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Protein
& Peptide Letters
ISSN: 0929-8665
Protein & Peptide Letters
Volume 15, Number 10, 2008
Contents
Regular Papers
Toward Prediction of Binding Affinities Between
the MHC Protein and Its Peptide Ligands Using Quantitative
Structure-Affinity Relationship Approach Pp.
1033-1043
F. Tian, F. Lv, P. Zhou, Q. Yang and A.F. Jalbout
[Abstract] [Purchase
Article]
Efficient Cleavage of Bid and Procaspase-7 by
Caspase-2 at Lower pH Pp. 1044-1049
P. Karki, G.R. Dahal, S.Y. Shin, J.S. Lee, B. Cho and
Il.-S. Park
[Abstract] [Purchase
Article]
Peptide Synthesis Using Carbamoylmethyl Esters
as Acyl Donors Mediated by Bacillus amyloliquefaciens
Protease Pp. 1050-1054
T. Miyazawa, T. Shindo, T. Murashima and T. Yamada
[Abstract] [Purchase
Article]
The Prefoldin of the Crenarchaeon Sulfolobus
solfataricus Pp. 1055-1062
A. D’Amaro, A. Valenti, A. Napoli, M. Rossi and
M. Ciaramella
[Abstract] [Purchase
Article]
Identification of Site(s) of Insulin Nitration
by Peroxynitrite and Characterization of Its Structural Change
Pp. 1063-1067
Y. Wang, Y. Luo, R. Zhong, D. Gao and S. Cui
[Abstract]
[Purchase
Article]
Synthesis of Acyl Carrier Protein Using a New Heterocyclic
Carboxyl Activating Group,3-Mercapto-5,6–Diphenyl-1,2,4–Triazine
Through SPPS Strategy Pp. 1068-1074
M.P. Rajan and E. Purushothaman
[Abstract]
[Purchase
Article]
Co-Expression of GroEL/ES Enhances the Expression
of Plant Catalase in Bacterial Cytosol Pp. 1075-1078
P. Mondal, M. Ray, S. Sahu and S.C. Sabat
[Abstract] [Purchase
Article]
Concerted Action of Metals and Macromolecular
Crowding on the Fibrillation of α-Synuclein
Pp. 1079-1085
L.A. Munishkina, A.L. Fink and V.N. Uversky
[Abstract] [Purchase
Article]
Antimicrobial Peptide Preferential Binding of E.
coli O157:H7 Pp. 1086-1093
J.W. Soares, R. Kirby, K.M. Morin and C.M. Mello
[Abstract] [Purchase
Article]
Synthesis and Characterization of Complex of
Glycyl-L-Glutamine and Bismuth Trichloride Pp. 1094-1099
S. Luan, Y. Zhu and Y. Jia
[Abstract] [Purchase
Article]
Enzymatic Profiling of Tetanus and Botulinum Neurotoxins
Based on Vesicle-Associated-Membrane Protein Derived Fluorogenic
Substrates Pp. 1100-1106
E.A. Perpetuo, L. Juliano, M.A. Juliano, F. Fratelli,
S.M.A. Prado, D.C. Pimenta and I. Lebrun
[Abstract] [Purchase
Article]
Function Prediction of Hypothetical Proteins Without
Sequence Similarity to Proteins of Known Function
Pp. 1107-1116
S. Kannan, A.M. Hauth and G. Burger
[Abstract] [Purchase
Article]
Structure-Function Study of a Plasmodium falciparum
Hsp70 Using Three-Dimensional Modelling and in Vitro
Analyses Pp. 1117-1125
A. Shonhai, M. Botha, T.A.P. de Beer, A. Boshoff and
G.L. Blatch
[Abstract] [Purchase
Article]
Analysis of Nickel-Binding Peptides in a Human
Hepidermoid Cancer Cell Line by Ni-NTA Affinity Chromatography
and Mass Spectrometry Pp. 1126-1131
A. Lamberti, C. Sanges, O. Longo, A. Chambery, A. Di Maro,
A. Parente, M. Masullo and P. Arcari
[Abstract] [Purchase
Article]
Predicting Lipase Types by Improved Chou’s
Pseudo-Amino Acid Composition Pp. 1132-1137
G.-Y. Zhang, H.-C. Li, J.-Q. Gao and B.-S. Fang
[Abstract] [Purchase
Article]
Crystallization Reports
Cloning, Expression, Purification, Crystallization
and Preliminary X-Ray Crystallographic Analysis of C-12 Hydroxylase
EryK from Saccharopolyspora erythraea Pp.
1138-1141
C. Savino, G. Sciara, A.E. Miele, S.G. Kendrew and
B. Vallone
[Abstract] [Purchase
Article]
Crystallization and Preliminary Crystallographic
Analysis of Laminarinase from Rhodothermus marinus:
A Case of Pseudomerohedral Twinning Pp. 1142-1144
A.M. Golubev, A.L. Rojas, A.S. Nascimento, L. Bleicher,
A.A. Kulminskaya, E.V. Eneyskaya and I. Polikarpov
[Abstract] [Purchase
Article]
Abstracts
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Toward Prediction of Binding Affinities Between the
MHC Protein and Its Peptide Ligands Using Quantitative Structure-Affinity
Relationship Approach
F. Tian, F. Lv, P. Zhou, Q. Yang and A.F. Jalbout
It is important but challenging to determine the binding
specificity of MHC-peptide interactions accurately and to
predict their binding affinity quantitatively. In this paper,
we discuss the application of an effective amino acid descriptor
to model and predict the binding affinities between the MHC
protein and its peptide ligands. This amino acid descriptor
was derived from 23 electronic properties, 37 steric properties,
54 hydrophobic properties and 5 hydrogen bond properties of
coded amino acids using principal component analysis (PCA),
called the divided physicochemical property scores (DPPS).
The DPPS descriptor was used to characterize a set of mouse
MHC (H-2KK) binding peptides,
and genetic algorithm-partial least square (GA-PLS) models
were then constructed. In analyses, these models were statistically
consistent with previous reports and molecular graphics exhibition.
Hydrophobic interactions and hydrogen bonds were important
to antigen recognition and presentation, especially exerting
effects on anchor residues of peptides.
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Efficient Cleavage of Bid and Procaspase-7 by Caspase-2 at
Lower pH
P. Karki, G.R. Dahal, S.Y. Shin, J.S. Lee, B. Cho
and Il.-S. Park
The activity of caspase-2 was examined under varying
biochemical conditions with the synthetic and protein substrates,
Bid and procaspase-7. The results indicate that it was largely
influenced by pH which might be one reason behind the inconsistency
for the cleavage of its established substrates during caspase-2-induced
apoptosis.
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Article]
Peptide Synthesis Using Carbamoylmethyl Esters as Acyl Donors
Mediated by Bacillus amyloliquefaciens Protease
T. Miyazawa, T. Shindo, T. Murashima and T. Yamada
Bacillus amyloliquefaciens protease-catalyzed peptide
bond formation was investigated using the carbamoylmethyl
(Cam) ester as the acyl donor. A series of N-protected
L-amino acid Cam esters were coupled with an L-amino acid
amide in acetonitrile in good to excellent yields. The superiority
of the Cam ester for segment condensations was demonstrated
in several 2+1 couplings. Furthermore, the couplings of racemic
amino acid Cam esters as carboxyl components afforded the
L-L-peptides in a highly diastereoselective manner.
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The Prefoldin of the Crenarchaeon Sulfolobus solfataricus
A. D’Amaro, A. Valenti, A. Napoli, M. Rossi and
M. Ciaramella
Prefoldin is a hetero-hexameric ATP-independent chaperone,
shared by eukaryotes and archaea, which binds non-native proteins
preventing them from aggregation. We report the identification
and characterization in vivo and in vitro
of the first prefoldin from a crenarchaeon, the hyperthermophile
Sulfolobus solfataricus. A functional complex was
obtained either co-expressing the α-
and β-prefoldin
subunits in Escherichia coli, or incubating at high
temperature the separately expressed subunits. In S. solfataricus,
prefoldin expression and apparent molecular weight were not
affected by either heat or cold shock.
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[Purchase Article]
Identification of Site(s) of Insulin Nitration by Peroxynitrite
and Characterization of Its Structural Change
Y. Wang, Y. Luo, R. Zhong, D. Gao and S. Cui
Insulin nitration mediated by peroxynitrite (ONOO-)
has been implicated in diabetes and diabetic cardiovascular
complications. In this study, we identified the nitration
sites of porcine insulin by infusion of ONOO-
and quantified its secondary structural change. Insulin was
cleaved with V8 protease to six peptides (four of them contained
each tyrosine residue), then analyzed by HPLC-MS and further
confirmed the nitration sites by HPLC-MS/MS. At low accumulated
doses of peroxynitrite, the main products were two different
mono-nitrated insulin species at Tyr-A19 and Tyr-B26 with
Tyr-A19 being predominant as shown by peptide mapping. Also,
the content of α-helix
structure of insulin reduced to 22.9 % and random-coil structure
increased to 30.2 % (compare with native insulin of 41.7 %
and 13.7 %, respectively) as de-termined by FTIR spectra.
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Article]
Synthesis of Acyl Carrier Protein Using a New Heterocyclic
Carboxyl Activating Group, 3-Mercapto-5,6–Diphenyl-1,2,4–Triazine
Through SPPS Strategy
M.P. Rajan and E. Purushothaman
A new, effective and easily accessible carboxyl activating
group , 3-mercapto-5, 6 - diphenyl-1, 2, 4 - triazine was
developed and the effectiveness was investigated using acyl
derivatives, chemically by the preparation of respective amides,
in addition to monitoring spectrophotometrically exploiting
the UV- visible spectra. The carboxyl activating nature of
the above mercapto heterocycle was further confirmed by solid
phase peptide synthesis. Here CLPSER resin as polymeric support
was applied. We synthesized Acyl Carrier Protein and smaller
peptides by replacing this thiol for other conventional carboxyl
activating reagents. These peptides synthesized were purified
by HPLC and characterized by molecular weight method.
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Article]
Co-Expression of GroEL/ES Enhances the Expression of Plant
Catalase in Bacterial Cytosol
P. Mondal, M. Ray, S. Sahu and S.C. Sabat
Expression of plant proteins in E. coli is frequently
unsuccessful, but soluble and functional rice catalase-B can
be produced in E. coli when it is co-expressed with
the chaperone GroEL/ES. The rice catalase exhibited properties
typical for a catalase including the decomposition of H2
O2 and inhibition by aminotriazole,
a specific inhibitor for plant and animal catalases. This
achievement records for first time the successful expression
of a both native and variant rice plant catalase in bacterial
cytosol suggesting that it may be an option to be considered
for the expression of other plant proteins in E. coli.
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Article]
Concerted Action of Metals and Macromolecular Crowding on
the Fibrillation of α-Synuclein
L.A. Munishkina, A.L. Fink and V.N. Uversky
Certain metals lead to increased risk of Parkinson’s
disease (PD) and the aggregation of α-synuclein
is implicated in the PD pathology. Although α-synuclein
fibrillation has been extensively studied in dilute solutions
in vitro, the intracellular environment is highly
crowded. We are showing here that certain metals cause a significant
acceleration of α-synuclein
fibrillation in the presence of high concentrations of various
macromolecules mostly through decreasing the fibrillation
lagtime. The faster fibrillation in crowded environments in
the presence of heavy metals suggests a simple molecular basis
for the observed elevated risk of PD due to exposure to metals.
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Article]
Antimicrobial Peptide Preferential Binding of E. coli
O157:H7
J.W. Soares, R. Kirby, K.M. Morin and C.M. Mello
The studies presented here explore antimicrobial peptide
preferential binding behavior for a target pathogen, Escherichia
coli O157:H7. A modified immunoassay and surface plasmon
resonance were employed to evaluate immobilized peptide binding
of whole bacterial cells. The knowledge gained may guide the
rational design of peptides with enhanced species binding
selectivity.
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Article]
Synthesis and Characterization of Complex of Glycyl-L-Glutamine
and Bismuth Trichloride
S. Luan, Y. Zhu and Y. Jia
A novel peptide complex was synthesized by a solid-solid reaction
of glycyl-L-glutamine monohydrate and bismuth trichloride
powders. The formula of the complex is (BiCl3)2[NH2CH2CONHCH(COOH)CH2CH2COOH·H2O]3.
The crystal structure of the complex belongs to monoclinic
system with the lattice parameters: a = 0.6914 nm, b = 0.7378
nm, c = 1.0005 nm, β
= 194.1o. The characterization
results of IR, Raman spectra and thermal analysis show that
complex is dimer and unidentate coordination. Each bismuth
atom and three chlorine atoms are coplanar in the complex.
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Article]
Enzymatic Profiling of Tetanus and Botulinum Neurotoxins Based
on Vesicle-Associated-Membrane Protein Derived Fluorogenic
Substrates
E.A. Perpetuo, L. Juliano, M.A. Juliano, F. Fratelli,
S.M.A. Prado, D.C. Pimenta and I. Lebrun
Botulinum (BoNT) and tetanus (TeNT) neurotoxins are bacterial
zinc metalloproteases that cleave and inactivate cellular
proteins essential for neurotransmitter release. There are
seven serotypes of BoNT, while TeNT is found in one serotype.
In order to characterize their enzymatic activities and to
propose serotype-differentiation an enzymatic assay based
on their metalloprotease activity was developed. The assays
were conducted with FRET peptides derived from SNAP-25, synaptobrevin
and syntaxin. The substrates were cleaved by 2 ng/mL of toxin
at different rates (Kcat
/KM from 0.028 to 75.9 μM.s-)
at a single bond, as confirmed by Q-TOF mass spectrometry.
Inhibition of the hydrolysis was obtained with EDTA or with
specific antibodies directed to each neurotoxin. Different
substrate selectivities, especially by BoNT- A and E, suggest
that these substrates can be used as a putative method for
clostridial toxin quantification and serotype differentiation
and could be easily adapted to a high-throughput protocols.
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Function Prediction of Hypothetical Proteins Without Sequence
Similarity to Proteins of Known Function
S. Kannan, A.M. Hauth and G. Burger
Function prediction by sequence-similarity based methods
identifies only ~50% of the proteins deduced from newly sequenced
genomes. We have developed an approach to annotate the ‘leftover
proteins’ i.e., those which cannot be assigned function
using sequence similarity. Our method (MOPS) is pan-taxonomic,
predicting fine-grained molecular function (rather than a
broad functional category) with high performance. In addition,
we developed a validation scheme that assesses predictions
using domain-specific knowledge.
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Structure-Function Study of a Plasmodium falciparum
Hsp70 Using Three-Dimensional Modelling and in Vitro
Analyses
A. Shonhai, M. Botha, T.A.P. de Beer, A. Boshoff and
G.L. Blatch
The spatial orientation of domains of the heat shock
protein 70 from Plasmodium falciparum (PfHsp70) were
mapped based on a three-dimensional model of the protein.
Purified PfHsp70 displayed chaperone activity in vitro.
Amino acid substitutions introduced in the chaperone’s
substrate binding cavity compromised the protein’s chaperone
function.
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Analysis of Nickel-Binding Peptides in a Human Hepidermoid
Cancer Cell Line by Ni-NTA Affinity Chromatography and Mass
Spectrometry
A. Lamberti, C. Sanges, O. Longo, A. Chambery, A. Di Maro,
A. Parente, M. Masullo and P. Arcari
To elucidate whether eukaryotic elongation factor 1A
(eEF-1A) in a human hepidermoid cancer cell line (H1355) belonged
to the family of the Ni-interacting protein, we analyzed the
sequence of peptides obtained by on-Ni-NTA-agarose tryptic
digestion of proteins from H1355 cell extract. LC/MS analysis
showed the presence of several peptides mainly from abundant
cellular proteins corresponding to eEF-1A, tubulin and actin.
The results indicated that F-actin strongly binds to Ni-NTA-agarose
whereas the other proteins are indirectly bound to the resin
because of the formation of a protein-protein complex with
actin.
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Predicting Lipase Types by Improved Chou’s Pseudo-Amino
Acid Composition
G.-Y. Zhang, H.-C. Li, J.-Q. Gao and B.-S. Fang
By proposing a improved Chou’s pseudo amino acid
composition approach to extract the features of the sequences,
a powerful predictor based on k-nearest neighbor
was introduced to identify the types of lipases according
to their sequences. To avoid redundancy and bias, demonstrations
were performed on a dataset where none of the proteins has
≥25%
sequence identity to any other. The overall success rate thus
obtained by the 10-fold cross-validation test was over 90%,
indicating that the improved Chou’s pseudo amino acid
composition might be a useful tool for extracting the features
of protein sequences, or at lease can play a complementary
role to many of the other existing approaches.
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Cloning, Expression, Purification, Crystallization
and Preliminary X-Ray Crystallographic Analysis of C-12 Hydroxylase
EryK from Saccharopolyspora erythraea
C. Savino, G. Sciara, A.E. Miele, S.G. Kendrew and
B. Vallone
Erythromycin A is produced by Saccharopolyspora erythraea
via a secondary metabolic pathway using several steps
including glycosylations and hydroxylations of the first macrolide
intermediate 6-deoxyerythronolide B. Erythromycin C-12 hydroxylase
(CYP113A1), the P450 cytochrome active in the final stages
of erythromycin biosynthesis, was cloned and expressed in
E. coli. Different crystal forms were harvested from
distinct crystallization conditions: two ligand-free forms,
one substrate bound and two inhibitors-bound. All crystals
belong either to the monoclinc P21
or to the ortho-rhombic P21
21 21
space groups, and exhibit diffraction limits ranging from
2.3 to 1.6 Å. The structures will be determined by molecular
replacement.
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Crystallization and Preliminary Crystallographic Analysis
of Laminarinase from Rhodothermus marinus: A Case
of Pseudomerohedral Twinning
A.M. Golubev, A.L. Rojas, A.S. Nascimento, L. Bleicher,
A.A. Kulminskaya, E.V. Eneyskaya and I. Polikarpov
Thermophilic endo-1,3(4) β-glucanase
(laminarinase) from Rhodothermus marinus was crystallized
by the hanging-drop vapor diffusion method. The needle-like
crystals belong to space group P21
and contain two protein molecules in the asymmetric unit with
a solvent content of 51.75 %. Diffraction data were collected
to a resolution of 1.95Å and resulted in a dataset with
an overall Rmerg
of 10.4% and a completeness of 97.8%. Analysis of the structure
factors revealed pseudomerohedral twinning of the crystals
with a twin fraction of approximately 42%.
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