|
Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 16, Number 7, 2009
Contents
Developments in Membrane Fusion
Guest Editor: Stefania Galdiero
Editorial Pp.711
[PMID:
19601898 PubMed - indexed for MEDLINE]
Membrane Fusion: Role of SNAREs and Calcium Pp.
712-717
B.P. Jena
[Abstract] [Purchase
Article] [PMID:
19601899 PubMed - indexed for MEDLINE]
The “Tilted Peptide Theory”
Links Membrane Insertion Properties and Fusogenicity of Viral
Fusion Peptides Pp. 718-725
B. Charloteaux, A. Lorin, R. Brasseur and
L. Lins
[Abstract] [Purchase
Article] [PMID:
19601900 PubMed - indexed for MEDLINE]
Characterization of Peptide-Induced Morphological
Alterations in Membranes by Fluorescence Resonance Energy
Transfer Pp. 726-735
L.M.S. Loura and M. Prieto
[Abstract] [Purchase
Article] [PMID:
19601901 PubMed - indexed for MEDLINE]
Membrane Permeabilization by Multivalent
Anti-Microbial Peptides Pp. 736-742
R.J. Pieters, C.J. Arnusch and
E. Breukink
[Abstract] [Purchase
Article] [PMID:
19601902 PubMed - indexed for MEDLINE]
Antimicrobial Peptides and Viral Fusion
Peptides : How Different They Are? Pp. 743-750
P. Joanne, P. Nicolas and C. El
Amri
[Abstract] [Purchase
Article] [PMID:
19601903 PubMed - indexed for MEDLINE]
Membrane Fusion and Fission: Enveloped
Viruses Pp. 751-759
A. Falanga, M. Cantisani, C. Pedone and
S. Galdiero
[Abstract] [Purchase
Article] [PMID:
19601904 PubMed - indexed for MEDLINE]
The Role of Glycoprotein H in Herpesvirus
Membrane Fusion Pp. 760-764
H.M. Browne
[Abstract] [Purchase
Article] [PMID:
19601905 PubMed - indexed for MEDLINE]
Composition and Functions of the Influenza
Fusion Peptide Pp. 765-778
K.J. Cross, W.A. Langley, R.J. Russell,
J.J. Skehel and D.A. Steinhauer
[Abstract] [Full
Text Article] [PMID:
19601906 PubMed - indexed for MEDLINE]
Viral Inactivation Based on Inhibition
of Membrane Fusion: Understanding the Role of Histidine Protonation
to Develop New Viral Vaccines Pp. 779-785
A.T. Da Poian, F.A. Carneiro and
F. Stauffer
[Abstract] [Purchase
Article] [PMID:
19601907 PubMed - indexed for MEDLINE]
Inhibition of Viral-Induced Membrane
Fusion by Peptides Pp. 786-793
M. Vitiello, M. Galdiero and M.
Galdiero
[Abstract] [Purchase
Article] [PMID:
19601908 PubMed - indexed for MEDLINE]
General Articles
Regular Papers
Describing Evolution of Hemagglutinins from
Influenza A Viruses Using a Differential Equation Pp.
794-804
S. Yan and G. Wu
[Abstract] [Purchase
Article] [PMID:
19601909 PubMed - indexed for MEDLINE]
The Use of Tripeptides for Lead Discovery
of 5-HT4 Receptor Ligands
Pp. 805-809
A. Hanna-Elias, P.E. Thompson, D.T. Manallack,
H.R. Irving, I.M. Coupar, I. Berque-Bestel and M.N.
Iskander
[Abstract] [Purchase
Article] [PMID:
19601910 PubMed - indexed for MEDLINE]
Efficient Manual Fmoc Solid-Phase Synthesis
of the N Terminal Segment of Surfactant Protein B (SP-B1-25)
Pp. 810-814
S. Ramli, I.R. Gentle and B.P.
Ross
[Abstract] [Purchase
Article] [PMID:
19601911 PubMed - indexed for MEDLINE]
Conservation of Hydrophobicity within
Viral Envelope Glycoproteins Reveals a Putative Hepatitis
C Virus Fusion Peptide Pp. 815-822
A. Taylor, J.M. O’Leary, S. Pollock
and N. Zitzmann
[Abstract] [Purchase
Article] [PMID:
19601912 PubMed - indexed for MEDLINE]
Improving the Classification of Nuclear
Receptors with Feature Selection Pp. 823-829
Q.-B. Gao, Z.-C. Jin, X.-F. Ye, C. Wu, J.
Lu and J. He
[Abstract] [Purchase
Article] [PMID:
19601913 PubMed - indexed for MEDLINE]
Plasma Ghrelin Levels in Patients with
Familial Mediterranean Fever Pp. 830-833
G. Keskin, A. Inal, R. Ilikçi and
O. Baysal
[Abstract] [Purchase
Article] [PMID:
19601914 PubMed - indexed for MEDLINE]
Investigation of Folding of Purified
Recombinant GRA1 Protein Using Web Based Protein Disorder
Servers and Trypsin Digestion Pp. 834-841
M. Döskaya, A. Caner, A. Degirmenci,
F. Jurnak and Y. Gürüz
[Abstract] [Purchase
Article] [PMID:
19601915 PubMed - indexed for MEDLINE]
Polytope DNA Vaccine Development Against
Hepatitis C Virus: A Streamlined Approach from In Silico
Design to In Vitro and Primary In Vivo
Analyses in BALB/c Mice Pp. 842-850
A. Memarnejadian, F. Roohvand, A. Arashkia,
S. Rafati and M.A. Shokrgozar
[Abstract] [Purchase
Article] [PMID:
19601916 PubMed - indexed for MEDLINE]
Abstracts
[Back to top]
[PMID:
19601898 PubMed - indexed for MEDLINE]
Editorial:
I am very pleased to offer to the readers of Protein
and Peptide Letters this special issue entitled “Developments
in membrane fusion” highlighting the latest findings
in the field. The aim of this issue is not to provide an exhaustive
collection of data on membrane fusion but rather to present
an updated, hopefully general, overview on this process and
provide ideas and information that could contribute to the
reader’s own research.
Membrane fusion has attracted great interest among scientists
in recent years. This process is fundamental to health and
disease: it occurs at fertilization, is needed for hormones
release into the bloodstream and during development, but it
is also the mechanism used by enveloped viruses to enter cells
or carcinogenesis. In the last few years, great strides have
been made in our understanding of the molecular machinery
and mechanism of membrane fusion. Fusion machines are adapted
to fit the needs of different reactions but operate by similar
principles in order to achieve merging of the bilayers. In
spite of the ubiquity of membrane fusion, scientists are still
trying to solve the mystery of how different molecules drive
vesicles fusion. Understanding the details of membrane fusion
may help scientists to find the appropriate conditions for
preventing viruses from fusing to and thereby infecting human
cells and could also lead to the design of systems in which
a drug, enclosed in a membrane known to fuse with specific
cells in our body, may be delivered or to improve gene therapy.
A number of research groups in the world are focused on cellular
and biophysical aspects of fusion and are directed at understanding
the protein components and/or membrane interactions that are
necessary to facilitate and trigger fusion. These groups are
making leading contributions to understanding the membrane
perturbations and protein interactions that promote fusion
as well as the cellular machinery that directs fusion. This
special issue includes several papers describing the know-how
on membrane fusion.
In the opening review by Jena the molecular mechanism of membrane
fusion is considered in terms of the role of the calcium ion
in the formation of conducting channel by SNARE proteins.
The characteristics of viral fusion peptides and their relation
to membranes are addressed in the following two reviews. Charloteaux
et al. describe the fusogenic properties of peptides
derived from glycoproteins of enveloped viruses and their
ability to insert obliquely in membranes. Loura and Prieto
present an overview of Resonance Energy Transfer (FRET) methods
for the understanding of interaction of fusogenic or membrane-perturbing
peptides with lipid bilayers.
The important issue of antimicrobial peptides and the permeabilization
of membranes has been taken up by Pieters et al.
and Joanne et al. In particular, the first review
is related to the activity of these peptides against resistant
pathogens, while Joanne et al. present an overview
on the molecular mechanisms of antimicrobial peptides (AMPs)
and of viral fusion peptides (FPs) that trigger membrane fusion
and focuses on the structural properties that are mainly responsible
for their different mode of interaction with membranes.
The next five reviews present specific topics concerning enveloped
viruses. Falanga et al. describe similarities in
fusion and fission mechanisms; Browne describes the herpes
virus glycoprotein gH which is involved in the fusion process;
Cross et al. provide a detailed overview on the structure
and sequence features of the fusion peptide of Influenza virus;
Da Poian et al. review several studies on the structural
rearrangements of vesicular stomatitis virus glycoprotein
G during cellular recognition and the crucial role played
by the protonation of His residues; Vitiello et al.
describe recent advances in the understanding of viral-mediated
fusion mechanisms concentrating on the development of peptidic
inhibitors of membrane fusion.
All papers were subjected to two rounds of review with a minimum
of two reviewers. We hope that the audience will find this
special issue both useful and enjoyable.
As guest editor, I would like to take this opportunity to
thank all the authors for their contributions to this special
issue, the reviewers for their valuable input, insight, and
expert comments, and the Editor-in-Chief, Distinguished Professor
Ben M. Dunn, for giving me the chance to compose this special
issue.
Stefania Galdiero
Guest Editor
Protein &
Peptide Letters
Department of Biological Science – Division of Biostructures
University of Naples “Federico II”
Via Mezzocannone 16, 80134, Napoli
Italy
Tel: +39-081-2534503
Fax: +39-081-2534560
E-mail: sgaldier@unina.it
[Back to top]
[Purchase Article] [PMID:
19601899 PubMed - indexed for MEDLINE]
Membrane Fusion: Role of SNAREs and Calcium
B.P. Jena
Life processes are governed at the chemical level, and
therefore knowledge of how single molecules interact, provides
a fundamental understanding of nature. The molecular mechanism
of membrane fusion essential to vital cellular activities
such as intracellular transport, hormone secretion, enzyme
release, or neurotransmission, involve the assembly and disassembly
of a specialized set of proteins present in opposing bilayers.
Target membrane proteins at the cell plasma membrane SNAP-25
and syntaxin termed t-SNAREs, and secretory vesicle-associated
protein VAMP or v-SNARE, are part of the conserved protein
complex involved in fusion of opposing membranes. It has been
demonstrated that in the presence of Ca2+,
t-SNAREs and v-SNARE in opposing bilayers interact and self-assemble
in a circular pattern, to form conducting channels. Such self-assembly
of t-/v-SNAREs in a ring conformation occurs only when the
respective SNAREs are in association with membrane. X-ray
diffraction measurements further demonstrate that t-SNAREs
in the target membrane and v-SNARE in the vesicle membrane
overcome repulsive forces to bring opposing membranes close
to within a distance of 2.8 Å.
Studies suggest that calcium bridging of the opposing bilayers,
lead to release of water from hydrated Ca2+ ions as well as
the loosely coordinated water at PO-lipid head groups, leading
to membrane destabilization and fusion. The t-/v-SNARE is
a tight complex, who’s disassembly requires an ATPase
called NSF, which functions as a right-handed molecular motor.
[Back to top]
[Purchase Article][PMID:
19601900 PubMed - indexed for MEDLINE]
The “Tilted Peptide Theory” Links Membrane Insertion
Properties and Fusogenicity of Viral Fusion Peptides
B. Charloteaux, A. Lorin, R. Brasseur and
L. Lins
Class I fusion glycoproteins of viruses are involved
in the fusion between viral envelope and cell membrane. A
region located in the N-terminal domain of these glycoproteins,
called the fusion peptide, is essential for fusion. Fusion
peptides are able to induce by themselves in vitro
membrane fusion. In this paper, we review the properties of
those peptides related to their fusogenicity, in particular
the correlation existing between their ability to insert obliquely
in membranes and fusogenicity. This relation notably allows
predicting successfully the minimal region of some fusion
peptides sufficient to induce significant in vitro
fusion. The notion of obliquity and fusogenicity is discussed
in terms of the existing proposed mechanisms for viral fusion.
[Back to top]
[Purchase Article] [PMID:
19601901 PubMed - indexed for MEDLINE]
Characterization of Peptide-Induced Morphological Alterations
in Membranes by Fluorescence Resonance Energy Transfer
L.M.S. Loura and M. Prieto
Interaction of fusogenic or membrane-perturbing peptides
with lipid bilayers often involves drastic rearrangements
of the membrane structure, with redistribution of lipids,
inducement of bilayer curvature, or formation of non-bilayer
or multibilayer structures. Fluorescence (or Förster)
Resonance Energy Transfer (FRET) is a photophysical technique
which has an acute sensitivity to distances in the nanometer
range, and, as such, is particularly suited to probe alterations
in membrane organization in this length scale. This article
reviews methods and selected applications of FRET in this
field, from the now classic (fusion induced) lipid-mixing
assay to examples where kinetic modeling of FRET enables the
recovery of topological information.
[Back to top]
[Purchase Article] [PMID:
19601902 PubMed - indexed for MEDLINE]
Membrane Permeabilization by Multivalent Anti-Microbial Peptides
R.J. Pieters, C.J. Arnusch and
E. Breukink
Antimicrobial peptides (AMP’s) are promising compounds
in the battle against antibiotic resistant pathogens. Many
AMP’s function by interacting with the bacterial membrane
and selectively permeabilizing it. Improvements are desired
in the potency and the in vivo stability of the AMP’s.
Both aspects have been approached by the preparation of multivalent
versions of AMP’s that contain several copies of the
peptide attached to a scaffold or core molecule. Both short
and long sequences have been used and in selected cases major
increases in antibacterial activity, membrane permeabilization
potency and in vivo stability have been obtained.
[Back to top]
[Purchase
Article] [PMID:
19601903 PubMed - indexed for MEDLINE]
Antimicrobial Peptides and Viral Fusion Peptides : How Different
They Are?
P. Joanne, P. Nicolas and C. El
Amri
Similarly to antimicrobial peptides (AMPs), viral fusion
peptides (FPs) are membrane-active peptides. This minireview
emphasizes the common properties of AMPs and FPs with a special
focus on the intrinsic flexibility and structural adaptability
of these peptides that are responsible for different mode
of interaction with the membrane bilayers. The potential use
of AMPs as multifunctional drugs with both antibacterial and
antiviral properties is discussed.
[Back to top]
[Purchase
Article] [PMID:
19601904 PubMed - indexed for MEDLINE]
Membrane Fusion and Fission: Enveloped Viruses
A. Falanga, M. Cantisani, C. Pedone and
S. Galdiero
Membrane fusion and fission are two key processes that
occur during the replication of enveloped viruses, namely
access to the interior of the host-cell (entry, which requires
fusion of the viral envelope with the target cell envelope)
and dissemination of viral progeny after replication (egress,
which involves budding and fission). These dynamic processes
are mediated by specialized proteins that modify and bend
the lipid bilayer transiently and locally. This review focuses
on fusion and fission reactions and on the hypothetical shared
mechanism that generates their driving force.
[Back to top]
[Purchase
Article] [PMID:
19601905 PubMed - indexed for MEDLINE]
The Role of Glycoprotein H in Herpesvirus Membrane Fusion
H.M. Browne
The mechanism by which herpesviruses fuse with cellular
membranes to permit virus entry is still relatively poorly
understood. This process is proving difficult to unravel,
largely due to the fact that multiple viral envelope proteins
appear to function in concert to mediate the fusion event.
For Herpes Simplex Virus Type 1 (HSV1), glycoproteins B, D
and the gHL heterodimer are all required for fusion, and gHL
counterparts are involved in the fusion process of all other
members of the herpesvirus family. An understanding of the
functional domains of gH that are critical for fusion may
offer the possibility of designing specific peptide inhibitors
of virus entry, and recent progress has highlighted the potential
usefulness of this approach. This review discusses these advances
and outlines some of the similarities and differences between
gH homologues of the different members of this diverse family
of viruses.
[Back to top]
[Full
Text Article] [PMID:
19601906 PubMed - indexed for MEDLINE]
Composition and Functions of the Influenza Fusion Peptide
K.J. Cross, W.A. Langley, R.J. Russell,
J.J. Skehel and D.A. Steinhauer
Fusion of the influenza virus envelope with the endosomal
membrane of host cells is mediated by the hemagglutinin glycoprotein
(HA). The most conserved region of HA is at the N-terminus
of the HA2 subunit, a relatively hydrophobic sequence of amino
acids referred to as the fusion peptide. This domain is critical
both for setting the trigger for fusion and for destabilizing
target membranes during the fusion process. The "trigger"
is set by cleavage of the HA precursor polypeptide, when the
newly-generated HA2 N-terminal fusion peptide positions itself
into the trimer interior and makes contacts with ionizable
residues to generate a fusion competent neutral pH structure.
This essentially "primes" the HA such that subsequent
acidification of the endosomal environment can induce the
irreversible conformational changes that result in membrane
fusion. A key component of these acid-induced structural rearrangements
involves the extrusion of the fusion peptide from its buried
position and its relocation to interact with the target membrane.
The role of the fusion peptide for both priming the neutral
pH structure and interacting with cellular membranes during
the fusion process is discussed.
[Back to top]
[Purchase
Article] [PMID:
19601907 PubMed - indexed for MEDLINE]
Viral Inactivation Based on Inhibition of Membrane Fusion:
Understanding the Role of Histidine Protonation to Develop
New Viral Vaccines
A.T. Da Poian, F.A. Carneiro and
F. Stauffer
Membrane fusion is an essential step in the entry of
enveloped viruses into their host cells, what makes it a potentially
attractive target for viral inactivation approaches. Fusion
is mediated by viral surface glycoproteins that undergo conformational
changes triggered by interaction with specific cellular receptors
or by the exposition to low pH of endossomal medium. Here
we review how several studies on the structural rearrangements
of vesicular stomatitis virus (VSV) glycoprotein G during
cellular recognition and fusion led us to propose a crucial
role of the protonation of His residues for G protein activity.
Moreover, we demonstrated that using diethylpyrocarbonate
(DEPC), a histidine-modifying compound, it was possible to
abolish viral infectivity and pathogenicity in mice, and to
elicit neutralizing antibodies that confer protection in these
animals against challenge using lethal doses of the virus.
The presence of conserved His residues in a wide range of
viral fusion proteins and the use of DEPC as a more general
means for vaccine development will be also discussed.
[Back to top]
[Purchase
Article] [PMID:
19601908 PubMed - indexed for MEDLINE]
Inhibition of Viral-Induced Membrane Fusion by Peptides
M. Vitiello, M. Galdiero and M.
Galdiero
Enveloped animal viruses fuse their membrane with a host
cell membrane in order to deliver their genome into the cytoplasm
of the cell and thus initiating infection. This crucial step
is mediated by virally encoded transmembrane proteins that,
following an appropriate triggering, insert their fusion peptides
into the target membrane and, through a cascade of conformational
changes, drive the merging of the two apposing membranes.
The battle against viruses is ongoing with the constant threat
of viruses developing resistance to present drugs and emerging
viruses, therefore there is a continuous challenge to improve
our defence strategies. Entry inhibitors are currently in
development for diverse human and animal viral pathogens,
and advances in our understanding on how viral entry proteins
undergo conformational changes that lead to entry offer a
huge potential for the development of novel therapeutics.
This review describes recent advances on viral-mediated fusion
mechanisms concentrating on the development of peptidic inhibitors
of membrane fusion.
[Back to top]
[Purchase
Article] [PMID:
19601909 PubMed - indexed for MEDLINE]
Describing Evolution of Hemagglutinins from Influenza A Viruses
Using a Differential Equation
S. Yan and G. Wu
Since 1999 we have developed three approaches to quantifying
each amino acid in a protein as well as a protein in whole
based on random mechanisms. With our approaches, we can reliably
describe the evolution of a protein family, for example, the
hemagglutinins from influenza A viruses along the time course
in a 2-dimensional graph, and then we use the fast Fourier
transform to find the mutation periodicity in order to time
the mutation. In this study, we realize that the changes in
quantified randomness in a hemagglutinin family over time
is the difference between randomness associated with mutant
amino acids and randomness associated with original amino
acids. This is a standard mass-balance relationship, by which
we can build a differential equation for a hemagglutinin family
or a system of differential equations for all hemagglutinins
in the family. In this context, the randomness defined by
us actually is the entropy, thus we have a general model to
describe the evolution, namely, the evolution is the exchange
of entropy between protein family and environment through
mutations quantified using our approaches.
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[Purchase Article] [PMID:
19601910 PubMed - indexed for MEDLINE]
The Use of Tripeptides for Lead Discovery of 5-HT4
Receptor Ligands
A. Hanna-Elias, P.E. Thompson, D.T. Manallack,
H.R. Irving, I.M. Coupar, I. Berque-Bestel and M.N.
Iskander
A series of 30 tripeptides were synthesized and tested
as novel 5-HT4 receptor ligands.
Receptor binding assays showed that a subset of compounds
had reasonable potency relative to the agonists serotonin
and 5-methoxytryptamine. Structure-activity analyses and molecular
docking have highlighted avenues for further synthetic work.
[Back to top]
[Purchase
Article] [PMID:
19601911 PubMed - indexed for MEDLINE]
Efficient Manual Fmoc Solid-Phase Synthesis of the N Terminal
Segment of Surfactant Protein B (SP-B1-25)
S. Ramli, I.R. Gentle and B.P.
Ross
The N-terminal 25 residue segment of human surfactant
protein B (SP-B1-25) was
synthesised in 26% yield by manual Fmoc solid-phase peptide
synthesis (Fmoc SPPS) using low-loading Fmoc-Gly-Wang resin.
Substantial oxidation of Met21
occurred during the synthesis, and the addition of Bu4NBr
to a TFA/water/EDT/TIS cleavage cocktail enabled facile reduction
of Met(O)21-SP-B1-25
to SP-B1-25. The methods
described herein are generally applicable to the Fmoc SPPS
of difficult sequences containing methionine.
[Back to top]
[Purchase
Article] [PMID:
19601912 PubMed - indexed for MEDLINE]
Conservation of Hydrophobicity within Viral Envelope Glycoproteins
Reveals a Putative Hepatitis C Virus Fusion Peptide
A. Taylor, J.M. O’Leary, S. Pollock
and N. Zitzmann
The mechanism(s) by which hepatitis C virus (HCV) enters
and infects cells remains unknown. Identifying the HCV fusion
peptide(s) and understanding the early stages of infection
may provide new opportunities for improved antiviral therapy.
The HCV envelope glycoprotein E2 is thought to be a class
II fusion protein. Class II fusion proteins are exemplified
by the E protein of the tick-borne encephalitis virus (TBEV)
and the E1 protein of the Semliki Forest virus (SFV). Analysis
of the hydrophobicity profiles of four HCV E2 envelope glycoproteins
revealed a region with a conserved three-pronged pattern of
hydrophobicity, termed the tridentate (TD) region. The primary
sequence of the TD region is highly conserved in all 490 HCV
strains currently reported. The known fusion peptide loops
of TBEV and SFV share the characteristic TD region hydrophobicity
profile and significant sequence conservation in the TD region
was identified in the E and E1 glycoproteins of members of
the Flaviviridae and Togaviridae families,
respectively. The HCV TD region peptides have membranotropic
activity; in molecular dynamics (MD) simulations, the HCV
TD region peptides insert into in a biomimetic bilayer in
a similar manner to the TBEV fusion peptide and the peptides
induce effective mixing of lipid membranes in a liposome fusion
assay. Together these results indicate that the highly conserved
TD region of the HCV E2 protein is a fusion peptide candidate
and may be an important factor in the class II fusion mechanism.
[Back to top]
[Purchase
Article] [PMID:
19601913 PubMed - indexed for MEDLINE]
Improving the Classification of Nuclear Receptors with Feature
Selection
Q.-B. Gao, Z.-C. Jin, X.-F. Ye, C. Wu, J.
Lu and J. He
Nuclear receptors are involved in multiple cellular signaling
pathways that affect and regulate processes. Because of their
physiology and pathophysiology significance, classification
of nuclear receptors is essential for the proper understanding
of their functions. Bhasin and Raghava have shown that the
subfamilies of nuclear receptors are closely correlated with
their amino acid composition and dipeptide composition [29].
They characterized each protein by a 400 dimensional feature
vector. However, using high dimensional feature vectors for
characterization of protein sequences will increase the computational
cost as well as the risk of overfitting. Therefore, using
only those features that are most relevant to the present
task might improve the prediction system, and might also provide
us with some biologically useful knowledge. In this paper
a feature selection approach was proposed to identify relevant
features and a prediction engine of support vector machines
was developed to estimate the prediction accuracy of classification
using the selected features. A reduced subset containing 30
features was accepted to characterize the protein sequences
in view of its good discriminative power towards the classes,
in which 18 are of amino acid composition and 12 are of dipeptide
composition. This reduced feature subset resulted in an overall
accuracy of 98.9% in a 5-fold cross-validation test, higher
than 88.7% of amino acid composition based method and almost
as high as 99.3% of dipeptide composition based method. Moreover,
an overall accuracy of 93.7% was reached when it was evaluated
on a blind data set of 63 nuclear receptors. On the other
hand, an overall accuracy of 96.1% and 95.2% based on the
reduced 12 dipeptide compositions was observed simultaneously
in the 5-fold cross-validation test and the blind data set
test, respectively. These results demonstrate the effectiveness
of the present method.
[Back to top]
[Purchase Article] [PMID:
19601914 PubMed - indexed for MEDLINE]
Plasma Ghrelin Levels in Patients with Familial Mediterranean
Fever
G. Keskin, A. Inal, R. Ilikçi and
O. Baysal
Familial mediterranean fever (FMF) is a familial disease
characterized by recurrent episodes of febrile serositis,
peritonitis, arthritis and pleuritis. Many studies have been
performed is an attempt to understand the basis of the inflammatory
attacts in FMF. Ghrelin, a recently described orexigene peptide
is predominantly produced by stomach. Ghrelin also exerts
multiple regulatory effects on immune system. It has reported
that grelin has anti-inflammatory effects. There is currently
no published evidence demonstrating a role for anti-inflammatory
effects of ghrelin in FMF. For this reason, we investigated
the role of plasma ghrelin levels in patients with FMF.
Thirty seven patients with FMF and 10 healthy controls (5
female, 5 male; mean age 35.4 ±
5.6 years) were enrolled in this study. Twenty-one patients
were in active stage (10 female, 11 male, mean age; 31.0 ±
5.4 years, mean disease duration 7.2 ±
3.3 years) and 16 patients were in inactive stage (7 female,9
male, mean age; 33.0 ±
6.0 years, mean disease duration; 8.7 ±
3.2 years). Plasma ghrelin levels were determined by EIA.
The mean plasma ghrelin levels were 158.4 ±
52.9 pg/ml in patients with FMF and 56.7 ±
7.5 pg/ml in healthy controls. The mean plasma ghrelin levels
were 190.5 ±
49.4 pg/ml in the active patients and 116.2 ±
11.7 pg/ml in the inactive patients. Plasma ghrelin levels
were significantly high in patients with FMF compared to healthy
controls (p<0.001).
Plasma ghrelin levels were significantly high in the active
patients compared to in the inactive patients and healthy
controls (p<0.001
and p<0.001
respectively). There was significantly difference between
in active and inactive patients with FMF (p<0.001).
As a results; Plasma ghrelin levels were high both in active
and inactive patients with FMF. It is showed that ghrelin
may play significant role of the pathogenesis of FMF.
[Back to top]
[Purchase
Article] [PMID:
19601915 PubMed - indexed for MEDLINE]
Investigation of Folding of Purified Recombinant GRA1 Protein
Using Web Based Protein Disorder Servers and Trypsin Digestion
M. Döskaya, A. Caner, A. Degirmenci,
F. Jurnak and Y. Gürüz
The successful folding of a recombinant protein after
expression and purification is essential for structural, biochemical
and vaccination studies. Toxoplasma gondii recombinant
GRA1 protein is a promising vaccine candidate against toxoplasmosis.
In the present study, the folding of recombinant GRA1 protein
has been evaluated by web based bioinformatics tools that
predict protein folding. Subsequently, trypsin digestion,
which is a simple indication of proper protein folding, has
been used to determine whether recombinant GRA1 protein is
likely to be folded. The results indicate that the recombinant
GRA1 protein is predicted to be folded by most of the web
based bioinformatics predictors. Moreover, in protease digestion
experiments, the recombinant GRA1, which was purified to homogeneity
without the use of denaturants, gives rise to a discrete band
pattern that is indicative of a folded protein. Together,
the results suggest that recombinant GRA1 protein is in a
folded conformation, suitable for structural, biochemical
and vaccination studies.
[Back to top]
[Purchase Article] [PMID:
19601916 PubMed - indexed for MEDLINE]
Polytope DNA Vaccine Development Against Hepatitis C Virus:
A Streamlined Approach from In Silico Design to In
Vitro and Primary In Vivo Analyses in BALB/c
Mice
A. Memarnejadian, F. Roohvand, A. Arashkia,
S. Rafati and M.A. Shokrgozar
For chronic viral infections like Hepatitis C, CD8-CTLs
have emerged as important protective tools. Hence, isolated
dominant epitopes arranged as polytope DNA or peptide vaccines
represent a promising approach. However, because of controversial
rules governing the polytope construction and epitope processing,
proper design and primary analysis of such vaccines are prior
to the costly transgenic animal studies.
In this study, based on in silico epitope selection,
four HLA-A2 (C132, E614 and N1406) and H-2d
(E405 and C132) immunodominant CD8-epitopes of HCV were selected.
The codon optimized nucleotide sequences of the epitopes were
assembled by overlap extension PCR in three different sequential
tandems for the best proteasomal cleavage predictions and
cloned into pcDNA3.1 vector. In addition, to enhance particulate
formation, three other plasmids containing the fusion of polytopes
with hepatitis B surface antigen gene (HBsAg) were also constructed.
Proper expression of all constructs in transfected Cos-7 cells
was verified by RT-PCR, immunofluorescence, Western-blot,
ELISA and dot blot techniques. Moreover, particle formation
of HBsAg-fused polytopes was manifested by their secretion
to the culture media albeit in lesser amounts compared to
sole HBsAg protein. Finally, the positive delayed-type hypersensitivity
(DTH) response of vaccinated mice indicated the in vivo
expression of all constructs and efficient stimulation of
immune response, which was stronger for HBsAg fusion constructs.
In addition, proper processing of the epitopes was evidenced
by the DTH response towards H-2d
epitopic peptides. These data provide enough support and merit
for the further evaluation of the designed constructs in HLA-A2
transgenic mice.
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