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Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 16, Number 11, 2009
Contents
Regular Papers
Structural and IR-Spectroscopic Elucidation of Dipeptide L-Threonyl-L-Methionine
in Solid State Pp. 1277-1280
A.G. Chapkanov and S.Y. Zareva
[Abstract] [Purchase
Article] [PMID:
20001919 PubMed - indexed for MEDLINE]
Confocal Microscopy Evidence of Prion Protein
Fragment hPrP[173-195] Internalization in Rat B104 Neuroblastoma
Cell Line Pp. 1281-1290
E. Urso, R. Acierno, M.G. Lionetto, A. Rizzello,
A. Papa, T. Schettino and M. Maffia
[Abstract] [Purchase
Article] [PMID:
20001920 PubMed - indexed for MEDLINE]
Neuronal Differentiation of Neural Progenitor Cells
by Intracellular Delivery of Synthetic Oligopeptide Derived
from Von Hippel-Lindau Protein Pp. 1291-1296
H. Kanno, S. Nakano, A. Kubo, T. Mimura, N. Tajima
and N. Sugimoto
[Abstract] [Purchase
Article] [PMID:
20001921 PubMed - indexed for MEDLINE]
Non-Globular Structures of Tandem Repeats
in Proteins Pp. 1297-1322
N. Matsushima, T. Tanaka and R.H. Kretsinger
[Abstract] [Purchase
Article] [PMID:
20001922 PubMed - indexed for MEDLINE]
Biochemical and PMF MALDI-TOF Analyses
of Two Novel Papain-Like Plant Proteinases Pp. 1323-1333
W.D. Obregón, C.S. Liggieri, S.R. Morcelle, S.A.
Trejo, F.X. Avilés and N.S. Priolo
[Abstract] [Purchase
Article] [PMID:
20001923 PubMed - indexed for MEDLINE]
Antibodies Against Refolded Recombinant Envelope
Protein (Domain III) of Japanese Encephalitis Virus Inhibit
the JEV Infection to Porcine Stable Kidney Cells
Pp. 1334-1341
S.K. Verma, N. Gupta, P. Pattnaik, J.P. Babu, P.V.L. Rao
and S. Kumar
[Abstract] [Purchase
Article] [PMID:
20001924 PubMed - indexed for MEDLINE]
Quantitative Prediction of Critical
Amino Acid Positions for Protein Folding Pp. 1342-1349
T. Thireou, V. Atlamazoglou, N.A. Papandreou, M. Lonquety,
J. Chomilier and E. Eliopoulos
[Abstract] [Purchase
Article] [PMID:
19508208 PubMed - indexed for MEDLINE]
Proteomic Analysis of Mitochondria in Raji Cells
Following Exposure to Radiation: Implications for Radiotherapy
Response Pp. 1350-1359
Y. Jiang, X. Liu, X. Fang and X. Wang
[Abstract] [Purchase
Article] [PMID:
20001925 PubMed - indexed for MEDLINE]
Deciphering the Flexibility and Dynamics of Geobacillus
zalihae Strain T1 Lipase at High Temperatures by Molecular
Dynamics Simulation Pp. 1360-1370
M.B.A. Rahman, R.A. Karjiban, A.B. Salleh, D.
Jacobs, M. Basri, A.L.T. Chor, H.A. Wahab and R.N.Z.R.A.
Rahman
[Abstract] [Purchase
Article] [Supplementary
Material] [PMID:
20001926 PubMed - indexed for MEDLINE]
Novel Antimicrobial Peptides Isolated from Skin
Secretions of the Mexican Frog Hyla eximia Pp.
1371-1378
O. Villa-Hernández, L. Hernández-Orihuela,
M.d.C. Rodríguez, F. Zamudio-Zuñiga, R. Castro-Franco,
V. Pando and C.V.F. Batista
[Abstract] [Purchase
Article]
Surface Plasmon Resonance Imaging Sensor
for Cathepsin Determination Based on Immobilized Cystatin
Pp. 1379-1385
E. Gorodkiewicz
[Abstract] [Purchase
Article] [PMID:
20001927 PubMed - indexed for MEDLINE]
Exploring the Structural Stability of a Potential
Antifungal Peptide Through Computational Analysis
Pp. 1386-1392
R. Rajasekaran and R. Sethumadhavan
[Abstract] [Purchase
Article]
Gibbs Sampling Shows Possibilities of B-Cell
Epitope Signatures Pp. 1393-1398
R.R. Joshi, U. Hira and D. Suri
[Abstract] [Purchase
Article]
Studies on an Antifungal Protein and a Chromatographically
and Structurally Related Protein Isolated from the Culture
Broth of Bacillus amyloliquefaciens Pp.
1399-1406
J.H. Wong and T.B. Ng
[Abstract] [Purchase
Article]
The In Situ Structural Characterization
of the Influenza A Virus Matrix M1 Protein within a Virion
Pp. 1407-1413
A.V. Shishkov, E.N. Bogacheva, A.A. Dolgov, A.L. Chulichkov,
D.G. Knyazev, N.V. Fedorova, A.L. Ksenofontov, L.V. Kordyukova,
E.V. Lukashina, V.M. Mirsky and L.A. Baratova
[Abstract] [Purchase
Article]
Interaction of the Chaperone Calreticulin with
Proteins and Peptides of Different Structural Classes
Pp. 1414-1423
K. Duus, N. Sandhu, C.S. Jørgensen, P.R. Hansen,
A. Steinø, M. Thaysen-Andersen, P. Højrup
and G. Houen
[Abstract] [Purchase
Article]
Abstracts
[Back to top]
[Purchase Article] [PMID:
20001919 PubMed - indexed for MEDLINE]
Structural and IR-Spectroscopic Elucidation
of Dipeptide L-Threonyl-L-Methionine
in Solid State
A.G. Chapkanov and S.Y. Zareva
Dipeptide L-threonyl-L-methionine
(Thr-Met) is characterized structurally by means
of a solid-state linear polarized IR- spectroscopy (IR-LD)
of oriented samples as a colloidal suspension in nematic liquid
crystal and quantum chemical ab initio calculations.
Vibrational analysis supports the experimental data as well.
The role of intermolecular hydrogen bonding on conformational
behavior and spectroscopic properties of the compound, studied
in solid state is determined.
[Back to top]
[Purchase Article] [PMID:
20001920 PubMed - indexed for MEDLINE]
Confocal Microscopy Evidence of Prion Protein
Fragment hPrP[173-195] Internalization in Rat B104 Neuroblastoma
Cell Line
E. Urso, R. Acierno, M.G. Lionetto, A. Rizzello,
A. Papa, T. Schettino and M. Maffia
The cytotoxicity of hPrP[173-195] prion peptide against
a neuroblastoma cell model was found independent of its tendency
to aggregate over time. Cytosolic and nuclear inclusions of
peptide were highlighted by confocal microscopy, suggesting
a role as a transcription factor in activating signal transduction
pathways involved in cell toxicity.
[Back to top]
[Purchase
Article] [PMID:
20001921 PubMed - indexed for MEDLINE]
Neuronal Differentiation of Neural Progenitor Cells
by Intracellular Delivery of Synthetic Oligopeptide Derived
from Von Hippel-Lindau Protein
H. Kanno, S. Nakano, A. Kubo, T. Mimura, N. Tajima
and N. Sugimoto
Intracellular delivery of synthetic oligopeptides has
the potential to promote the occurrence of various cellular
events such as cell death, proliferation, growth inhibition,
metabolic changes, and morphological changes. However, the
regulation of cellular differentiation by intracellular delivery
of synthetic oligopeptides has been little studied. Von Hippel-Lindau
protein (pVHL) is one of the proteins that functions to induce
the differentiation of neural progenitor cells (NPCs). To
function in these cells, pVHL forms a complex composed of
itself, elongin BC, Clu-2, and Rbx-1. It is suggested that
the binding site of elongin BC in pVHL plays a critical role
in pVHL function, i.e., ubiquitination, which is related to
neuronal differentiation. So, we synthesized an oligopeptide
corresponding to the elongin BC binding site, and delivered
the oligopeptide into NPCs by using a mixture of trifluoroacetylated
lipopolyamine and diloeoyl phosphatidylethanolamine (BioPorter)
to form a peptide-lipid complex. After intracellular delivery
of the oligopeptide, induction of differentiation of NPCs
was shown in terms of neurite outgrowth and by immunocytochemical
and electrophysiological means. The intracellular delivery
of the synthetic oligopeptide derived from pVHL may provide
a safe and valuable approach for the neu-ronal differentiation
of NPCs.
[Back to top]
[Purchase
Article] [PMID:
20001922 PubMed - indexed for MEDLINE]
Non-Globular Structures of Tandem Repeats
in Proteins
N. Matsushima, T. Tanaka and R.H. Kretsinger
There are two classes of tandem repeats in proteins -
globular and non-globular. There are two subclasses of non-globular
repeats. The first, such as collagen, form stable helices.
Members of the second are flexible and somewhat disordered
both in vitro and in vivo. This review focuses
on this second subclass.
[Back to top]
[Purchase Article] [PMID:
20001923 PubMed - indexed for MEDLINE]
Biochemical and PMF MALDI-TOF Analyses
of Two Novel Papain-Like Plant Proteinases
W.D. Obregón, C.S. Liggieri, S.R. Morcelle, S.A.
Trejo, F.X. Avilés and N.S. Priolo
Two cysteine endopeptidases from latex of Araujia
angustifolia (araujiain aI and araujiain aIII) were purified
and characterized by means of conventional and proteomics
techniques (MALDI-TOF). N?terminal sequences showed a high
percentage of identity with cysteine proteinases belonging
to the papain family. The peptide mass fingerprint analysis
demonstrated a close homology among both proteinases.
[Back to top]
[Purchase Article] [PMID:
20001924 PubMed - indexed for MEDLINE]
Antibodies Against Refolded Recombinant Envelope
Protein (Domain III) of Japanese Encephalitis Virus Inhibit
the JEV Infection to Porcine Stable Kidney Cells
S.K. Verma, N. Gupta, P. Pattnaik, J.P. Babu, P.V.L. Rao
and S. Kumar
Japanese encephalitis virus (JEV) is a mosquito-borne
viral zoonosis of public health importance. Global efforts
have been made towards development of vaccine for prevention
of Japanese encephalitis. The envelope protein of JEV is associated
with viral binding to cellular receptors, membrane fusion,
and the induction of protective neutralizing antibody response
in hosts. Here we report that the antibodies raised against
refolded domain III of envelope protein of JEV neutralize
the JE virus and inhibit the JEV infection to Porcine Stable
Kidney (PS) cells. A reverse transcriptase-PCR amplified gene
encoding domain III of JEV envelope protein was cloned into
pET28a+ vector and over expressed in E. coli. The
recombinant JEV-DIII protein was purified by affinity chromatography
under denaturing conditions. The rJEV-DIII was refolded by
oxido-redux shuffle and purified to homogeneity by ion-exchange
chromatography. Refolded rJEV-DIII was characterized using
biochemical and biophysical methods. The polyclonal antibodies
were raised against in vitro refolded rJEV-DIII protein
in BALB/c mice with Freunds adjuvant. Ninety percent JEV is
neutralized when the serum against refolded rJEV-DIII is used
at a dilution of 1:80 as against 60.5% neutralization capacity
with the same dilution of serum raised against denatured rJEV-DIII.
The method of expression and purification of biologically
functional rJEV-DIII protein described in this study may help
in better understanding the biology of JE virus and the development
of better vaccine candidate. Since the expression system uses
E. coli as the heterologous host, the process is
easy and amenable to in-expensive scale-up.
[Back to top]
[Purchase Article] [PMID:
19508208 PubMed - indexed for MEDLINE]
Quantitative Prediction of Critical
Amino Acid Positions for Protein Folding
T. Thireou, V. Atlamazoglou, N.A. Papandreou, M. Lonquety,
J. Chomilier and E. Eliopoulos
The MIR algorithm provides an ab initio prediction
of a protein's core residues. An improved version, the MIR2,
is presented and validated on 3203 proteins from PDB. Structures
are decomposed in Closed Loops, their limits constituting
the observed core residues. They are predicted by MIR2 with
an accuracy approaching 80%.
[Back to top]
[Purchase
Article] [PMID:
20001925 PubMed - indexed for MEDLINE]
Proteomic Analysis of Mitochondria in Raji Cells
Following Exposure to Radiation: Implications for Radiotherapy
Response
Y. Jiang, X. Liu, X. Fang and X. Wang
Radioresistance represents a major obstacle to a successful
outcome for the treatment of non-Hodgkin’s lymphoma
(NHL). Here we performed a global differential proteome analysis
of the mitochondria in Raji cells exposed to radiation. The
results showed that 23 differentially expressed proteins were
identified. Furthermore, GAPDH, RECQL4, MKI67, and ATAD3B
could serve as potential biomarkers of radioresistance.
[Back to top]
[Purchase Article] [PMID:
20001926 PubMed - indexed for MEDLINE]
Deciphering the Flexibility and Dynamics of Geobacillus
zalihae Strain T1 Lipase at High Temperatures by Molecular
Dynamics Simulation
M.B.A. Rahman, R.A. Karjiban, A.B. Salleh, D.
Jacobs, M. Basri, A.L.T. Chor, H.A. Wahab and R.N.Z.R.A.
Rahman
[Supplementary
Material]
The stability of biocatalysts is an important criterion
for a sustainable industrial operation economically. T1 lipase
is a thermoalkalophilic enzyme derived from Geobacillus
zalihae strain T1 (T1 lipase) that was isolated from
palm oil mill effluent (POME) in Malaysia. We report here
the results of high temperatures molecular dynamics (MD) simulations
of T1 lipase in explicit solvent. We found that the N-terminal
moiety of this enzyme was accompanied by a large flexibility
and dynamics during temperature-induced unfolding simulations
which preceded and followed by clear structural changes in
two specific regions; the small domain (consisting of helices
α3
and α5,
strands β1
and β2,
and connecting loops) and the main catalytic domain or core
domain (consisting of helices α6-
α9
and connecting loops which located above the active site)
of the enzyme. The results suggest that the small domain of
model enzyme is a critical region to the thermostability of
this organism.
[Back to top]
[Purchase
Article]
Novel Antimicrobial Peptides Isolated from Skin
Secretions of the Mexican Frog Hyla eximia
O. Villa-Hernández, L. Hernández-Orihuela,
M.d.C. Rodríguez, F. Zamudio-Zuñiga, R. Castro-Franco,
V. Pando and C.V.F. Batista
In this work, we describe the original characterization
of peptides and proteins present in the skin secretions of
the Mexican amphibian Hyla eximia. To this purpose,
a novel water/dark extraction method, as well as the classic
electrical stimulation procedure, was applied in order to
extract the skin secretion. Two novel antimicrobial peptides
He-1 and He-2 were sequenced. In addition, a molecular mass
fingerprint revealed more than one hundred different molecules.
Eight peptides in homogeneous form were assayed against five
species of bacteria. Thereafter, the peptide He-2 demonstrated
high antiparasitic activity against ookinete forms of malaria
parasites at low concentration.
[Back to top]
[Purchase
Article] [PMID:
20001927 PubMed - indexed for MEDLINE]
Surface Plasmon Resonance Imaging Sensor
for Cathepsin Determination Based on Immobilized Cystatin
E. Gorodkiewicz
A specific SPRI sensor for cathepsin determination based
on the interaction between immobilized cystatin and cathepsins
has been developed. All cathepsins form the same calibration
curve. The sensor dynamic response range is between 0.5 and
2.0 ng ml-1 and the detection
limit is equal to 0.1 ng ml-1.
[Back to top]
[Purchase Article]
Exploring the Structural Stability of a Potential
Antifungal Peptide Through Computational Analysis
R. Rajasekaran and R. Sethumadhavan
We analyzed 27 antifungal peptides (AFPs) to understand
their stability by various parameters like, stabilization
centers, GROMOS, OPLS and FOLDEF force fields. Subsequently,
we propose that AFP, NK-Lysin could be considered a potential
candidate and also could act as a template for designing the
therapeutic peptide drug against pathogenic fungi.
[Back to top]
[Purchase Article]
Gibbs Sampling Shows Possibilities of B-Cell
Epitope Signatures
R.R. Joshi, U. Hira and D. Suri
We have attempted finding common sequential patterns
among protein antigens. For this, we have used Gibbs multiple
motif sampler on the set of all non-redundant antigenic sequences
available in curated databanks. Several sequential motifs
are obtained on these sequences when the amino acids are represented
according to their similarity clusters. Significantly high
proportions of known B-cell epitope sites are found
within or adjacent to these motifs, thus indicating
a possibility of linear epitope signatures. These
findings may offer important applications in synthesis of
peptide vaccines. A predictive example in this regard is presented.
[Back to top]
[Purchase Article]
Studies on an Antifungal Protein and a Chromatographically
and Structurally Related Protein Isolated from the Culture
Broth of Bacillus amyloliquefaciens
J.H. Wong and T.B. Ng
An antifungal protein with multiple stable biological
activities unaffected by chemical modification of tyrosine
and tryptophan, and a protein with N-terminal sequence and
molecular mass resemblance to the antifungal protein but no
identifiable activities were isolated from culture broth of
Bacillus amyloliquefaciens. The findings are analogous
to previous reports on thaumatin and thaumatin-like proteins.
[Back to top]
[Purchase
Article]
The In Situ Structural Characterization
of the Influenza A Virus Matrix M1 Protein within a Virion
A.V. Shishkov, E.N. Bogacheva, A.A. Dolgov, A.L. Chulichkov,
D.G. Knyazev, N.V. Fedorova, A.L. Ksenofontov, L.V. Kordyukova,
E.V. Lukashina, V.M. Mirsky and L.A. Baratova
The first attempt has been made to suggest a model of
influenza A virus matrix M1 protein spatial structure and
molecule orientation within a virion on the basis of tritium
planigraphy data and theoretical prediction results. Limited
in situ proteolysis of the intact virions with bromelain
and surface plasmon resonance spectroscopy study of the M1
protein interaction with lipid coated surfaces were used for
independent confirmation of the proposed model.
[Back to top]
[Purchase Article]
Interaction of the Chaperone Calreticulin with
Proteins and Peptides of Different Structural Classes
K. Duus, N. Sandhu, C.S. Jørgensen, P.R. Hansen,
A. Steinø, M. Thaysen-Andersen, P. Højrup
and G. Houen
The interaction of calreticulin with native and denatured
forms and polypeptides in proteolytic digests of proteins
representing structural classes of all-α-helix
(hemoglobin, serum albumin), all-β-sheet
(IgG) and α-helix
+ β-sheets
(lysozyme, ovalbumin) was investigated. The binding of calreticulin
to denatured proteins was found to depend on con-formation
and structural class of the protein. No interaction was observed
with the native proteins, whereas binding was seen for the
denatured proteins, the order of interaction being lysozyme
= IgG >
ovalbumin >>
hemoglobin = serum al-bumin. Moreover, the interaction between
calreticulin and the heat-denatured proteins depended on the
temperature and time used for denaturation and the degree
of proteolytic fragmentation. Calreticulin bound well to peptides
in proteolytic digests from protease K or chymotrypsin treatment
of lysozyme, IgG and ovalbumin but weakly or not at all to
peptides in proteolytic digests of hemoglobin and serum albumin.
Synthetic peptides from lysozyme and ovalbumin confirmed binding
to hydrophobic peptides from these proteins. These results
show that calreticulin has the ability to interact with denatured
and fragmented forms of proteins with a preference for β-strand
structure and hydrophobicity.
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