPV 58 Long and Short L1 Capsid Proteins
in Primary Mouse Keratinocyte Cultures
X. Wang, J. Liu, W.M. Zhao and K.-N.
Zhao
We studied expression of HPV 58 long and short L1 proteins
in primary mouse keratinocyte (KC) cultures by transient transfection
of the L1 expression constructs. Following transient transfection,
long and short L1 open reading frames (ORFs) were transcribed
continuously for 9 days; however, no significant difference
was detected between the long and short L1 mRNA levels measured
by quantitative RT-PCR. Western blot analysis showed that
both long and short L1 proteins were continuously detected
in L1-transfected KCs for 9 days post-transfection and the
significantly increased signals of the L1 proteins over time
were associated with KC differentiation. Moreover, L1 protein
was more abundant in KCs transfected with the short L1 ORF
than the long L1 ORF. In vitro translation of the
L1 mRNAs indicated further that the short L1 mRNA had significantly
higher translation efficiency than the long L1 mRNA in cell-free
lysate system. The L1 proteins expressed from the two L1 mRNAs
in KCs were similarly stable. Thus, approximate 40% lower
level of expression of the L1 protein in KCs transfected with
the long L1 ORF was probably due to a stem-loop structure
with high ΔG
value downstream the first AUG codon in its mRNA secondary
structure. This stem-loop structure might prevent efficient
binding of the ribosome to mRNA and therefore reduced translation.
[Back to top]
[Full Text Article]
[PMID:
19149677 PubMed - indexed for MEDLINE]
Molecular Cloning and Expression of Several New Anopheles
cracens Epsilon Class Glutathione Transferases
J. Wongtrakul, J. Wongsantichon, A. Vararattanavech,
P. Leelapat, L.-a. Prapanthadara and A.J. Ketterman
Glutathione transferases, GSTs, are detoxification proteins
that are found in most organisms. The acGSTE3-3 had the ability
to conjugate 4-hydroxynonenal, a cytotoxic lipid peroxidation
product. Although other Epsilon GSTs showed roles in insecticide
metabolism, the acGSTE3-3 appeared to have a major role in
detoxifying lipid peroxidation products conferring protection
against oxidative damage.
[Back to top]
[Full Text Article]
[PMID:
19149678 PubMed - indexed for MEDLINE]
Pomegranin, An Antifungal Peptide from Pomegranate
Peels
G. Guo, H.X. Wang and T.B. Ng
A new antifungal peptide designated as pomegranin, with
an N-terminal sequence resembling that of rice disease resistance
NB-S-LRR-like protein, was isolated from fresh pomegranate
peels by ion exchange chromatography on DEAE-cellulose, affinity
chromatography on Affi-gel blue gel, and gel filtration by
fast protein liquid chromatography on Superdex 75. Pomegranin
was unadsorbed on DEAE-cellulose but adsorbed on Affi-gel
blue gel. It exhibited a molecular mass of 11 kDa in both
gel filtration and sodium dodecyl sulfate-polyacrylamide gel
electrophoresis. It inhibited mycelial growth in the fungi
Botrytis cinerea and Fusarium oxysporum with
an IC50 of 2 μM
and 6.1 μM,
respectively. It was devoid of hemagglutinating, ribonuclease,
deoxyribonuclease and protease inhibitory activities.
[Back to top]
[Full Text Article]
[PMID:
19149679 PubMed - indexed for MEDLINE]
Design, Synthesis and Docking Studies of Hydroxyethylamine
and Hydroxyethylsulfide BACE-1 Inhibitors
L. Rizzi, N. Vaiana, F. Sagui, E. Genesio,
E. Pilli, V. Porcari and S. Romeo
Both stereoisomer of hydroxyethylamine (HEA) and hydroxyethylsulfide
(HES) transition-state isostere inhibitors of BACE-1 were
synthesized. The syn-HEA epimer resulted always more active
than the anti stereoisomer independently from the P1
and the P1’ substituents.
On the contrary, the anti epimer of the HES isostere resulted
more active than the syn stereoisomer. The change of stereopreference
was studied by molecular modelling.
[Back to top]
[Full Text Article]
[PMID:
19149680 PubMed - indexed for MEDLINE]
Proteinase K-Resistant Aggregates of Recombinant
Prion Protein PrP-(23-98) Are Toxic to Cultured Cells
N. Shiraishi, Y. Inai and Y. Ihara
Here, we show for the first time that non-fibrillar and
spherical aggregates produced from PrP-(23-98) in the presence
of NADPH plus copper ions are toxic to cultured cells and
induce apoptotic signals. It is also confirmed that endogenous
cellular PrP isoform is not required for toxicity to occur.
[Back to top]
[Full Text Article]
[PMID:
19149681 PubMed - indexed for MEDLINE]
Crystallization and Preliminary X-Ray Crystallographic
Analysis of Human Plasma Platelet Activating Factor Acetylhydrolase
U. Samanta, C. Wilder and B.J.
Bahnson
The plasma form of the human enzyme platelet activating
factor acetylhydrolase (PAF-AH) has been crystallized, and
X-ray diffraction data were collected at a synchrotron source
to a resolution of 1.47 Å. The crystals belong to space
group C2, with unit cell parameters of α
= 116.18, b = 83.06, c = 96.71 Å,
and β=
115.09°
and two molecules in the asymmetric unit. PAF-AH functions
as a general anti-inflammatory scavenger by reducing the levels
of the signaling molecule PAF. Additionally, the LDL bound
enzyme has been linked to atherosclerosis due to its hydrolytic
activities of pro-inflammatory agents, such as sn-2
oxidatively fragmented phospholipids.
[Back to top]
[Full Text Article]
[PMID:
19149682 PubMed - indexed for MEDLINE]
Crystallization and Preliminary Diffraction Studies
of Nudix Hydrolase YmfB from Escherichia coli K-1
M.-K. Hong, J.-K. Kim, Y.-J. Ahn and
L.-W. Kang
Nudix hydrolases are a family of proteins that contains
the Nudix signature of the characteristic amino-acid sequence
Gx5Ex5[UA]xREx2EExGU,
where x represents any amino acid and U usually a bulky hydrophobic
amino acid, such as Leu, Val, or Ile. They ubiquitously exist
in more than 200 species. YmfB, a novel Nudix hydrolase found
in Escherichia coli, is a nonspecific nucleoside
tri- and di-phosphatase, which atypically releases inorganic
orthophosphate from triphosphates instead of pyrophosphate.
In this study, YmfB was cloned, overexpressed, and crystallized.
Two different crystals, one belonging to an orthorhombic space
group C2221 and the other a monoclinic space group P21, diffracted
to 2.7 Ä
and 2.6 Ä
resolution, and had unit cell parameters of α
= 68.7 Ä,
b = 283.1 Ä,
c = 70.4 Ä
and α
= 69.1 Ä,
b = 70.3 Ä,
c = 145.6 Ä,
β =
103.3°,
respectively. For the C2221
space group, four or five monomers exist in the asymmetric
unit, with a corresponding Vm
of 2.48 or 1.99 Ä3
Da-1 and a solvent content of 50.5 or 38.2%. For
the P21 space group, eight
or nine monomers exist in the asymmetric unit, with a corresponding
Vm of 2.49 or 2.21 Ä3
Da-1and a solvent content of 50.7 or 44.5%.
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