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Protein & Peptide Letters
ISSN: 0929-8665
Protein & Peptide Letters
Volume 14, Number 7, 2007
Contents
Protein Peptide Informatics and Drug Designing –
Some Computational Techniques for Structural Genomics Based
Approaches (Part II)
Guest Editor: Rajani R. Joshi
Editorial Pp. 625
R.R. Joshi
PEPstr: A de novo Method for Tertiary
Structure Prediction of Small Bioactive Peptides
Pp. 626-631
H. Kaur, A. Garg and G.P.S. Raghava
[Abstract]
ParDOCK: An All Atom Energy Based Monte Carlo Docking
Protocol for Protein-Ligand Complexes Pp. 632-646
A. Gupta, A. Gandhimathi, P. Sharma and B. Jayaram
[Abstract]
An Alignment-Free Method for Classification of Protein
Sequences Pp. 647-657
S. Deshmukh, S. Khaitan, D. Das, M. Gupta and P.P. Wangikar
[Abstract]
Protein Structure Classification Using Geometric Invariants
and Dynamic Programming Pp. 658-664
A. Dalal, S. Deshmukh and P.P. Wangikar
[Abstract]
Conformational Angles Database (CADB-3.0)
Pp. 665-668
K. Gopalakrishnan, S.S. Sheik, C.V. Ranjani, A. Udayakumar
and K. Sekar
[Abstract]
Ramachandran Plot on the Web (2.0) Pp. 669-671
K. Gopalakrishnan, G. Sowmiya, S.S. Sheik and K. Sekar
[Abstract]
Structural Compromise of Disallowed Conformations
in Peptide and Protein Structures Pp. 672-682
C. Ramakrishnan, B. Lakshmi, A. Kurien, D. Devipriya and
N. Srinivasan
[Abstract]
Scanning the Genome of Mycobacterium tuberculosis
to Identify Potential Lectins Pp. 683-691
D.D. Singh, D. Chandran, J. Jeyakani and N. Chandra
[Abstract]
Identification and Analysis of Novel Amino Acid Sequence
Repeats and Domains in Pyrobaculum aerophilum Using
Computational Tools Pp. 692-697
G. Hemalatha, I.K. Kishore, R.S. Rao and L. Guruprasad
[Abstract]
General Articles
Preliminary X-Ray Crystallographic Studies of a Lys49
Phospholipase A2 Homologue
from Bothrops pirajai Venom Complexed with p-Bromo-phenacyl
Bromide and α
Tocopherol Inhibitors Pp. 698-701
J.I. dos Santos, D.P. Marchi-Salvador, C.A.H. Fernandes,
L.B. Silveira, A.M. Soares and M.R.M. Fontes
[Abstract]
Insulin-Releasing Properties of the Temporin Family
of Antimicrobial Peptides Pp. 702-707
Y.H.A. Abdel-Wahab, L. Marenah, P.R Flatt and J.M. Conlon
[Abstract]
Serum Leptin, Insulin-Like Growth Factor-I Components
and Sex Hormone Binding Globulin: Relationship with Sex, Age,
and Body Composition in Healthy Population Pp. 708-711
J.-M. Gómez
[Abstract]
Ultrasensitive Staining-Free Protein Detection After
PAA Gel Electrophoresis Using Deep UV Fluorescence
Pp. 712-715
E. Riaplov, Q. Li and S. Seeger
[Abstract]
Radical Damage Involving Sulfur-Containing Enzymes
and Membrane Lipids Pp. 716-722
A. Torreggiani, M. Tamba and C. Ferreri
[Abstract]
Recent Developments in the Understanding of Nuclear
Protein Import Pp. 723-733
S.M. Liu and W.M. Liu
[Abstract]
A Surface Immobilization Method of Endoglucanase from
Cellulomonas biazotea Mutant Improved Catalytic Properties
of Biocatalyst During Processing Pp. 734-741
M.I. Rajoka, Y. Zia and Khalil-ur-Rehman
[Abstract]
Abstracts
[Back to top]
Editorial
R.R. Joshi
This is the second and concluding part of the special
issue of “Protein Peptide Letters” which presents
some state-of-the art contributions in multi-dimensional research
at the interface of Protein Peptide Informatics and Drug Designing.
The first part focused at specific experimental and computational
studies on Protein Kinases, GRPs, and peptide based vaccine
designs and structural-binding properties of several drug
targets in Plasmodium falciparum, HIV-I and Japanese
Encephalitis Virus.
This issue presents some novel algorithms, computational techniques,
servers, softwares and databases providing wider applications
in Structure Based Drug Design (SBDD) and related issues in
Genomics and Proteomics.
Drug development research in the past decades has focused
on the enzyme-binding-pocket model of drug targets. Advances
headed towards peptide and gene based rational drug and vaccine
designs now require knowledge of the structural biology of
the target, co-receptor and inhibitor molecules. The ab-initio
method (PEPstr) and corresponding web-server developed
by H. Kaur, A. Garg and G. P. S. Raghava for prediction of
tertiary structure of small bioactive peptides makes a useful
contribution in this context.
Prediction and analysis of the binding interactions of the
drug with the receptor (target) molecules is crucial in drug
designing projects. Computational methods based on surface
complementarity and stereochemistry are widely used for this
purpose to enable docking of protein - protein and protein
- ligands. However, modifications in the existing docking
algorithms are often required in deciphering the stochastic
interactions that account for diversity and affinity in surface-complementarity.
The all-atom based Monte Carlo method and useful application
software named ParDOCK developed by Prof. B. Jayaram’s
research group in the supercomputing lab at IIT Delhi is an
important contribution in this regard. The paper by A. Gupta,
A. Gandhimathi, P. Sharma and B. Jayaram presents this procedure
with validation results and applications.
The applications and scope of gene and protein data banks
in next generation research and development in Medical Biotechnology
and Pharmacology are remarkable. Multiple sequence alignment
and homology modeling have no doubt made the major chunk of
harvesting the fruits of knowledge from the ever-expanding
databases of experimental data on the Internet. However these
data-mining techniques are not limitation-free to meet the
challenges of Nature. The innovative approach of alignment-free
classification of protein sequences presented in the paper
by S. Deshmukh, S. Khaitan, D. Das, M. Gupta and P. P. Wangikar
provides a distinct alternative with significant scope.
Dr. Wangikar’s research group had recently reported
a new method of classifying protein structure using geometrically
invariant structural patterns. Extended application of this
algorithm together with dynamic programming, as reported in
his paper with A. Dalal and S. Deshmukh, provides an efficient
method for protein structure alignment. This method is found
to reduce the computational time by 30 to 60 times as compared
to the execution time of the conventional methods for average
sized protein chains.
Two useful contributions to protein structure modeling, analysis
or comparison of specific structural attributes are made by
Dr. Sekar’s group, viz – (i) comprehensive data
base (CADB-3.0) of conformation angles of known protein structures
(ii) advanced web server for online display of Ramchandran
Plot of the confirmation angles of the polypeptide chain of
a protein with demarcation of secondary structural elements
and regions within any given set or range of values of these
angels. Applications illustrated in the corresponding papers
– (i) by K. Gopalakrishnan, S. S. Sheik, C. Vasuki Ranjani,
A. Udayakumar and K. Sekar; and (ii) K. Gopalakrishnan, G.
Sowmiya, S. S. Sheik and K. Sekar – include targets
of certain drugs.
C. Ramakrishnan, B. Lakshmi, A. Kurien, D. Devipriya and Dr.
N. Srinivasan have analyzed the presence of conformational
angles (Φ,
φ)
in non-redundant, high resolution crystal structures of proteins
and peptides focusing on those ranges of pair of these angles
that are disallowed in the Ramchandran plots. Their results
give new insight into the inter-atomic bonds and structural
conformation. Application of this study in identifying occurrences
of disallowed Ramchandran angles in the linker regions or
flexible activity pockets would offer new directions to drug
designing.
D.D. Singh, D. Chandran, Justin J. and Dr. Nagasuma C. demonstrate
an interesting application of web-tools and bioinformatics
techniques in genome annotation. In particular they have identified
several lectins by scanning the genome (of H37Rv) of Mycobacterium
tubercular. Their result offers useful clues for molecular
mapping of pathogenesis of the complex bacterium. The lectins
traced here may also serve as potential targets for anti-tuberculosis
therapy.
G. Hemalatha, I. K. Kishore, R. S. Rao and Dr. L. Guruprasad
present in-silico identification of conserved sequential patterns
in proteins encoded by the Pyrobaculum aerophilum
proteome. Occurrence of similar patterns and corresponding
secondary structural folds and domains in proteins translated
by other genomes is also discussed. Such research findings
offer potential application in gene-based peptide drug research
via annotation of genomes with respect to activity pockets
in protein domains characterized by specific structural motifs.
Rajani R. Joshi
Guest Editor
Protein & Peptide Letters
Professor, Department of Mathematics and
Associated Faculty (as Professor), School of Bioscience &
Bioengineering
Indian Institute of Technology Bombay, Powai
Mumbai 400076
India
Email: rrj@math.iitb.ac.in
[Back to top]
PEPstr: A de novo Method for Tertiary
Structure Prediction of Small Bioactive Peptides
H. Kaur, A. Garg and G.P.S. Raghava
Among secondary structure elements, β-turns
are ubiquitous and major feature of bioactive peptides. We
analyzed 77 biologically active peptides with length varying
from 9 to 20 residues. Out of 77 peptides, 58 peptides were
found to contain at least one β-turn.
Further, at the residue level, 34.9% of total peptide residues
were found to be in β-turns,
higher than the number of helical (32.3%) and β-sheet
residues (6.9%). So, we utilized the predicted β-turns
information to develop an improved method for predicting the
three-dimensional (3D) structure of small peptides. In principle,
we built four different structural models for each peptide.
The first ‘model I’ was built by assigning all
the peptide residues an extended conformation (Φ
= Ψ
= 180o). Second ‘model
II’ was built using the information of regular secondary
structures (helices, β-strands
and coil) predicted from PSIPRED. In third ‘model III’,
secondary structure information including β-turn
types predicted from BetaTurns method was used. The fourth
‘model IV’ had main-chain Φ,
Ψ angles
of model III and side chain angles assigned using standard
Dunbrack backbone dependent rotamer library. These models
were further refined using AMBER package and the resultant
Cα
rmsd values were calculated. It was found
that adding the β-turns
to the regular secondary structures greatly reduces the rmsd
values both before and after the energy minimization. Hence,
the results indicate that regular and irregular secondary
structures, particularly β-turns
information can provide valuable and vital information in
the tertiary structure prediction of small bioactive peptides.
Based on the above study, a web server PEPstr (http://www.imtech.res.in/raghava/pepstr/)
was developed for predicting the tertiary structure of small
bioactive peptides.
[Back to top]
ParDOCK: An All Atom Energy Based Monte Carlo Docking
Protocol for Protein-Ligand Complexes
A. Gupta, A. Gandhimathi, P. Sharma and B. Jayaram
We report here an all-atom energy based Monte Carlo docking
procedure tested on a dataset of 226 protein-ligand complexes.
Average root mean square deviation (RMSD) from crystal conformation
was observed to be ~ 0.53 Å. The correlation coefficient
(r2) for the predicted binding
free energies calculated using the docked structures against
experimental binding affinities was 0.72. The docking protocol
is web-enabled as a free software at www.scfbioiitd.res.in/dock.
[Back to top]
An Alignment-Free Method for Classification of Protein
Sequences
S. Deshmukh, S. Khaitan, D. Das, M. Gupta and P.P. Wangikar
Protein sequences vary in their length and are not readily
amenable to conventional data mining techniques that need
mapping in a fixed dimensional space. Thus, majority of the
current methods for protein sequence classification are based
on alignment of the query sequence either with a sequence
or a profile of the sequence family. We present a method for
mapping of protein sequences in a fixed dimensional descriptor
space. The descriptors such as amino acid content and amino
acid pair association rules were used along with routinely
available classification methods. An experiment on one hundred
Pfam families showed classification accuracy of 98% with support
vector machines classifier. Information gain based feature
selection helped simplify the model and improve accuracy.
Interestingly, a large number of the selected features were
based on the association rules of Glycine or Aspartic acid
residues suggesting their role in the conserved loops among
evolutionarily related proteins. Further, in another experiment,
the approach was tested for classification of proteins from
39 Pfam families of protein kinases. Support vector machines
classifier provided an accuracy of approximately 96%. The
method provides an alternative to conventional profile based
methods for protein sequence classification.
[Back to top]
Protein Structure Classification Using Geometric Invariants
and Dynamic Programming
A. Dalal, S. Deshmukh and P.P. Wangikar
Classification of newly determined protein structures is important
in understanding their function and mechanism of action. Currently
available methods employ a global structure alignment strategy
and are computationally expensive. We propose a two-step methodology
with a quick screen to significantly reduce the number of
candidate structures followed by global structure alignment
of the query structure with the reduced set. We represent
a protein structure as a sequence of local structures, codified
in the form of geometric invariants. Geometric invariants
are quantities that remain unchanged under transformations
such as translation and rotation. Protein structures represented
as multi-attribute sequences are aligned via dynamic programming
to identify close neighbors of the query structure. The query
structure is then compared with this reduced dataset using
conventional structure comparison methods to predict its functional
class. For a typical protein structure, the screening method
was able to reduce the protein data bank to mere 200 proteins
while preserving structurally closest neighbor in the reduced
set. This has resulted in 30 to 60 fold improvement in the
execution time. We present the results of leave-one-out classification
experiment on ASTRAL-95 domains and comparison with SCOP classification
hierarchy.
[Back to top]
Conformational Angles Database (CADB-3.0)
K. Gopalakrishnan, S.S. Sheik, C.V. Ranjani, A. Udayakumar
and K. Sekar
Transitions in amino-acid conformation angles tend to accompany
various structural modifications in protein structures. Thus,
to benefit the modeling of protein structures, the Conformation
Angles DataBase (CADB-3.0) has been updated to visualize the
conformational angles in varied regions (fully, generously,
additionally and disallowed regions). In addition, options
are provided to display the angles in the secondary structural
elements (α-helix,
β-sheet
and 310-helix) of the Ramachandran
plot. The database is being updated periodically and can be
accessed over the World Wide Web at the following URL: http://cluster.physics.iisc.ernet.in/cadb/.
[Back to top]
Ramachandran Plot on the Web (2.0)
K. Gopalakrishnan, G. Sowmiya, S.S. Sheik and K. Sekar
The Ramachandran plot displays the main chain conformation
angles (Φ
and Ψ)
of the polypeptide chain of a protein molecule. The paper
reports the updated version of the Ramachandran plot web server
and has several improved options for displaying the conformation
angles in various regions. In addition, options are provided
to display the conformation angles in various secondary structural
elements and regions within the user specified Φ
and Ψ
values in the plot. The updated version is accessible at the
following URL: http://dicsoft1.physics.iisc.ernet.in/rp/
[Back to top]
Structural Compromise of Disallowed Conformations
in Peptide and Protein Structures
C. Ramakrishnan, B. Lakshmi, A. Kurien, D. Devipriya and
N. Srinivasan
Using a data set of 454 crystal structures of peptides and
80 crystal structures of non-homologous proteins solved at
ultra high resolution of 1.2 Å or better we have analyzed
the occurrence of disallowed Ramachandran (Φ,
Ψ)
angles. Out of 1492 and 13508 non-glycyl residues in peptides
and proteins respectively 12 and 76 residues in the two datasets
adopt clearly disallowed combinations of Ramachandran angles.
These examples include a number of conformational points which
are far away from any of the allowed regions in the Ramachandran
map. According to the Ramachandran map a given (Φ,
Ψ)
combination is considered disallowed when two non-bonded atoms
in a system of two-linked peptide units with ideal geometry
are prohibitively proximal in space. However, analysis of
the disallowed conformations in peptide and protein structures
reveals that none of the observations of disallowed conformations
in the crystal structures correspond to a short contact between
non-bonded atoms. A further analysis of deviations of bond
lengths and angles, from the ideal peptide geometry, at the
residue positions of disallowed conformations in the crystal
structures suggest that individual bond lengths and angles
are all within acceptable limits. Thus, it appears that the
rare tolerance of disallowed conformations is possible by
gentle and acceptable deviations in a number of bond lengths
and angles, from ideal geometry, over a series of bonds resulting
in a net gross effect of acceptable non-bonded inter-atomic
distances.
[Back to top]
Scanning the Genome of Mycobacterium tuberculosis
to Identify Potential Lectins
D.D. Singh, D. Chandran, J. Jeyakani and N. Chandra
Lectins are carbohydrate binding proteins with important roles
in many biological processes such as adhesion. Here we have
identified 11 potential lectins from Mycobacterium tuberculosis
H37Rv genome, using a comprehensive bioinformatics analysis,
which will provide helpful clues in molecular mapping of pathogenesis
and perhaps also serve as potential drug targets.
[Back to top]
Identification and Analysis of Novel Amino Acid Sequence
Repeats and Domains in Pyrobaculum aerophilum Using
Computational Tools
G. Hemalatha, I.K. Kishore, R.S. Rao and L. Guruprasad
We have identified four repeats and five domains that are
novel in proteins encoded by the Pyrobaculum aerophilum
str. IM2 proteome using automated in silico methods.
A “repeat” corresponds to a region comprising
less than 55 amino acid residues that occurs more than once
in the protein sequence and sometimes present in tandem. A
“domain” corresponds to a conserved region comprising
greater than 55 amino acid residues and may be present as
single or multiple copies in the protein sequence. These correspond
to (1) 85 amino acid residues AAG domain, (2) 72 amino acid
residues GFGN domain, (3) 43 amino acid residues KGG repeat,
(4) 25 amino acid residues RWE repeat, (5) 25 amino acid residues
RID repeat, (6) 108 amino acid residues NDFA domain, (7) 140
amino acid residues VxY domain, (8) 35 amino acid residues
LLPN repeat and (9) 98 amino acid residues GxY domain. A repeat
or domain is characterized by specific conserved sequence
motifs. We discuss the presence of these repeats and domains
in proteins from other genomes and their probable secondary
structure.
[Back to top]
Preliminary X-Ray Crystallographic Studies of a Lys49
Phospholipase A2 Homologue
from Bothrops pirajai Venom Complexed with p-Bromo-phenacyl
Bromide and α
Tocopherol Inhibitors
J.I. dos Santos, D.P. Marchi-Salvador, C.A.H. Fernandes,
L.B. Silveira, A.M. Soares and M.R.M. Fontes
PrTX-I, a non-catalytic and myotoxic Lys49-PLA2
from Bothrops pirajai venom has been crystallized alone and
in complex with bromophenacyl bromide (BPB), α
tocopherol and α
tocopherol acetate inhibitors. These crystals have shown to
diffract X-rays between 2.34 and 1.65 Å resolution.
All complexes crystals are isomorphous and belong to the space
group P21 whereas native
PrTX-I crystals belong to the P3121.
[Back to top]
Insulin-Releasing Properties of the Temporin Family
of Antimicrobial Peptides
Y.H.A. Abdel-Wahab, L. Marenah, P.R Flatt and J.M. Conlon
Temporin-1Vb, -1Oe, -1DRb, and -1TGb (10-8
- 10-6M) produced significant
(p<0.05) and concentration-dependent stimulatory effects
on insulin secretion from clonal rat BRIN-BD11 cells without
increased release of lactate dehydrogenase. Temporin-1Va and
temporin-1Vc (10-8 - 10-6M)
also stimulated insulin-release but were cytotoxic at 10-6M.
Temporin-1DRa was without effect. The temporins at 10-7
M had no effect on intracellular calcium concentrations suggesting
that they stimulate insulin release via a KATP channel- independent
pathway.
[Back to top]
Serum Leptin, Insulin-Like Growth Factor-I Components
and Sex Hormone Binding Globulin: Relationship with Sex, Age,
and Body Composition in Healthy Population
J.-M. Gómez
Leptin plays an important role in the regulation of food intake
and thermogenesis, regulates long term energy balance and
reproductive function and its concentrations are closely linked
to body mass index. Leptin secretion is influenced by many
factors and the age-related changes in different hormones
might modify circulating leptin concentrations. Sex dimorphism
in leptin concentrations has been clearly shown in previous
studies and its concentrations were lower in men than in women
in all decades of life. Insulin growth factor-I (IGF-I) is
a peptide growth factor that is present in all types of physiologic
fluids and is also produced by connective tissue cell types
and its autocrine/paracrine secretion is nearly always present
within tissues. There is a physiological decline of the growth
hormone (GH)/IGF-I axis with ageing and in addition, insulin,
thyroid hormones and the supply of dietary energy may directly
regulate the circulating levels of the IGFs and growth hormone
binding protein (GHBP). Furthermore, there is no doubt that
GH participates in the regulation of body composition, and
with advanced age there is a decrease in muscle and an increase
in adiposity associated with a decline in GH and total IGF-I.
The biological activities of the IGF ligands are modulated
by the family of high affinity GHBP. Sex hormone binding globulin
(SHBG) concentrations are thought to be regulated primarily
through opposing actions of sex steroids on hepatic SHBG production,
with oestrogen stimulating and androgen inhibiting SHBG production,
and thyroid hormones are also a potent stimulator of SHBG
production concentrations. Some studies support an independent
IGFBP3 contribution to SHBG variability and these findings
are compatible with the hypothesis that some of the anabolic
effects ascribed to the GH/IGF axis may be caused by SHBG-mediated
changes in testosterone activity or SHBG/total testosterone
index.
[Back to top]
Ultrasensitive Staining-Free Protein Detection After
PAA Gel Electrophoresis Using Deep UV Fluorescence
E. Riaplov, Q. Li and S. Seeger
We present the observation of separated protein bands after
polyacrylamide (PAA) gel electrophoresis based on the staining-free
detection of their ultra violet (UV)-induced fluorescence
employing deep UV confocal fluorescence microscopy. Mixtures
of the three biological compounds β-Galactosidase
(from Escherichia coli), apo-Transferrin (bovine)
and bovine serum albumin (BSA) have been separated and a staining
free detection limit below 80 pg (7.0×108
molecules) per band has been achieved. This corresponds to
~270 molecules in the detection volume for confocal microscopy.
[Back to top]
Radical Damage Involving Sulfur-Containing Enzymes
and Membrane Lipids
A. Torreggiani, M. Tamba and C. Ferreri
Free radicals induce protein modifications, often associated
to many biological phenomena. This mini-review overviews the
approaches we have used to elucidate the radical-induced damages
on sulfur-containing enzymes, such as ribonuclease and lysozyme,
and the possible post-translational mechanism of the damage
to another cell compartment, such as lipid domain.
[Back to top]
Recent Developments in the Understanding of Nuclear
Protein Import
S.M. Liu and W.M. Liu
The process of nucleocytoplasmic exchange of various macromolecules
and metabolites between the nuclear and cytoplasmic compartment
is crucial for cell function and survival. It is also closely
involved with several pathogeneses including cancer and viral
infections. Here, we will discuss the current understanding
of the classical nuclear import pathway and the factors that
are essential for this process.
[Back to top]
A Surface Immobilization Method of Endoglucanase from
Cellulomonas biazotea Mutant Improved Catalytic Properties
of Biocatalyst During Processing
M.I. Rajoka, Y. Zia and Khalil-ur-Rehman
Purified endoglucanase from C. biazotea mutant 51SMr
was successfully immobilized on Eudragit L-100, with 75 %
yield of immobilization. This method improved the kinetic
and thermodynamic properties of the enzyme. Immobilization
significantly decreased entropy and enthalpy of inactivation
of biocatalyst and made it functionally and thermodynamically
more stable and reusable compared to free one.
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