|
Protein
& Peptide Letters
ISSN: 0929-8665
Protein &
Peptide Letters
Volume 17, Number 6,
2010
Contents
Regular Papers
Using Affinity Propagation Combined Post-Processing
to Cluster Protein Sequences Pp. 681-689
F. Yang, Q.X. Zhu, D.M. Tang and M.Y.
Zhao
[Abstract] [Purchase
Article] [PMID:
19594428 PubMed - indexed for MEDLINE]
Biochemical and Functional Properties
of a Lectin Purified from Korean Large Black Soybeans ―
A Cultivar of Glycine Max Pp. 690-698
E.F. Fang, J.H. Wong, P. Lin and T.B. Ng
[Abstract] [Purchase
Article] [PMID:
19715533 PubMed - indexed for MEDLINE]
On the Importance of the Small Domain
in the Thermostability of Thermoalkalophilic Lipases from
L1 and T1: Insights from Molecular Dynamics Simulation
Pp. 699-707
R.A. Karjiban, M.B.A. Rahman, A.B. Salleh, M. Basri, R.N.Z.RA.
Rahman and A.L.T. Chor
[Abstract] [Purchase
Article] [PMID:
19958281 PubMed - indexed for MEDLINE]
Conformational Stability and Activity
of Circular Enterocin AS-48 Derivatives Pp. 708-714
M. Sánchez-Hidalgo, A.M Fernández-Escamilla,
M. Martínez-Bueno, E. Valdivia, L. Serrano and
M. Maqueda
[Abstract] [Purchase
Article] [PMID:
19958277 PubMed - indexed for MEDLINE]
Using the Concept of Chou's Pseudo Amino Acid Composition
to Predict Enzyme Family Classes: An Approach with Support
Vector Machine Based on Discrete Wavelet Transform
Pp. 715-722
J.-D. Qiu, J.-H. Huang, S.-P. Shi and
R.-P. Liang
[Abstract] [Purchase
Article] [PMID:
19961429 PubMed - indexed for MEDLINE]
Novel Detection System for Plant Protein
Production of Pharmaceuticals and Impact on Conformational
Diseases Pp. 723-731
K.A. Nagel, B. Kastenholz, F. Gilmer, U. Schurr and
A. Walter
[Abstract] [Purchase
Article] [PMID:
20015023 PubMed - indexed for MEDLINE]
Homology Modeling Studies of Yeast Mitogen-Activated
Protein Kinases (MAPKS): Structural Motifs as a Basis for
Specificity Pp. 732-738
D.L. Smith and S.H. Nilar
[Abstract] [Purchase
Article] [PMID:
19995338 PubMed - indexed for MEDLINE]
Isothermal Calorimetry Study of the
Interactions of Type I Antifreeze Proteins with a Lipid Model
Membrane Pp. 739-743
H. Kun and Y. Mastai
[Abstract] [Purchase
Article] [PMID:
19995337 PubMed - indexed for MEDLINE]
Effects of Cisplatin Binding to DNA
on the Dynamics of the E. coli MutS Dimer
Pp. 744-750
F.R. Salsbury Jr.
[Abstract] [Purchase
Article] [PMID:
19995335 PubMed - indexed for MEDLINE]
Importance of a Potential Salt Bridge
and Hydrophobic Core in the Function and Oligomerization of
a Small Heat Shock Protein Pp. 751-758
Z. Wen, Y. Wang, X. Xu, B. Yang, W. Li and M.
Xie
[Abstract] [Purchase
Article] [PMID:
20015024 PubMed - indexed for MEDLINE]
Molecular Modeling Studies of the Conserved
B`12-Binding Motif and Its
Variants from Clostridium tetanomorphum Glutamate Mutase
Pp. 759-764
C.-H. Hsu and H.-P. Chen
[Abstract] [Purchase
Article] [PMID:
20397969 PubMed - indexed for MEDLINE]
Development of Tools and Database for
Analysis of Metal Binding Sites in Protein Pp. 765-773
B.K. Kuntal, P. Aparoy and P. Reddanna
[Abstract] [Purchase
Article] [PMID:
20205657 PubMed - indexed for MEDLINE]
Antibodies Against Recombinant Shiga
Toxin Subunit B Neutralize Shiga Toxin Toxicity in HeLa Cells
Pp. 774-781
P. Gupta, M.K. Singh, P. Singh, M. Tiwari and
R.K. Dhaked
[Abstract] [Purchase
Article] [PMID:
20044923 PubMed - indexed for MEDLINE]
A Storage Protein-Like Trypsin Inhibitor
from the Moth Bean (Phaseolus acutifolius)
with Antiproliferative Activity Toward
Lymphoma Cells Pp.782-788
D.Z. Ma, J. Sun, G.Q. Zhang, H.X. Wang and
T.B. Ng
[Abstract] [Purchase
Article] [PMID:
20044920 PubMed - indexed for MEDLINE]
Gene Ontology-Based Protein Function
Prediction by Using Sequence Composition Information
Pp. 789-795
Q. Dong, S. Zhou, L. Deng and J. Guan
[Abstract] [Purchase
Article] [PMID:
19995340 PubMed - indexed for MEDLINE]
Salt Effect on Substrate Specificity
of a Subtilisin-Like Halophilic Protease Pp. 796-802
D.N. Okamoto, M.Y. Kondo, K. Hiraga, M.A. Juliano, L.
Juliano,
I.E. Gouvea and K. Oda
[Abstract] [Purchase
Article] [PMID:
20205649 PubMed - indexed for MEDLINE]
Cloning and Characterization of an Exo-Xylogucanase
from Rumenal Microbial Metagenome Pp. 803-808
D.D.W.S. Wong, V.J. Chan, A.A. McCormack and
S.B. Batt
[Abstract] [Purchase
Article] [PMID:
20044921 PubMed - indexed for MEDLINE]
Abstracts
[Back to top] [Purchase
Article] [PMID:
19594428 PubMed - indexed for MEDLINE]
Using Affinity Propagation Combined
Post-Processing to Cluster Protein Sequences
F. Yang, Q.X. Zhu, D.M. Tang and M.Y.
Zhao
The sizes of the protein databases are growing
rapidly nowadays thus clustering protein sequences based only
on sequence information becomes increasingly important. In
this paper, we analyze the limitation of Affinity propagation
(AP) algorithm when clustering a dataset generated randomly.
Then we propose a post-processing method to improve the AP
algorithm. This method uses the median of the input similarities
as the shared preference value, and then employs post-processing
phase combined mergence and reassignment strategy on the results
of the AP algorithm. We have tested our method extensively
and compared its performance with other five methods on several
datasets of COG (Clusters of Orthologous Groups of proteins)
database, SCOP and G-protein family. The number of clusters
obtained for a given set of proteins approximate to the correct
number of clusters in that set. Moreover, in our experiments,
the quality of the clusters as quantified by F-measure was
better than that of others (on average, 9% better than BlastClust,
33% better than TribeMCL, 34% better than CLUSS, 59% better
than Spectral clustering and 41% better than AP).
[Back to top]
[Purchase
Article] [PMID:
19715533 PubMed - indexed for MEDLINE]
Biochemical and Functional Properties
of a Lectin Purified from Korean Large Black Soybeans ―
A Cultivar of Glycine Max
E.F. Fang, J.H. Wong, P. Lin and T.B. Ng
Lectins, a class of proteins that reversibly
and non-enzymatically bind specific sugars, have been purified
from different kinds of legumes. In this study, a 48-kDa lectin
(KBL) was purified from Korean large black soybeans using
liquid chromatography. The specific hemagglutinating activity
of the KBL was 4096 titer/mg. EDTA-induced loss of hemagglutinating
activity of KBL could be recovered by addition of Fe3+
ions and some divalent cations as Ca2+,
Mn2+, Fe2+,
Cu2+, Zn2+,
and Pb2+. Sugars such as
D-(+)-galactose, D-(+)-raffinose, L-(+)-arabinose, α-D-(+)-melibiose,
and α-lactose
could inhibit the hemagglutinating activity of the lectin.
Furthermore, the protein showed high thermal stability as
well as stability over a wide range of pH values. KBL inhibited
HIV-1 reverse transcriptase activity with an IC50
of 1.38 μM.
However, it was destitute of cytokine releasing, mitogenic,
ribonuclease and antifungal activities. In addition, inhibitory
activity toward nasopharyngeal cell lines was undetectable
in KBL at concentrations up to 20 μM.
[Back to top]
[Purchase
Article] [PMID:
19958281 PubMed - indexed for MEDLINE]
On the Importance of the Small Domain
in the Thermostability of Thermoalkalophilic Lipases from
L1 and T1: Insights from Molecular Dynamics Simulation
R.A. Karjiban, M.B.A. Rahman, A.B. Salleh, M. Basri, R.N.Z.RA.
Rahman and A.L.T. Chor
An all-atom level MD simulation in explicit
solvent at high temperature is a powerful technique to increase
our knowledge about the structurally important regions modulating
thermal stability in thermoenzymes. In this respect, two large-sized
thermoalkalophilic enzymes from Bacillus stearothermophilus
L1 (L1 lipase) and Geobacillus zalihae strain T1
(T1 lipase) are well-established representatives. In this
paper, comparative results from temperature-induced MD simulations
of both model systems at 300 K, 400 K and 500 K are presented
and discussed with respect to identification of highly flexible
regions critical to thermostability. From our MD simulation
results, specific regions along the L1 lipase and T1 lipase
polypeptide chain including the small domain and the main
catalytic domain or core domain of both enzymes show a marked
increase in fluctuations and dynamics followed by clear structural
changes. Overall, the N-terminal moiety of both enzymes and
their small domains exhibit hyper-sensitivity to thermal stress.
The results appear to propose that these regions are critical
in determining of the overall thermal stability of both organisms.
[Back to top]
[Purchase
Article] [PMID:
19958277 PubMed - indexed for MEDLINE]
Conformational Stability and Activity
of Circular Enterocin AS-48 Derivatives
M. Sánchez-Hidalgo, A.M Fernández-Escamilla,
M. Martínez-Bueno, E. Valdivia, L. Serrano and
M. Maqueda
Four AS-48 mutants (Trp24Ala, Gly13Lys, Leu40Lys
and Ala53Ser) were obtained by site-directed mutagenesis.
The minimal inhibitory concentration of each peptide showed
that only residue Trp24 was unquestionably involved in the
biological activity. Guanidine hydrochloride-induced unfolding
assays showed a three-state transition denaturation process,
suggesting a molten-globule-like conformation after the first
transition.
[Back to top]
[Purchase
Article] [PMID:
19961429 PubMed - indexed for MEDLINE]
Using the Concept of Chou's Pseudo Amino Acid Composition
to Predict Enzyme Family Classes: An Approach with Support
Vector Machine Based on Discrete Wavelet Transform
J.-D. Qiu, J.-H. Huang, S.-P. Shi and
R.-P. Liang
The early determination of family for a newly
found enzyme molecule becomes important because it is directly
related to the detail information about which specific target
it acts on, as well as to its catalytic process and biological
function. Unfortunately, it is still a hard work to distinguish
enzyme classes by experiments. With an enormous amount of
protein sequences uncovered in the genome research, it is
both challenging and indispensable to develop an automatic
method for fast and reliably classifying the enzyme family.
Using the concept of Chou's pseudo amino acid composition,
we developed a new method that coupled discrete wavelet transform
with support vector machine based on the amino acid hydrophobicity
to predict enzyme family. The overall success rate obtained
by the 10-cross-validation for the identification of the six
enzyme families was 91.9%, indicating the current method could
be an effective and promising high-throughput method in the
enzyme research.
[Back to top]
[Purchase
Article] [PMID:
20015023 PubMed - indexed for MEDLINE]
Novel Detection System for Plant Protein
Production of Pharmaceuticals and Impact on Conformational
Diseases
K.A. Nagel, B. Kastenholz, F. Gilmer, U. Schurr and
A. Walter
State-of-the-art biochemistry methods in combination
with an automated phenotyping method demonstrate the high
potential of transgenic tobacco plants in producing properly-folded
therapeutic proteins for the treatment of protein-misfolding
diseases (e.g., Alzheimer's disease). This molecular farming
approach led to highest protein production of hydroponically-grown
tobacco compared to other growth substrates generally used
in plant cultivation.
[Back to top]
[Purchase
Article] [PMID:
19995338 PubMed - indexed for MEDLINE]
Homology Modeling Studies of Yeast Mitogen-Activated
Protein Kinases (MAPKS): Structural Motifs as a Basis for
Specificity
D.L. Smith and S.H. Nilar
Mitogen-activated protein kinases (MAPKs) are
key components of cellular signal transduction. It is the
objective of this communication to demonstrate that insight
into protein-protein interactions in the Common Docking motif
of yeast mitogen-activated protein kinases can be obtained
based on homology models. Homology models for four yeast MAPKs,
FUS3, KSS1, HOG1 and MPK1 were built based on the X-ray structures
of active and inactive rat ERK2. The structural motifs required
for the basis of specificity were rationalized based on these
structures.
[Back to top]
[Purchase
Article] [PMID:
19995337 PubMed - indexed for MEDLINE]
Isothermal Calorimetry Study of the Interactions of Type I
Antifreeze Proteins with a Lipid Model Membrane
H. Kun and Y. Mastai
In this paper, we report our study of thermodynamic
parameters of the interactions of antifreeze proteins (AFP)
type I and it short segments with DMPC unilamellar vesicles
as model for cell membrane. The heat of interactions between
AFP's and the model cell membrane were studied by Isothermal
Titration Calorimetry (ITC) at temperatures above and below
phase transition temperatures of the membrane. It is shown
that heat of interactions is linearly dependent on the temperatures
below the phase transition of the membrane and constant at
temperatures above phase. The heat of interaction above phase
transition is assigned to the interaction of the AFP with
the membrane, while below phase transition the ordering effect
of the AFP influence the heat of interaction.
[Back to top]
[Purchase
Article] [PMID:
19995335 PubMed - indexed for MEDLINE]
Effects of Cisplatin Binding to DNA
on the Dynamics of the E. coli MutS Dimer
F.R. Salsbury Jr.
MSH proteins are capable of recognizing damage
in DNA due to a common chemotheraputic, cisplatin, and consequently
participate in the initiation of cell death pathways. While
previous studies have used computational modeling and cell
biology to demonstrate that there are specific structural
responses to cisplatin damage that are critical to the initiation
of apoptosis, this study demonstrates that there are also
specific dynamical changes that are also associated with cisplatin
binding. These changes further distinguish the undamaged MutS/DNA
complex from the damaged MutS/DNA complex and suggest that
there are dynamical aspects to the response of MSH proteins
to the binding of DNA damaged by therapeutics; consideration
of these responses may influence further drug design and development.
[Back to top]
[Purchase
Article] [PMID:
20015024 PubMed - indexed for MEDLINE]
Importance of a Potential Salt Bridge
and Hydrophobic Core in the Function and Oligomerization of
a Small Heat Shock Protein
Z. Wen, Y. Wang, X. Xu, B. Yang, W. Li and M.
Xie
SsHSP14.1, a novel sHSP from the hyper-thermophilic
archaeon Sulfolobus solfataricus (S. solfataricus),
is reported herein to function to protect EcoR I
from heat-induced inactivation. A predicted salt bridge and
hydrophobic interactions were found to be important for this
function.
[Back to top]
[Purchase
Article] [PMID:
20397969 PubMed - indexed for MEDLINE]
Molecular Modeling Studies of the Conserved B12-Binding
Motif and Its Variants from Clostridium tetanomorphum
Glutamate Mutase
C.-H. Hsu and H.-P. Chen
The coupling of an aspartate residue with an
active site histidine plays a pivotal role in enzyme catalysis.
The His-Asp pair in glutamate mutase and other B12-dependent
mutases is not only responsible for coenzyme-binding, but
is also involved in fine-tuning the enzymatic activities.
Our modeling results show that the His-Asp pair is arranged
in a highly organized manner. Except for carboxymethylated
Cys or Glu, a less hindered or non-charged amino acid residue
is preferred between the conserved histidine and aspartate
residue.
[Back to top]
[Purchase
Article] [PMID:
20205657 PubMed - indexed for MEDLINE]
Development of Tools and Database for
Analysis of Metal Binding Sites in Protein
B.K. Kuntal, P. Aparoy and P. Reddanna
In this study, we have developed a standalone tool called
as ANAMBS (Analysis of Metal Binding Site) to derive metal
neighbourhood information using PERL as the programming language.
The tool accepts the structures in the pdb format. The cut
off distance to define the metal binding region can be specified.
The metal binding site composition, orientation of various
amino acids and atoms along with the Hydropathy index within
the metal binding site region can be measured. Its speed and
efficiency makes it a beneficial tool for various structural
biology projects, especially when the characterization of
the metal binding domain is needed. Additionally, the database
MEDB (Metal Environment Database) was developed which presents
quantitative information on metal-binding sites in protein
structures. It can be used for identification of trends or
patterns in the metal-binding sites. The information obtained
can be used to generate structural templates from metal binding
sites of known enzymes and to develop constraints for computational
modeling of metalloproteins. The tool and database are available
at http://www.uohyd.ernet.in/anambs/
[Back to top]
[Purchase
Article] [PMID:
20044923 PubMed - indexed for MEDLINE]
Antibodies Against Recombinant Shiga
Toxin Subunit B Neutralize Shiga Toxin Toxicity in HeLa Cells
P. Gupta, M.K. Singh, P. Singh, M. Tiwari and
R.K. Dhaked
Shigella dysenteriae type 1 and Escherichia coli
O157:H7 produce Shiga toxin (Stx) and Shiga toxin (Stx1),
respectively and these two toxins are almost identical. E.
coli O157:H7 is the major cause of diarrhea-associated
hemolytic uremic syndrome. Stx and Stx1 are AB5 type of toxin
with a molecular weight of 70 kDa, comprising an enzymaticaly-active
A subunit (32 kDa) and five receptor-binding B subunits (7.7
kDa). In this study DNA fragment (289 bp, Gene Bank Accn No.
EF685161) coding for B chain of Stx was amplified from
S. dysenteriae type1 and cloned. Shiga toxin-binding
subunit was expressed and purified in native conditions by
affinity and gel permeation chromatography with the yield
of 5.1 mg/L in shake flask culture. For the purpose of immunization,
the polypeptide was polymerized with glutaraldehyde. Hyper
immune serum produced in mice reacted with the purified polypeptide
and intact Shiga toxin. The anti-StxB antiserum effectively
neutralized the cytotoxicity of Shiga toxin towards HeLa cells.
[Back to top]
[Purchase
Article] [PMID:
20044920 PubMed - indexed for MEDLINE]
A Storage Protein-Like Trypsin Inhibitor
from the Moth Bean (Phaseolus acutifolius)
with Antiproliferative Activity Toward
Lymphoma Cells
D.Z. Ma, J. Sun, G.Q. Zhang, H.X. Wang and
T.B. Ng
A 26-kDa trypsin inhibitor with an N-terminal
sequence resembling storage proteins was purified from moth
beans (Phaseolus acutifolius). It dose-dependently inhibited
trypsin with an IC50 value
of about 0.38 μM.
It inhibited [methyl-3H]
thymidine incorporation by lymphoma MBL2 cells with an IC50
value of 20 μM.
[Back to top]
[Purchase
Article] [PMID:
19995340 PubMed - indexed for MEDLINE]
Gene Ontology-Based Protein Function
Prediction by Using Sequence Composition Information
Q. Dong, S. Zhou, L. Deng and J. Guan
The prediction of protein function is a difficult and
important problem in computational biology. In this study,
an efficient method is presented to predict protein function
with sequence composition information. Four kinds of basic
building blocks of protein sequences are investigated, including
N-grams, binary profiles, PFAM domains and InterPro domains.
The protein sequences are mapped into high-dimensional vectors
by using the occurrence frequencies of each kind of building
blocks. The resulting vectors are then taken as input to support
vector machine to predict their function based on gene ontology.
Experiments are conducted over the subset of GOA database.
The experimental results show that the protein function can
be predicted from primary sequence information. The method
based on InterPro domains outperforms the other building blocks,
and gets an overall accuracy of 0.87 and ROC score is 0.93.
We also demonstrate that the use of feature extraction algorithms
such as latent semantic analysis and nonnegative matrix factorization,
can efficiently remove noise and improve the prediction efficiency
without significantly degrading the performance. The results
obtained here are helpful for the prediction of protein function
by using only sequence information.
[Back to top]
[Purchase
Article] [PMID:
20205649 PubMed - indexed for MEDLINE]
Salt Effect on Substrate Specificity
of a Subtilisin-Like Halophilic Protease
D.N. Okamoto, M.Y. Kondo, K. Hiraga, M.A. Juliano, L.
Juliano, I.E. Gouvea and K. Oda
Enzyme-substrate interaction under the presence
of high concentration of salts is of great interest for biotechnology
applications and basic enzymology. In our previous work, the
salt effect on halophilic subtilase SR5-3 was evaluated with
Suc-AAPF-MCA and with the FRET peptide Abz-AAPFSSKQ-EDDnp.
It was demonstrated that the magnitude of catalytic activity
enhancement was affected by the presence of the prime site
residues. In this work, a detailed analysis of the salt effect
on SR5-3 protease substrate specificity was performed using
chromogenic and coumarin substrates as well as FRET peptides
derived from Abz-KLRSSKQ-EDDnp. The followings were demonstrated:
1) Preference of amino acid of SR5-3 protease at the P3,
P2, P1,
P1’ or P2’
position of FRET substrates was almost similar with that of
subtilisin. 2) Under the presence of the salts (3M NaCl or
1M Na2SO4),
SR5-3 protease showed higher kcat values, lower Km values
and totally 2-6 times higher kcat/Km values
compared with those of control for FRET substrates, and salts
did not significantly affect the preference of amino acid
residues at the primary positions (P1 and P1-), but it affected
the preference at the P2
and P2’ position. In
contrast, for smaller substrates with only non-prime sites,
SR5-3 protease showed 20-75 times higher kcat/Km
values compared with those of control. These findings are
in agreement with the notion that increases in enzyme-substrate
interactions in subtilases alter the rate-determining step
in peptide hydrolysis.
[Back to top]
[Purchase
Article] [PMID:
20044921 PubMed - indexed for MEDLINE]
Cloning and Characterization of an Exo-Xylogucanase
from Rumenal Microbial Metagenome
D.D.W.S. Wong, V.J. Chan, A.A. McCormack and
S.B. Batt
A novel exo-glucanase gene (xeg5B)
was isolated from a rumenal microbial metagenome, cloned,
and expressed in E. coli. The 1548 bp gene coded
for a protein of 516 amino acids, which assumed an (α/β)8
fold typical of glycoside hydrolase (GH) family 5. The protein
molecule consisted of a loop segment blocking one end of the
active site, which potentially provided the enzyme with exo-acting
property. The recombinant enzyme showed exclusive specificity
towards xyloglucan and oligoxyloglucan substrates with no
detectable activity on unsubstituted linear glucans, CMC,
laminarin, and lichenan. The major end products of exhaustive
hydrolysis were XX (tetrasaccharide) and XG (trisaccharide).
The hydrolysis of tamarind xyloglucan followed the Michaelis-Menten
kinetics, yielding Km
and Vmax of 2.12±0.13
mg/ml and 0.17±0.01 mg/ml/min (37°C,
pH 6.0), respectivel.
|
