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Protein
& Peptide Letters
ISSN: 0929-8665
Protein &
Peptide Letters
Volume 17, Number 7,
2010
Contents
Regular Papers
Synthetic Strategies to a Backbone-Side Chain Cyclic
SHP-1 N-SH2 Ligand Containing N-Functionalized Alkyl Phosphotyrosine† Pp. 809-816
K. Teichmann, T. Niksch, K. Wieligmann, M. Zacharias
and D. Imhof
[Abstract] [Purchase
Article] [PMID:
19747152 PubMed - indexed for MEDLINE]
Acafusin, a Dimeric Antifungal Protein
from Acacia confusa Seeds Pp. 817-822
S.K. Lam and T.B. Ng
[Abstract] [Purchase
Article] [PMID:
19958279 PubMed - indexed for MEDLINE]
A Cytokine-Inducing Hemagglutinin from Small
Taros Pp. 823-830
Y.S. Chan, J.H. Wong and T.B. Ng
[Abstract] [Purchase
Article] [PMID:
19807671 PubMed - indexed for MEDLINE]
Circular Dichroism Studies on the Deinococcus
radiodurans Nudix Hydrolase DR_0079: An Atypical Thermal
Melt Pp. 831-835
G.W. Buchko
[Abstract] [Purchase
Article] [PMID:
20156187 PubMed - indexed for MEDLINE]
Determination of Proteins Induced in Response
to Jasmonic Acid and Salicylic Acid in Resistant and Susceptible
Cultivars of Tomato Pp. 836-846
A. Afroz, M.R. Khan and S. Komatsu
[Abstract] [Purchase
Article] [PMID:
20156185 PubMed - indexed for MEDLINE]
Design, Synthesis and Preliminary Activity Evaluation
of Novel L-Lysine Derivatives as Aminopeptidase N/CD13 Inhibitors
Pp. 847-853
Q. Wang, F. Xu, J. Mou, J. Zhang, L. Shang, Y. Luan, Y.
Yuan, Y. Liu, M. Li, H. Fang, B. Wang and W. Xu
[Abstract] [Purchase
Article] [PMID:
20156182 PubMed - indexed for MEDLINE]
Why Inverse Proteins Are Relatively Abundant
Pp. 854-860
J.-C. Nebel and C.G.C. Walawage
[Abstract] [Purchase
Article] [PMID:
20205652 PubMed - indexed for MEDLINE]
Biochemical Characterization and NMR Study of the
Region E748-A785 of the Human Protein MRP6/ABCC6 Pp.
861-866
A. Ostuni, R. Miglionico, F. Bisaccia and
M.A.C. Morelli
[Abstract] [Purchase
Article] [PMID:
20226001 PubMed - indexed for MEDLINE]
Protein Engineering of Bacterial Histidine
Kinase Receptor Systems Pp. 867-873
W. Xie, K.Y. Blain, M.M.-C. Kuo and S. Choe
[Abstract] [Purchase
Article] [PMID:
20205655 PubMed - indexed for MEDLINE]
In Vitro Unfolding of Insulin: Characterization
of Intermediates and Putative Unfolding Pathway Pp.
874-880
J. Zhao, Q.-L. Huang, Y.-H. Tang, F.-K. Zhao and
Y.-M. Feng
[Abstract] [Purchase
Article] [PMID:
20205654 PubMed - indexed for MEDLINE]
Study on the Influences of Palindromes in Protein
Coding Sequences on the Folding Rates of Peptide Chains
Pp. 881-888
R.-F. Li and H. Li
[Abstract] [Purchase
Article] [PMID:
20205658 PubMed - indexed for MEDLINE]
The Two Pathways for Effective Orthogonal
Protection of L-Ornithine, for Amino Acylation of 5’-O-Pivaloyl
Nucleosides, Describe the General and Important Role for the
Successful Imitation, During the Synthesis of the Model Substrates
for the Ribosomal Mimic Reaction Pp.
889-898
S.G. Bayryamov, N.G. Vassilev and
D.D. Petkov
[Abstract] [Purchase
Article] [PMID:
20205650 PubMed - indexed for MEDLINE]
Classification of Transcription Factors Using
Protein Primary Structure Pp. 899-908
X.-Y. Yang, X.-H. Shi, X. Meng, X.-L. Li, K. Lin, Z.-L.
Qian, K.-Y. Feng, X.-Y. Kong and Y.-D. Cai
[Abstract] [Purchase
Article] [Supplementary
Material] [PMID:
20394581 PubMed - indexed for MEDLINE]
Histatins In Non-Human Primates: Gene Variations
and Functional Effects Pp. 909-918
L. Padovan, L. Segat, A. Pontillo, N. Antcheva, A. Tossi and S. Crovella
[Abstract] [Purchase
Article] [PMID:
20423320 PubMed - indexed for MEDLINE]
Transient Expression of Recombinant sPDGFRα
-Fc in CHO DG44 Cells using 50-mL Orbitally Shaking
Disposable Bioreactors Pp. 919-924
Y.-X. Sang, X.-W. Zhang, X.-J. Chen, K. Xie, C.-W. Qian,
A. Hong, Q.-L. Xie and S. Xiong
[Abstract] [Purchase
Article] [PMID:
20205651 PubMed - indexed for MEDLINE]
N-(tert)-Butyloxycarbonyl-β,
β -Cyclopentyl-Cysteine (Acetamidomethyl)-Methyl
Ester for Synthesis of Novel Peptidomimetic Derivatives
Pp. 925-929
A. Mollica, F. Feliciani, A. Stefanucci, I. Cacciatore,
C. Cornacchia, D. Torino and F. Pinnen
[Abstract] [Purchase
Article] [PMID:
20205656 PubMed - indexed for MEDLINE]
Abstracts
[Back to top] [Purchase
Article] [PMID:
19747152 PubMed - indexed for MEDLINE]
Synthetic Strategies to a Backbone-Side Chain Cyclic
SHP-1 N-SH2 Ligand Containing N-Functionalized Alkyl Phosphotyrosine†
K. Teichmann, T. Niksch, K. Wieligmann, M. Zacharias
and D. Imhof
The cyclic peptid EGLNcΨ[CON((CH2)3NH)pYNleE(NHCH2CO)]L-NH2
(1) was designed and synthesized according to a native interaction
partner of tyrosine phosphatase SHP-1. We introduced N-aminopropyl-phosphotyrosine
to enable backbone-side chain cyclization with a glutamic
acid derivative as counterpart for cyclization. Different
approaches have been compared to find a strategy for the generation
of backbone and backbone-side chain cyclic phosphopeptides.
[Back to top]
[Purchase
Article] [PMID:
19958279 PubMed - indexed for MEDLINE]
Acafusin, a Dimeric Antifungal Protein
from Acacia confusa Seeds
S.K. Lam and T.B. Ng
A dimeric 34-kDa antifungal protein, designated as acafusin,
was purified from Acacia confusa seeds using Q-Sepharose,
DEAE-cellulose, Mono S and Superdex S75. It demonstrated antifungal
activity toward Rhizoctonia solani with an IC50
of 28 μM.
Acafusin inhibited the activity of HIV-1 reverse transcriptase
mildly with an IC50 of 80
μM.
[Back to top]
[Purchase
Article] [PMID:
19807671 PubMed-indexed for MEDLINE]
A Cytokine-Inducing Hemagglutinin from Small
Taros
Y.S. Chan, J.H. Wong and T.B. Ng
A 22.4-kDa dimeric hemagglutinin was isolated from tubers
of Colocasia esculenta cv. ‘Small Taro’
by employing a purification protocol that involved ion exchange
chromatography on Q-Sepharose, fast protein liquid chromatography
(FPLC)-ion exchange chromatography on Mono Q, and FPLC-gel
filtration on Superdex 75. The hemagglutinin was isolated
from the fraction of the taro extract adsorbed on Q-Sepharose
and subsequently adsorbed on Mono Q. The major absorbance
peak from the Superdex 75 column constituted purified hemagglutinin.
Its hemagglutinating activity could not be inhibited by simple
sugars, and was stable after exposure for 30 minutes to temperatures
up to 40°C
and to ambient pH in the range of pH 2 to pH 13. The activity
decreased progressively when the ambient temperature was raised
from 40°C
to 100°C.
Negligible activity was detected at 100°C.
The activity plummeted, with about 40% and 10% remaining,
4 minutes and 20 minutes after exposure to 100°C,
respectively. About half of the activity remained at pH 0
and pH 1 whereas the activity was completely abolished at
pH 14. The hemagglutinin exhibited slight anti-tumor activity
toward hepatoma HepG2 cells, and weak mitogenic activity toward
murine splenocytes. It induced expression of the cytokines
interleukin-1β,
inteleukin-2, interferon-γ
and tumor necrosis factor-α.
However, it was devoid of anti-fungal activity toward a number
of fungal species.
[Back to top]
[Purchase
Article] [PMID:
20156187 PubMed - indexed for MEDLINE]
Circular Dichroism Studies on the Deinococcus
radiodurans Nudix Hydrolase DR_0079: An Atypical Thermal
Melt
G.W. Buchko
The crystal structure for the Deinococcus radiodurans Nudix protein DR_0079 was recently determined in the metal-free
form at 1.9 Å resolution (2O5F). The protein adopts
the fundamental fold common to the Nudix family of proteins,
a large mixed β-sheet
sandwiched between the α-helix
of the “Nudix box” and a second α-helix.
The protein’s physical properties were further characterized
by circular dichroism (CD) spectroscopy. A CD thermal melt
at 220 nm indentifies an inflection point at ~52ºC. However,
unlike typical CD thermal melts, the negative ellipticity
at 220 nm becomes more negative upon passing through the inflection
point. Both NMR spectroscopy and size exclusion chromatography
indicate that heating effects the irreversible formation of
a large molecular weight complex. After cooling, the negative
ellipiticity at 220 nm increases further, and overall, the
CD spectrum at 25ºC suggests that heat-treated DR_0079
has more α-helical
and β-sheet
structure than non-heat treated DR_0079.
[Back to top]
[Purchase
Article] [PMID:
20156185 PubMed - indexed for MEDLINE]
Determination of Proteins Induced in Response
to Jasmonic Acid and Salicylic Acid in Resistant and Susceptible
Cultivars of Tomato
A. Afroz, M.R. Khan and S. Komatsu
Jasmonic acid (JA) and salicylic acid (SA) are signaling
molecules that play key roles in the regulation of metabolic
processes, reproduction, and defense against pathogens. The
proteomics approach was used to identify proteins that are
induced by JA and SA in the tomato cultivars Roma and Pant
Bahr, which are susceptible and resistant to bacterial wilt,
respectively. Threonine deaminase and leucine amino peptidase
were upregulated, and ribulose-1,5-bisphosphate carboxylase/oxygenase
small chain was downregulated by time-course application of
JA. Translationally controlled tumor protein was upregulated
by time-course application of SA. Protein disulfide isomerase
was upregulated by application of either JA or SA. Proteins
related to defense, energy, and protein destination/storage
are suspected to be responsible for the susceptibility or
resistance of the cultivars. Furthermore, in Roma, iron ABC
transporter was upregulated by JA and down-regulated by SA.
Iron ABC transporter plays a part in the signal transduction
of both JA and SA in cultivars of tomato that are resistant
to bacterial wilt.
[Back to top]
[Purchase
Article] [PMID:
20156182 PubMed-indexed for MEDLINE]
Design, Synthesis and Preliminary Activity Evaluation
of Novel L-Lysine Derivatives as Aminopeptidase N/CD13 Inhibitors
Q. Wang, F. Xu, J. Mou, J. Zhang, L. Shang, Y. Luan, Y.
Yuan, Y. Liu, M. Li, H. Fang, B. Wang and W. Xu
A novel class of L-lysine derivatives as aminopeptidase
N (APN) inhibitors was designed and synthesized. Activity
evaluation showed that compound C7 (IC50 = 9.6 ± 1.3 µM) and C20 (IC50
= 13.6 ± 1.9 µM) were equivalent to the positive
control Bestatin (IC50 =
11.3 ± 1.6 µM).
[Back to top]
[Purchase
Article] [PMID:
20205652 PubMed - indexed for MEDLINE]
Why Inverse Proteins Are Relatively Abundant
J.-C. Nebel and C.G.C. Walawage
Studies have shown that inverse proteins are relatively
abundant. In this work, we investigate the proposition that
the repeat patterns they share with protein sequences explain
this phenomenon. Using a new artificial set of peptide sequences
which also display these features and a random set, we show
that the presence of repeats contributes to protein sequence
similarity. Further analysis confirms that most inverse proteins
exhibit repeats. Therefore, we suggest the relative abundance
of inverse proteins can be explained by the fact they display
the same repeat structures and amino acid propensity of existing
proteins.
[Back to top]
[Purchase
Article] [PMID:
20226001 PubMed - indexed for MEDLINE]
Biochemical Characterization and NMR Study of
the Region E748-A785 of the Human Protein MRP6/ABCC6
A. Ostuni, R. Miglionico, F. Bisaccia and
M.A.C. Morelli
Multidrug-resistance-associated protein 6 (MRP6/ABCC6)
is a protein belonging to the ABC transporter family which
couple ATP hydrolysis with the transport of molecules across
biological membranes. MRP6 topology presents three transmembrane
domains and two nucleotide-binding domains (NBDs). The protein
is structurally and functionally poorly characterized. Mutations
in ABCC6 gene cause Pseudoxanthoma elasticum, a recessive
genetic disorder affecting the elastic tissues. Most mutations
have been found in NBDs that are critical for ATP binding
and hydrolysis.
With the aim to better characterize MRP6, we have performed
a preliminary study on the fragment E748-A785 of MRP6-NBD1,
with the wild type sequence and the R765Q mutation found in
PXE affected patients. CD and NMR spectroscopy show the presence
of helical structures in both peptides. Fluorescence experiments
demonstrate that peptides bind ATP. The NMR structure of the
mutated peptide is compared with the corresponding region
of the MRP6-NBD1 modeled structure using as a template the
X-ray structure of MRP1-NBD1. The finding that both wild type
and mutated peptide present the same structure and similar
affinity for ATP suggests that the onset of PXE symptoms is
a consequence of the different type of interactions involving
residue 765 R/Q inside the protein.
[Back to top]
[Purchase
Article] [PMID:
20205655 PubMed - indexed for MEDLINE]
Protein Engineering of Bacterial Histidine
Kinase Receptor Systems
W. Xie, K.Y. Blain, M.M.-C. Kuo and S. Choe
Two-component systems (TCS) involving the His-Asp phosphotransfer
are commonly utilized for signal transduction in prokaryotes
in which the two essential components are a sensor histidine
kinase (HK) receptor and a response regulator (RR). Despite
great efforts in structural and functional characterization
of signal perception mechanisms, the exact signaling mechanisms
remain elusive for many TCSs. Mimicking the natural TCS signaling
pathways, chimeric receptor kinases and response regulators
have been constructed through the process of swapping modular
domains of related TCSs. To design chimeras with new signaling
pathways, domains from different proteins that have little
relationship at the primary structural level but carrying
desirable functional properties can be conjoined to engineer
novel TCSs. These chimeras maintain the ability to respond
to environmental stimulants by regulating protein phosphorylation
to produce downstream output signals. Depending on the nature
of external signals, chimeric TCSs can serve as a novel tool
not only to examine the natural signaling mechanisms in TCSs,
but also for industrial and clinical applications.
[Back to top]
[Purchase
Article] [PMID:
20205654 PubMed - indexed for MEDLINE]
In Vitro Unfolding of Insulin: Characterization
of Intermediates and Putative Unfolding Pathway
J. Zhao, Q.-L. Huang, Y.-H. Tang, F.-K. Zhao and
Y.-M. Feng
The in vitro insulin unfolding had been studied
using the “equilibrium unfolding” method where
protein is unfolded by reducing reagents in the presence of
trace amounts of oxidants such as oxidized glutathione. Nine
intermediates were captured in the unfolding process, named
as P1A, P2A, P3A, P4A, P3B, P4B, P5B, P6B, and P7B, which
were all either A chain derivatives or B chain derivatives.
No intermediate with inter-A-B chain disulfide was captured.
Based on the character of the intermediates, their distribution
during the unfolding process and the hypothetic “transient”
intermediates, an in vitro putative unfolding pathway
of insulin had been proposed. Besides, the comparison of the
intermediates captured in unfolding with the intermediates
captured in the refolding process of insulin revealed that
both unfolding/refolding processes of insulin shared common
intermediates. Based on these observations we suggested that
the unfolding pathway of insulin was similar to the refolding
pathway but flowed in the opposite direction.
[Back to top]
[Purchase
Article] [PMID:
20205658 PubMed - indexed for MEDLINE]
Study on the Influences of Palindromes in Protein
Coding Sequences on the Folding Rates of Peptide Chains
R.-F. Li and H. Li
Taking all the proteins of four virus genomes
as samples, the segments of α-helix
and β-strand
in proteins of the four viruses were obtained. Linear regression
analyses between the average polarities and the folding rates
of peptide chains were performed for α-helices
and β-strands
respectively. The results indicated that the folding rates
show significant positive linear correlation for α-helices
and negative linear correlation for β-strands
with the average polarities. Based on the corresponding protein
coding sequences of these amino acid segments, the influences
of GC content of palindromes and palindrome densities in protein
coding segments on the relations between the folding rates
and the average polarities were studied. Results showed that
the folding rates correlated positively with the GC content
of palindromes and the palindrome density, and protein coding
sequences do carry the information which can influence the
folding rates of peptide chains or protein structures. Our
analysis indicates that this kind of effect mostly comes from
the information of palindrome structure itself or from the
synonymous codon usage, but not from the translation information
from codons to amino acids.
[Back to top] [Purchase
Article] [PMID:
20205650 PubMed - indexed for MEDLINE]
The Two Pathways for Effective Orthogonal
Protection of L-Ornithine, for Amino Acylation of 5’-O-Pivaloyl
Nucleosides, Describe the General and Important Role for the
Successful Imitation, During the Synthesis of the Model Substrates
for the Ribosomal Mimic Reaction
S.G. Bayryamov, N.G. Vassilev and
D.D. Petkov
Bz(NO2)-Orn(Boc)-OCH2CN
was synthesized as an amino acid component with effective
and successful orthogonal protection for amino acylation of
5’-O-Pivaloyl nucleosides and preparation of substrates
for model ribosome reactions. The synthesis was carried out
using suitable combinations of the methods of peptide synthesis
and modification of amino acids.
[Back to top]
[Purchase
Article] [PMID:
20394581 PubMed - indexed for MEDLINE]
Classification of Transcription Factors Using
Protein Primary Structure
X.-Y. Yang, X.-H. Shi, X. Meng, X.-L. Li, K. Lin, Z.-L.
Qian, K.-Y. Feng, X.-Y. Kong and Y.-D. Cai
[Supplementary
Material]
The transcription factor (TF) is a protein that binds
DNA at specific site to help regulate the transcription from
DNA to RNA. The mechanism of transcriptional regulatory can
be much better understood if the category of transcription
factors is known. We introduce a system which can automatically
categorize transcription factors using their primary structures.
A feature analysis strategy called “mRMR” (Minimum
Redundancy, Maximum Relevance) is used to analyze the contribution
of the TF properties towards the TF classification. mRMR is
coupled with forward feature selection to choose an optimized
feature subset for the classification. TF properties are composed
of the amino acid composition and the physiochemical characters
of the proteins. These properties will generate over a hundred
features/parameters. We put all the features/parameters into
a classifier, called NNA (nearest neighbor algorithm), for
the classification. The classification accuracy is 93.81%,
evaluated by a Jackknife test. Feature analysis using mRMR
algorithm shows that secondary structure, amino acid composition
and hydrophobicity are the most relevant features for classification.
A free online classifier is available at http://app3.biosino.org/132dvc/tf/.
[Back to top]
[Purchase
Article] [PMID:
20423320 PubMed - indexed for MEDLINE]
Histatins In Non-Human Primates: Gene Variations
and Functional Effects
L. Padovan, L. Segat, A. Pontillo, N. Antcheva, A. Tossi and S. Crovella
Human histatins are histidine-rich, low molecular weight
salivary proteins that contribute to the immune system of
the oral cavity. In this work, nucleotide sequences of the
HIS1 (coding for histatin 1) and HIS2 (coding
for histatin 3) genes, homologous to the human ones, have
been sequenced and analysed in five primates species including
Great Ape, Hylobatidae and Cercopithecidae. In HIS1,
the region corresponding to the putative mature peptide shows
a premature stop codon in Macaca and Cercopithecus,
while HIS2 a six codon insertion in the Cercopithecidae.
Histatin 5, a 24-residue peptide derived from histatin 3,
is the most antimicrobially active among human histatins,
thus macaque and nomascus orthologues of histatin 5 were selected
for chemical synthesis and functional characterization, in
comparison to the human peptide. All synthesized histatins
are predicted to be poorly amphipathic, depending on the charged
state of His residues and assume partially α-helical
conformations only in lipophilic conditions. Antimicrobial
assays against Candida and Criptococcus spp.
indicate somewhat different spectra of in vitro activity
against the tested fungi.
We have described HIS1 and HIS2 gene variations
in primates and have analysed their functional effects on
selected Hst5 orthologues. The human antimicrobial peptide
has been proposed to represent an important lead for new generation
of antimicrobial compounds for the treatment of oral mycoses,
thus the information from the non-human primates histatins
studied may aid strategies for drugs design.
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[Purchase
Article] [PMID:
20205651 PubMed-indexed for MEDLINE]
Transient Expression of Recombinant sPDGFRα
-Fc in CHO DG44 Cells using 50-mL Orbitally Shaking
Disposable Bioreactors
Y.-X. Sang, X.-W. Zhang, X.-J. Chen, K. Xie, C.-W. Qian,
A. Hong, Q.-L. Xie and S. Xiong
Overactivity of platelet-derived growth factor (PDGF)
has been linked to malignant cancers. High levels of PDGF
result in the activation of its receptors (PDGFRs) and the
over-proliferation of cells. Therefore, interfering with this
signaling pathway in cancer cells could be significant for
anti-cancer drug development. In a previous study, the sPDGFRα-Fc
fusion protein expressed in static CHO-k1
cells showed an anti-proliferative effect on vascular endothelial
cells. However, it was difficult to obtain a large quantity
of this fusion protein for further functional studies. In
the present study, the sPDGFRα-Fc
fusion protein was transiently expressed in Chinese Hamster
Ovary (CHO) DG44 cells in 50-mL orbital shaking bioreactors.
sPDGFRα-Fc
was expressed as a 250-kDa dimeric protein with potential
glycosylation. The final yield of sPDGFRα-Fc
in the culture supernatant was as high as 16.68 mg/L. Our
results suggest that transient expression in orbital shaking
bioreactors may be feasible for preparation of recombinant
proteins used for preclinical studies.
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[Purchase
Article] [PMID:
20205656 PubMed - indexed for MEDLINE]
N-(tert)-Butyloxycarbonyl-β,
β -Cyclopentyl-Cysteine (Acetamidomethyl)-Methyl
Ester for Synthesis of Novel Peptidomimetic Derivatives
A. Mollica, F. Feliciani, A. Stefanucci, I. Cacciatore,
C. Cornacchia, D. Torino and F. Pinnen
It has been recently reported that thiol groups
could play an important role in the protection of neuronal
cells in Alzheimer's disease (AD), prion disease (CJD) and
Parkinson's disease (PD). Also bucillamine, that is a pseudo
dipeptide possessing a thiol group capable to form an internal
disulfide bridge, has relevant scavenger properties used in
therapy for the treatment of arthritis. Furthermore, many
sulphur containing compounds show strong chelating properties
to heavy metals. Due to the crucial role of thiol groups in
a variety of detoxicant biological systems, we report the
synthesis of a racemic β,β-dialkyl-substituted,
fully protected, cysteine derivative as a suitable intermediate
in the synthesis of novel biological active peptides.
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