|
Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 16, Number 9, 2009
Contents
Regular Papers
Molecular and Functional Characterization of
Polynucleotide Phosphorylase from the Antarctic Eubacterium
Pseudoalteromonas haloplanktis
Pp. 999-1005
G. Evangelista, P. Falasca, I. Ruggiero, M. Masullo and
G. Raimo
[Abstract] [Purchase
Article]
Peptoid Analogues of Anoplin Show Antibacterial Activity
Pp. 1006-1011
K. Meinike and P.R. Hansen
[Abstract] [Purchase
Article]
Recognition of the N-Terminal Histone H2A and H3 Peptides
by Peptidylarginine Deiminase IV Pp. 1012-1016
M. Saiki, M. Watase, H. Matsubayashi and Y. Hidaka
[Abstract] [Purchase
Article]
Bioinformatics Comparison of G Protein of Isfahan
Virus with the Same Proteins of Two Other Closely Related
Viruses of the Genus Vesiculovirus Pp. 1017-1023
H. Mohabatkar and S. Mohsenzadeh
[Abstract] [Purchase
Article]
Synthesis and Characterization of New Galanthamine
Derivatives Comprising Peptide Moiety Pp. 1024-1028
L.T. Vezenkov, M.G. Georgieva, D.L. Danalev, T.B. Ivanov
and G.I. Ivanova
[Abstract] [Purchase
Article]
Synthesis of 4-Amino-Thiazole Analogs of Fmoc-Amino
Acids and Thiazole Linked N-Orthogonally Protected Dipeptidomimetics
Pp. 1029-1035
N. Narendra, T.M. Vishwanatha, N.S. Sudarshan and
V.V. Sureshbabu
[Abstract] [Purchase
Article]
Identification and Characterization of a Novel Oligomeric
Decaprenyl Diphosphate Synthase Pp. 1036-1040
H.H. Choe, H. Hwang, S. Kim, S. Yoon, D.H. Jo, Y. Ryu
and T.D. Kim
[Abstract] [Purchase
Article]
Proteome Analysis of Probenazole-Effect in Rice-Bacterial
Blight Interactions Pp. 1041-1052
T. Mahmood, M. Kakishima and S. Komatsu
[Abstract] [Purchase
Article]
Gβγ-Copurified
Lipid Kinase Impurity from Sf9 Cells Pp. 1053-1056
A. Shymanets, M.R. Ahmadian and B. Nürnberg
[Abstract] [Full
Text Article]
Human Prion Protein Helices: Studying Their Stability
by Molecular Dynamics Simulations Pp. 1057-1062
S. Costantini and A.M. Facchiano
[Abstract] [Purchase
Article]
Overlapping Double Turn Conformations Adopted by Tetrapeptides
Containing Non-Coded α-Amino
Isobutyric Acid (AIB) and Formation of Tape-Like Structures
Through Supramolecular Helix Mediated Self-Assembly Pp.
1063-1073
S. Kar, A. Dutta, M.G.B. Drew, P. Koley and A.
Pramanik
[Abstract] [Purchase
Article]
Regulation of Endochondral Ossification by Osteogenic
Growth Peptide C-Terminal Pentapeptide [OGP(10-14)]
Pp. 1074-1080
Z. Chen, M. Chang, Y. Peng, L. Zhao, Y. Zhan, L. Wang
and R. Wang
[Abstract] [Purchase
Article]
Functional Roles of EF-Hands in Human Potassium Channel-Interacting
Protein 2.2 Pp. 1081-1087
L. Lee, K.-C. Chen and L.-S. Chang
[Abstract] [Purchase
Article]
Antinociceptive Activity of Lectins from Diocleinae
Seeds on Acetic Acid-Induced Writhing Test in Mice
Pp. 1088-1092
F.R. Holanda, A.N. Coelho-de-Sousa, A.M.S. Assreuy, J.H.
Leal-Cardoso, A.F. Pires, K.S. do Nascimento, C.S. Teixeira,
B.S. Cavada and C.F. Santos
[Abstract] [Purchase
Article]
Investigating the Effect of Temperature on Transient
Partial Unfolding by Proteolysis Pp. 1093-1097
K. Youn and C. Park
[Abstract] [Purchase
Article]
Invertase from Hyper Producer Strain of Aspergillus
niger: Physiochemical Properties, Thermodynamics and
Active Site Residues Heat of Ionization Pp. 1098-1105
H. Nadeem, M.H. Rashid, M. Riaz, B. Asma, M.R. Javed and
R. Perveen
[Abstract] [Purchase
Article]
Insulin-Binding Canavalin Is Present in Canavalia
ensiformis Seed Coat Pp. 1106-1111
E.D.S. Ribeiro, A.F. Uchôa, L.G. da Silva, D.G.
Beghini, A.T. da Silva Ferreira, J. Perales, T. Jacinto, K.V.S.
Fernandes, J. Xavier-Filho and A.E.A. Oliveira
[Abstract] [Purchase
Article]
The Recognition of 27-Class Protein Folds: Approached
by Increment of Diversity Based on Multi-Characteristic Parameters
Pp. 1112-1119
H. Zhang, X. Hu and Q. Li
[Abstract] [Purchase
Article]
Stability, Subunit Interactions and Carbohydrate-Binding
of the Seed Lectin from Pterocarpus angolensis
Pp. 1120-1134
D. Echemendia-Blanco, E.V. Driessche, I. Ncube, J.S. Read
and S. Beeckmans
[Abstract] [Purchase
Article]
Abstracts
[Back to top] [Purchase
Article]
Molecular and Functional Characterization of Polynucleotide
Phosphorylase from the Antarctic Eubacterium Pseudoalteromonas
haloplanktis
G. Evangelista, P. Falasca, I. Ruggiero, M. Masullo and
G. Raimo
Polyribonucleotide phosphorilase from the psychrophilic
Antarctic eubacterium Pseudoalteromonas haloplanktis
(PhPNPase) has been purified. This enzyme catalyzes
both the RNA polymerisation and degradation reaction, showing
the highest activity at temperatures below 40°C.
PhPNPase is quite sensitive to heat treatment and
it is endowed with remarkable halotolerance.
[Back to top]
[Purchase
Article]
Peptoid Analogues of Anoplin Show Antibacterial Activity
K. Meinike and P.R. Hansen
We have synthesised nine analogues of the antibacterial peptide
anoplin with a peptoid residue at position 5 (H-GLLKXIKTLL-NH2).
The most active compounds showed MIC-values of 12.5 and 25
μM
against E.coli and S.aureus. These MIC-values
are comparable with anoplin which showed 23 μM
and 11 μM
against E.coli and S.aureus. However, the
selectivity was reversed. Our results indicate that peptoid
analogues of anoplin are promising lead structures for developing
new antibacterial agents.
[Back to top]
[Purchase
Article]
Recognition of the N-Terminal Histone H2A and H3 Peptides
by Peptidylarginine Deiminase IV
M. Saiki, M. Watase, H. Matsubayashi and Y. Hidaka
Peptidylarginine deiminase IV (PAD4) catalyzes the conversion
of an Arg residue to a citrulline residue in various proteins.
In particular, citrullination of histone subunits, such as
H2A and H3, by PAD4 is thought to be related to rheumatoid
arthritis. However, the details of the citrullination mechanism
of histone H2A and H3 are not yet well known. Moreover, the
effects of N-terminal acetylation on histone subunits with
respect to PAD4 recognition have not yet been studied. To
further study the mechanism of PAD4 recognition of histone
H2A and H3 subunits, a series of the N-terminal peptides was
chemically synthesized and the citrullination sites were identified
using MALDI-TOF/MS. N-terminal acetylation of histone H2A
was not significant with respect to PAD4 recognition in
vitro, but the acetylation of H3 peptide had a significant
effect on PAD4 recognition in vitro, resulting in
predominant citrullination at the Arg2 residue.
[Back to top]
[Purchase
Article]
Bioinformatics Comparison of G Protein of Isfahan
Virus with the Same Proteins of Two Other Closely Related
Viruses of the Genus Vesiculovirus
H. Mohabatkar and S. Mohsenzadeh
Since there are not much experimental data available
about different structural properties of Isfahan virus (ISFV),
in the present investigation, computational study of G protein
of ISFV was performed and the results were compared with G
proteins of Chandipura virus (CHPV) and Piry virus (PV). Calculation
of amino acid compositions of G proteins of viruses was done
by PseAAC server. Predictions of localization, sequence of
signal peptides, C, N and O glycosylation sites, transmembrane
helices, cysteine bond positions and B cell epitopes of G
proteins were performed by Virus-PLoc, Signal-CF, EnsembleGly,
MemBrain, DiANNA and BCPREDS servers respectively. Similarities
and differences between these glycoproteins were predicted
and discussed.
[Back to top]
[Purchase
Article]
Synthesis and Characterization of New Galanthamine
Derivatives Comprising Peptide Moiety
L.T. Vezenkov, M.G. Georgieva, D.L. Danalev, T.B. Ivanov
and G.I. Ivanova
New analogues of galanthamine containing peptide fragments
either at 6 or 11 position, were synthesized by reaction between
galanthamine molecule and dipeptides and tripeptide, derivatives
of N-(3,4-dichlorophenyl)-D,L-Ala-OH. The best results according
to yields, easily purification of the target products, and
simplicity of the scheme realisation was achieved by using
of cyanomethyl ester of Boc-Gly-OH as activated compound.
[Back to top]
[Purchase
Article]
Synthesis of 4-Amino-Thiazole Analogs of Fmoc-Amino
Acids and Thiazole Linked N-Orthogonally Protected Dipeptidomimetics
N. Narendra, T.M. Vishwanatha, N.S. Sudarshan and
V.V. Sureshbabu
We report a one pot synthesis of Fmoc amino acid derived
4-amino-thiazole derivatives and thiazole linked N-orthogonally
protected dipeptidomimetics by the condensation of Nα-Fmoc
α-halomethylketones
with thiourea and Boc/Z-α-amino
acid thioamides via modified Hantzch protocol. Side
chain modified Fmoc amino acids containing 4-amino thiazole
moiety have also been synthesized following the similar protocol.
[Back to top]
[Purchase
Article]
Identification and Characterization of a Novel Oligomeric
Decaprenyl Diphosphate Synthase
H.H. Choe, H. Hwang, S. Kim, S. Yoon, D.H. Jo, Y. Ryu
and T.D. Kim
A novel oligomeric decaprenyl pyrophosphate synthase was identified.
Circular dichroism measurements indicated that it is alpha-helical,
and stable against pH changes and denaturants. Three peptides
corresponding to the conserved regions were synthesized and
metal affinities were investigated. Crystallographic analyses
of this oligomeric DDS are currently in progress.
[Back to top]
[Purchase
Article]
Proteome Analysis of Probenazole-Effect in Rice-Bacterial
Blight Interactions
T. Mahmood, M. Kakishima and S. Komatsu
To study the effect of probenazole on the induced systemic
resistance mechanism of rice-bacterial interaction, a proteomic
approach was applied. Oryza sativa cv. Java 14 seedlings
were treated with probenazole, followed by inoculation with
compatible (Xo7435) and incompatible (T7174) races of Xanthomonas
oryzae pv. oryzae. Cytosolic proteins were
fractionated from leaf blades, separated by two-dimensional
polyacrylamide gel electrophoresis. Pathogenesis-related protein
5 (PR5) was significantly induced with probenazole treatment
followed by inoculation with T7174 or Xo7435. The sense PR5
transgenic rice plants were more highly resistant than the
susceptible vector control against Xo7435. These results indicate
that probenazole strongly induces PR5 in the interaction between
rice and X. oryzae pv. oryzae, and might
be involved in the resistance mechanism of rice against bacterial
blight.
[Back to top]
[Full
Text Article]
Gβγ-Copurified
Lipid Kinase Impurity from Sf9 Cells
A. Shymanets, M.R. Ahmadian and B. Nürnberg
G-protein βγ
dimers are prime regulators transmitting extracellular signals
to wide-ranging cellular effectors including phosphoinositide
3-kinase (PI3K) isoforms β
and γ.
Recombinant Gβγ
purified from Sf9 cells via metal-affinity and anion exchange
chromatography exhibited a wortmannin-insensitive phospholipid
kinase activity that copurified from the insect cells. To
exclude false-positive results of Gβγ-dependent
lipid kinase activity, the elimination of insect phospholipid
kinase from Gβγ
protein samples is necessary to avoid interference with the
intrinsic lipid kinase activity of PI3K isoforms in reconstitution
experiments. Here we describe an improved procedure of Gβ1γ2
purification from cell membranes that separates the contaminating
phospholipid kinase.
[Back to top]
[Purchase
Article]
Human Prion Protein Helices: Studying Their Stability
by Molecular Dynamics Simulations
S. Costantini and A.M. Facchiano
To study the intrinsic structural properties of three human
prion helices and analyse their stability, we conducted molecular
dynamics simulations, applied helix propensity predictions
and evaluated the energetic contribution of the helical regions
to the PrP protein stability. Our results suggest that three
helices present different stability and the helix 2 results
the least stable.
[Back to top]
[Purchase
Article]
Overlapping Double Turn Conformations Adopted by Tetrapeptides
Containing Non-Coded α-Amino
Isobutyric Acid (AIB) and Formation of Tape-Like Structures
Through Supramolecular Helix Mediated Self-Assembly
S. Kar, A. Dutta, M.G.B. Drew, P. Koley and A.
Pramanik
Single crystal X-ray diffraction studies and solvent dependent
1H NMR titrations reveal
that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe,
where Xx, Yy and Zz are coded L-amino acids, adopt equivalent
conformations that can be described as overlapping double
turn conformations stabilized by two 4→1
intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O
and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double
turn structures are packed in head-to-tail fashion through
intermolecular hydrogen bonds to create supramolecular helical
structures. Field emission scanning electron microscopic (FE-SEM)
images of the tetrapeptides in the solid state reveal that
they can form flat tape-like structures. The results establish
that synthetic Aib containing supramolecular helices can form
highly ordered self-aggregated amyloid plaque like human amylin.
[Back to top]
[Purchase
Article]
Regulation of Endochondral Ossification by Osteogenic
Growth Peptide C-Terminal Pentapeptide [OGP(10-14)]
Z. Chen, M. Chang, Y. Peng, L. Zhao, Y. Zhan, L. Wang
and R. Wang
In neonatal rat metatarsal organ culture, a bell-shaped dose-related
curve in length of mineralized area, increases in the height
of proliferative and hypertrophic zones, in the number of
hypertrophic chondrocyte and in the amount of Runx2 mRNA,
were revealed after treatment with OGP(10-14). We conclude
that OGP(10-14) accelerates bone growth.
[Back to top]
[Purchase
Article]
Functional Roles of EF-Hands in Human Potassium Channel-Interacting
Protein 2.2
L. Lee, K.-C. Chen and L.-S. Chang
Single site-directed mutations at each of the four EF-hand
loops of potassium channel-interacting protein 2.2 (KChIP2.2)
were carried out to explore the functional roles of EF-hands
in KChIP2.2. In contrast to those on EF-hands 1 and 2, mutations
on EF-hands 3 or 4 distorted the high affinity Ca2+-binding
site of KChIP2.2. However, the Mg2+-binding
ability of KChIP2.2 was marginally affected by the mutations.
The gross conformation of mutated KChIP2.2 was indistinguishable
from wild-type KChIP2.2 as revealed by CD spectra. The results
of size exclusion chromatography showed that, with exception
of EF-hand 4 mutant, mutations on EF-hands 1, 2 or 3 caused
KChIP2.2 to form oligomer. Pull-down assay revealed that,
unlike wild-type KChIP2.2, the interaction between mutated
KChIP2.2 and Kv4.2 was not notably enhanced by Ca2+
and Mg2+. Coexpression of
Kv4.2 and KChIP2.2 in HeLa cells revealed that mutations on
EF-hands did not alter the intracellular co-localization of
KChIP2.2 and Kv4.2. Together with previous findings that EF-hand
mutants of KChIP proteins are unable to regulate the kinetics
of Kv4.2, our data show that the intact EF-hands should be
crucial for the formation of active conformation of KChIP2.2
when the protein is loaded with Ca2+
and Mg2+.
[Back to top]
[Purchase
Article]
Antinociceptive Activity of Lectins from Diocleinae
Seeds on Acetic Acid-Induced Writhing Test in Mice
F.R. Holanda, A.N. Coelho-de-Sousa, A.M.S. Assreuy, J.H.
Leal-Cardoso, A.F. Pires, K.S. do Nascimento, C.S. Teixeira,
B.S. Cavada and C.F. Santos
Diocleinae lectins administered per oral route in mice inhibited
the abdominal constrictions induced by acetic acid. The percentage
of the lectins antinociception varied from 61% for Canavalia
grandiflora (ConGf) to 20% for Dioclea violacea.
ConGf inhibited contortions at all doses tested but not in
a dose-dependent manner, involving carbohydrate recognition.
[Back to top]
[Purchase
Article]
Investigating the Effect of Temperature on Transient
Partial Unfolding by Proteolysis
K. Youn and C. Park
Protein inactivation frequently occurs through partially unfolded
states under native conditions, and temperature is an important
parameter that affects the susceptibility of proteins to inactivation.
While the effect of temperature on global unfolding is well
documented, however, experimental characterizations of the
temperature effect on partial unfolding are rare. Proteolysis
offers a valuable chance to investigate the temperature effect
on partial unfolding. By investigating proteolysis kinetics,
the energetics of the partially unfolded state responsible
for proteolysis (the cleavable state) can be studied. E.
coli ribonuclease H (RNase H) has been shown to be cleaved
by thermolysin at the amide bond between Thr92 and Ala93 through
partial unfolding. Using this cleavage as a model system,
we evaluated quantitatively the temperature effect on conformational
equilibrium between the native state and a cleavable state.
The analysis shows that decrease in temperature from 37°C
to 4°C
decreases the population in the cleavable state and reduces
proteolytic susceptibility of the substrate protein. The conformational
change leading to the cleavable state has a temperature-independent
positive ∆H°
with negligible ∆Cp°.
This thermodynamic characteristic of partial unfolding for
proteolysis is quite distinct from that of global unfolding
of RNase H that has a considerable ∆Cp°
and a negative ∆H°
at low temperature. The distinct thermodynamic characteristics
of partial unfolding from global unfolding mainly result from
the difference in the changes of solvent-accessible surface
area, which confirms that the temperature effect on partial
unfolding is strongly scale-dependent.
[Back to top]
[Purchase
Article]
Invertase from Hyper Producer Strain of Aspergillus
niger: Physiochemical Properties, Thermodynamics and
Active Site Residues Heat of Ionization
H. Nadeem, M.H. Rashid, M. Riaz, B. Asma, M.R. Javed and
R. Perveen
Here we report for the first time heat of ionizationof invertase
(E.C.3.2.1.26) active site residues from hyper-producer strain
of Aspergillus niger (34.1 U ml-1),
along with its physiochemical properties, kinetics and thermodynamics
of stability-function. The Invertase showed great potential
for industry as being highly efficient (kcat
= 24167 s-1 at 65 °C,
pH 5.0) and stable (half life= 12 h at 56°C).
[Back to top]
[Purchase
Article]
Insulin-Binding Canavalin Is Present in Canavalia
ensiformis Seed Coat
E.D.S. Ribeiro, A.F. Uchôa, L.G. da Silva, D.G.
Beghini, A.T. da Silva Ferreira, J. Perales, T. Jacinto, K.V.S.
Fernandes, J. Xavier-Filho and A.E.A. Oliveira
An insulin-binding protein was isolated from Canavalia
ensiformis seed coat, by using an insulin-Sepharose 4B
affinity chromatography, and the protein was identified as
canavalin (Canavalia 7S globulin) by mass spectrometry
analysis. The major novelty of these data is the acidic nature
of this globulin insulin-binding, in contrast to the basic
Bg-like insulin-binding proteins so far reported in plants.
[Back to top]
[Purchase
Article]
The Recognition of 27-Class Protein Folds: Approached
by Increment of Diversity Based on Multi-Characteristic Parameters
H. Zhang, X. Hu and Q. Li
Based on the primary sequence, by selecting the pseudo amino
acid composition, position weight matrix score, the predicted
secondary structure and the second neighbor dipeptide composition
as characteristic parameters, an approach of diversity increment
for predicting 27-class protein folds is proposed. Overall
recognition accuracy reaches 61.10% in the independent testing.
[Back to top]
[Purchase
Article]
Stability, Subunit Interactions and Carbohydrate-Binding
of the Seed Lectin from Pterocarpus angolensis
D. Echemendia-Blanco, E.V. Driessche, I. Ncube, J.S. Read
and S. Beeckmans
From 1 kg of defatted Pterocarpus angolensis
(mukwa tree) seed meal, 21.6 grams of an α,D-mannose/glucose-specific
lectin can be purified on mannose-Sepharose. Relative affinities
for several (oligo)saccharides and glycoproteins were studied
by haemagglutination-inhibition. Gel filtration shows that
the lectin exists as a dimer above pH 5 and as a monomer below
pH 3.5. This is confirmed by studies on the release of lectin
subunits that were adsorbed from solution to lectin monomers
immobilized onto Eupergit-c. From the gel filtration patterns
it is calculated that a residue with pKa
of about 4.4 is involved in dimer dissociation. Titration
of glutamic acids (E60, E209) is postulated to be involved.
CD spectroscopy shows that the secondary structure of the
lectin is unchanged between pH 1 and 12.5, and that the tertiary
structure remains unchanged between pH 5 and 12. In the acid
pH region, reversible spectral changes occur that may be due
to the titration of one or more amino acids with a pKa
value of 3.9-4.2, probably aspartic acid. These residues are
implicated in sugar-binding but not in dimerization of the
lectin. Only at pH 12.5, irreversible denaturation occurs.
Mukwa lectin displays full carbohydrate-binding capacity between
pH 4 and 12, as is concluded from ELLA (Enzyme Linked Lectin
Assay) using ovalbumin and fetuin, and from binding of the
same glycoproteins to immobilized lectin monomers. The lectin
is rapidly and fully reversibly demetallized at pH 2.5 with
5 mM EDTA. The demetallized lectin is completely devoid of
sugar-binding activity. Mukwa lectin is a very thermostable
molecule (at least till 85°C).
However, addition of non-ionic detergents substantially lowers
its thermostability.
|
