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Interaction pattern for the complex of B-DNAFullerene compounds with a set of known replication proteins using docking study

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Hypothesis
Volume 11(3)
ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 11(3): 122-126 (2015)
122
© 2015 Biomedical Informatics
Interaction pattern for the complex of B-DNA-
Fullerene compounds with a set of known
replication proteins using docking study
Sumbul Firdaus1, Anupam Dhasmana2, Vandana Srivastava2, Tasneem Bano2, Afreen Fatima2,
Qazi Mohammad Sajid Jamal3, Roshan Jahan3, Gulshan Wadhwad4 & Mohtashim Lohani3*
1Department of Physics, Integral University, Lucknow, India; 2Departments of Bioengineering, Integral University, Lucknow,
India; 3Departments of Biosciences, Integral University, Lucknow, India; 4Department of Biotechnology, Ministry of Science and
Technology, CGO complex, Lodhi Road, New Delhi-110003, India; Mohtashim Lohani Email: mlohani@rediffmail.com; Phone:
+91-522- 2890730, 2890812 (O) +91-9161984134 (Personal); Fax: +91-522- 2890809; *Corresponding author
Received January 21, 2015; Accepted February 23, 2015; Published March 31, 2015
Abs
tr
a
ct:
Fullerenes have attracted considerable attention due to their unique chemical structure and potential applications which has
opened wide venues for possible human exposure to various fullerene types. Therefore, in depth knowledge of how fullerene may
interfere with various cellular processes becomes quite imperative. The present study was designed to investigate how the
presence of fullerene affect the binding of DNA with different enzymes involved in replication process. Different fullerenes were
first docked with DNA and then binding scores of different enzymes was analyzed with fullerene docked DNA. C30, C40 & C50
once docked with DNA, reduced the binding score of primase, whereas no significant change in the binding score was observed
with the helicase, ssb protein, dna pol δ, dna pol ɛ, ligase, DNA clamp, and topoisomerases. On the contrast, the binding score of
RPA14 decreases in fluctuating manner while interacting with increasing molecular weight of fullerene bound single-stranded
DNA complex. The study revealed the affect of fullerene family interacting with DNA on the binding pattern of enzymes involved
in replication process. Study suggests that the presence of most of fullerenes may not affect the activity of these enzymes necessary
for replication process whereas C30, C40 & C50 may disrupt the activity of primase, (strating point for DNA polymerase) its
docking score decreases from 13820 to 10702.
Keywords: Fullerene, Fullerene family, RPA, replication enzymes.
B
a
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o
und
:
Nanotechnology, actually means the exploitation of the
substances at their nano-meter size, and is expected to enhance
the quality of life and economic development on the global
basis. A decade ago, nanoparticles were studied because of
their size-dependent physical and chemical properties, but now
they have crossed the threshold of commercial exploration
period. Understanding of biological processes on the nanoscale
level is a strong driving force behind development of
nanotechnology [1]. Out of surplus of size-dependant physical
properties of nanomaterials like optical and magnetic effects
have been exploited for a number of biological/medical
applications, e.g.: their use as fluorescent biological labels for
the drug and gene delivery, Probing of DNA structure, for the
treatment of cancer, for the separation and purification of
biological molecules and cells etc.. These unlimited advantages
of nanoparticles lead to thier mass-production, making the
exposure of almost enevitable. The human exposure to these
nanoparticles raises concern about their potential risk to human
health. Nanoparticles could easily enter the body through the
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food or water we consume, both accidently or intentionally via
nose and lungs just like other aerosols. Some nanoparticles
readily travel throughout the body, deposit in target organs,
penetrate cell membranes, lodge in mitochondria, and may
trigger injurious responses. As related research on smoking's
effects on lung tissue has found, foreign particles inhaled into
the lungs have the potential to do great damage [2]. Earlier
studies revealed that inhaled nanoparticles not only cause lung
damage, but also can move into the bloodstream; potentially
causing cardiac damage and other observations indicate that
inhaled nanoparticles in humans caused damage both to the
point of entry, and to the brain itself. There are some special
kinds of nanoparticles made up of carbon are termed as
fullerenes which occur naturally in the form of C20, C60, C70,
C82, molecules whereas C24, C30, C40 etc can be produced by
various industrial processes. Because of small size and easy
entry into the human body, they get readily adsorbed to
macromolecules affecting the regulatory mechanism of
macromolecules, proteins and genetic materials.
A number of in vitro as well as in vivo studies have proven that
these nanomaterials are also capable of inducing DNA damages
[3, 4 & 5]. C60 and its derivatives were reported to inhibit the
replication of simian immunodeficiency virus (SIV) in vitro and
the activity of Moloney murine leukaemia virus (M-MuLV)
reverse transcriptase [6]. Large numbers of researches are being
done on DNA replication and causes of mutations, checkpoint
control and also on the enzymes involved in replication process
[7, 8 & 9]. Simulation studies conducted earlier revealed that
C60 strongly binds to nucleotides in aqueous solution at the
hydrophobic ends or at the minor groove of the nucleotide [10].
This C60-ssDNA binding can significantly deform the
nucleotides. Some studies revealed CNP -DNA binding leading
to DNA aggregation in vivo and in vitro [11] .The binding
mechanism of water-soluble C60 derivative-ss-DNA was found
to be similar to native C60DNA, while forming more stable
C60DNA complex. Molecular dynamics study reveals the
distortion of DNA/RNA by the fullerene [12]. It has been
already reported that C60 can binds to DNA via hydrophobic
interactions in silico. Some in vitro studies are also done to
investigate the toxicity mechanism of C60 in biological system
show that C60 molecules may interfere with the biological
functions performed by DNA, resulting in disruptions to DNA
replication, transcription and repair processes [13]. More
studies are needed to establish the interactions of fullerenes
with the molecular machineries and processes and how these
interactions may affect various biological functions. In depth
studies are required to investigate the interference of fullerenes
in DNA replication machinery, how fullerene bound DNA is
interacts with the enzymes involved in replication process etc.
Here, we propose the application of in-silico approach to
investigate the interaction of enzymes involved in DNA
replication process with fullerene (C20 to C180) bound DNA.
Methodology:
In one set of investigation, the docking scores of DNA with
eight different enzymes involved in replication process were
determined. Further, the docking score of eight enzymes were
determined with the fullerene (C20 to C180) bound DNA
complexes. The two sets were compared to determine the effect
of fullerene on the binding of enzymes with DNA.
Generation and procurement of macromolecules
Double stranded & single stranded DNA structures were
constructed using Discovery Studio Visualizer (Version 2.5.5).
And the structures of enzymes involved in the DNA
Replication process were obtained from RCSB Protein Data
Bank. Published structures were edited to remove HETATM
using Discovery Studio Visualizer (Version 2.5.5). Chimera was
used for energy minimization, removal of steric collision with
the steepest descent steps 1000, steepest descent size 0.02 Å,
Conjugated gradient steps 1000 and the conjugate gradient step
size 0.02 Å for the conjugate gradient minimization [14, 15].
Procurement of fullerene family
Nanotube Modeller is a program for generating XYZ co-
ordinates of nano geometries (nanocone, nanotube, fullerenes,
viruses etc.). Fullerenes of various molecular sizes were
obtained through fullerene library of Nanotube Modeller.
Generated geometries of C20, C30, C40, C50, C60, C70, C80,
C90, and C100 & C180 were viewed using the integrated
viewer.
Molecular Docking Studies
All the in silico docking analyses were performed using
PatchDock (Schneidman et al, 2005) [16]. The fullerenes were
docked with the DNA. The resultant pdb file obtained after
fullerenes and DNA docking was used as fullerene-DNA
complex, and was docked with different enzymes along with
some replication factors involved in the replication process of
DNA by uploading them as a receptor and ligand molecules in
PatchDock Server, an automatic server for molecular docking.
Clustering RMSD was chosen as 4.0Å.
Figure 1: Presence of some fullerene molecules affects the
binding of Primase and RPA14 1(a): shows the interaction of
primase with c30 bound DNA, 1(b): shows the interaction of
primase with c40 bound DNA, 1(c): shows the interaction of
primase with c50 bound DNA, 1(d): shows the interaction of
RPA14 with c30 bound ss-DNA, 1(e): shows the interaction of
RPA14 with c70 bound ss-DNA.
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Results:
Fullerenes of various molecular weights (c20, c30, c40, c50, c60,
c70, c80, c90, c100, c180) were separately docked with DNA to
form fullerene-DNA complex. Docking score ranged from
2062(C20) to 3888(C180). Further, fullerene-DNA complexes
were used as a receptor and enzymes involved in replication
process as a ligand to show the effects of fullerenes on the DNA
replication process. Each of the eight enzymes was docked with
the different forms of fullerene-DNA complex. Then, each of
these enzymes involved in replication process were separately
docked with DNA alone i.e. in the absence of fullerene. And
their docking scores were compared and analyzed to
investigate the effect of presence of fullerene. Analysis of all the
docking results revealed that c30, c40 and c50 may affects the
activity of Primase as the docking score of primase with B-DNA
is 13820, but the docking score of primase with B-DNA-C30,
BDNA-C40, BDNA-C50 complexes are 10702, 11734 & 11270
respectively (Figure1).
Apart from the enzymes, replication proteins A (RPA14, RPA32
& RPA70) were docked with single-stranded DNA alone then
with the fullerene bound ssDNA in order to analyse the affect
of of fullerene. Figure 2 Graph 1 showed the docking result
which explains that the presence of fullerene caused
considerable reduction in the docking score of RPA14, whereas
RPA32 & RPA70 binding score increased in the presence of
fullerene. Docking score of RPA14 with ssDNA is11170
whereas the docking score decreases when RPA14 interact with
fullerene bound ssDNA, ranged from 10116(ssDNA-C20) to
10284(ssDNA-C180). All these scores are shown in Table 1 (see
supplementary material).
Figure 2: Graph shows functional loss analysis in expressions of
docking score of B-DNA in the presence of fullerene with
enzymes and factors involved in replication machinery.
Discussion:
Buckminsterfullerene (C (60)) has received great research
interest due to its extraordinary properties and increasing
applications in manufacturing industry and biomedical
technology. AN H et al. [17] recently reported C (60) could enter
bacterial cells and bind to DNA molecules and determine how
the DNA-C60 binding affected the thermal stability and
enzymatic digestion of DNA molecules, and DNA mutations.
Some in vitro studies have also been done to investigate the
toxicity mechanism of C60 in biological system show that C60
molecules may interfere with the biological functions
performed by DNA, resulting in disruptions to DNA
replication, transcription, and repair processes [18]. More
studies are needed to reveal the interactions of various species
of fullerenes with enzymes involved in DNA processes, and
how this interaction may affect the biological functions.
However to the best of our knowledge no such study has been
done involving fullerene and fullerene family interaction with
all the enzymes of eukaryotic DNA replication process.
Therefore, the present study was designed to reveal the effect of
molecular weight and size of fullerene on its capacity to interact
with different enzymes of DNA replication.
We have previously shown the applicability of PatchDock to
determine interaction between nanoparticles and biomolecules
[19]. In the present study, we performed molecular docking
between various enzymes & factors involved in replication with
the DNA bound with fullerene molecule of different sizes (C20
to C180) separately in order to evaluate the effect of fullerene
on the binding receptor of enzymes with DNA. Docking score
of DNA-enzyme complexes were compared with the fullerene
bound DNA- enzyme complexes, which reveals that most of
the enzymes activity were not affected by the presence of
fullerene. Docking score of only Primase and RPA14 decreased
when they interacts with the fullerene-DNA complex in
comparison to the score when they were interacted directly
with the DNA. So this decrease in the score may be considered
because of the presence of fullerene and in-vitro and in vivo
studies are needed to conclude that the presence of fullerene
may hamper the activity of enzymes during replication process
of DNA. All these enzymes are having their specific function;
involvement of fullerene may affect its functionality. Previous
studies have shown that the nanoparticle was found to bind
with the minor grooves of double-stranded DNA and trigger
unwinding and disrupting of the DNA helix, which indicates
C60 can potentially inhibit the DNA replication and induce
potential side effects and it has been proved that
pristine fullerene nanoparticles are capable of adsorbing
polymerase and significantly inhibiting its biologically
important replication activity; however, the inhibition can be
partially mitigated by abundant proteins through competitive
binding [20]. Zhao et.al work theoretically to show how C60
binds to and deforms a DNA fragment suggesting the potential
for C60 molecules to disrupt the replication and repair of DNA
[10]. The DNA-C60 complexes depend on the nature of the
nucleotide. Yong Liang et.al, shows that that C60 can disrupt
DNA replication in vitro by binding to DNA and changing the
conformation of DNA templates.
Our finding suggests that activity of primase might be affected
by C30, C40 & C50 fullerene-DNA complex. Interaction shows
significant decrease in their docking score such as c30, 40, 50-
DNA complexes with Primase (Figure 1). Primase provides a
starting point of RNA (or DNA) for DNA polymerase to begin
synthesis of the new DNA strand but the presence of fullerene
may hamper the replication at the starting point itself. Whereas
interaction of fullerene with other enzymes showed, no
significant change in the docking scores. But the interaction of
replication factor RPA14 with ssDNA-fullerene complex shows
significant decrease in the docking score from 11170 to10284
shown in Table 1 (see supplementary material). As the
Replication protein A ( RPA) binds with high affinity to ssDNA
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© 2015 Biomedical Informatics
that is formed transiently during DNA replication,
recombination and repair, protecting it from nucleases, and
destabilizing unwanted secondary structures (e.g., hairpins
and G-quadruplexes) but the decrease in binding score is due to
fullerene presence which may affect the proper functioning of
these particular enzymes, necessary for replication process;
suggesting that defect in DNA replication may be the source of
this damage.
Conclusion:
Primase provides a starting point of RNA (or DNA) for DNA
polymerase to begin synthesis of the new DNA strand but this
activity of primase might be impaired by fullerene (C30, C40 &
C50). While the interaction of fullerenes with other enzymes
(helicases, ssb protein, dna pol δ, dna pol ɛ, ligase, DNA clamp,
and topoisomerases) do not show significant reduction in their
docking score. Apart from enzymes replication factor RPA14
when docked with ssDNA-fullerene complex shows significant
decrease in the docking score, which means RPA14 would not
able to destabilize unwanted secondary structures of ssDNA
and may leads to poor replication.
R
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14520400]
[2] Ryu JH et al. Eur Respir J. 2001 17: 122 [PMID: 11307741]
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[5] Srivastava RK et al. Hum Exp Toxicol. 2013 32: 153 [PMID:
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[6] Nacsa J et al. Fullerenes, Nanotubes and Carbon
Nanostructures. 1997 969976.
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[8] Das-Bradoo S & Bielinsky A, Nature Education. 2010 3: 50
[9] Pursell ZF & Kunkel TA, Prog Nucleic Acid Res Mol Biol.
2008 82: 101 [PMID: 18929140]
[10] Zhao X et al. Biophys J. 2005 89: 3856 [ PMID:16183879]
[11] An H et al. Biochem Biophys Res Commun. 2010 393: 571
[PMID: 20156419]
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Edited by P Kangueane
Citation: Firdaus et al. Bioinformation 11(3): 122-126 (2015)
License statement: This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited
open access
ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 11(3):122-126 (2015)
126
© 2015 Biomedical Informatics
Supplementary material:
Table 1: Functional loss analysis of activity of enzymes and factors involved in replication machinery when docking score/ binding
values of BDNA with enzymes and factors were compared in the presence and absence of fullerene molecule of different molecular
sizes.
S.NO.
Enzymes
Bdna
bdna-
c20
bdna-
c30
bdna-
c40
bdna-
c50
bdna-
c60
bdna-
c70
bdna-
c80
bdna-
c90
bdna-
c100
bdna-
c180
1.
Helicase
10170
13822
14368
15252
13478
10496
15254
15794
15720
14932
14794
2.
ssb protein
13764
13768
13580
12989
13550
13610
13632
13236
13178
12896
13876
3.
Primase
13820
13386
10702
11734
11270
14990
15102
15588
14050
14804
16570
4.
Dnapoldelta
12038
13038
12572
12876
12578
12764
12958
13678
13498
13470
13880
5.
dnapolepsilon
7674
7482
8010
8662
7804
8592
8302
8104
8504
8074
8676
6.
Ligase
14966
15526
15338
15610
14450
15108
15140
14874
15120
14916
16394
7.
DNA clamp
12218
12084
11832
12512
11706
11916
11688
11740
12328
14916
13094
8.
topoisomerase
17310
17730
17168
18924
17692
18884
18402
11740
17078
11428
19100
9.
RPA14*
11170
10116
9928
10182
10528
10020
9984
10278
10834
10186
10284
10.
RPA32*
8714
8268
9106
8330
8782
9274
9034
8726
8970
8874
8814
11.
RPA70*
9892
9990
9656
10048
9680
9582
10304
10724
11082
10156
9820
NOTE: “*” sign denotes replication factors interacting with singlestrand DNA, scores in red color denote major functional loss of
enzymes activity.
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Significant environmental and health risks due to the increasing applications of engineered nanoparticles in medical and industrial activities have been concerned by many communities. The interactions between nanomaterials and genomes have been poorly studied so far. This study examined interactions of DNA with carbon nanoparticles (CNP) using atomic force microscopy (AFM). We experimentally assessed how CNP affect DNA molecule and bacterial growth of Escherichia coli. We found that CNP were bound to the DNA molecules during the DNA replication in vivo. The results revealed that the interaction of DNA with CNP resulted in DNA molecule binding and aggregation both in vivo and in vitro in a dose-dependent manner, and consequently inhabiting the E. coli growth. While this was a preliminary study, our results showed that this nanoparticle may have a significant impact on genomic activities.
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DNA polymerase epsilon (Pol epsilon) is a large, multi-subunit polymerase that is conserved throughout all eukaryotes. In addition to its role as one of the three DNA polymerases responsible for bulk chromosomal replication, Pol epsilon is implicated in a wide variety of important cellular processes, including the repair of damaged DNA, DNA recombination, and the regulation of proper cell cycle progression. Pol ε catalyzes DNA template-dependent DNA synthesis by a phosphoryl transfer reaction involving nucleophilic attack by the 30 hydroxyl of the primer terminus on the a-phosphate of the incoming deoxynucleoside triphosphate (dNTP). The products of this reaction are pyrophosphate and a DNA chain increased in length by one nucleotide. The catalytic mechanism is conserved among DNA polymerases. It begins with binding of a primer template to the polymerase. Like all polymerases, Pol ε ultimately does not generate all types of errors at equal rates, but rather has distinctive error specificity. Two features of Pol ε error specificity are particularly interesting in light of its proposed biological roles in DNA replication. One is that Pol ε is among the most accurate of DNA polymerases for single base deletion/insertion errors. Because indels are typically generated more frequently within repetitive sequences, this property may be relevant to the proposal that Pol ε has a particularly important role in replicating heterochromatic DNA, which is enriched in repetitive sequences. Another is that a mutant derivative of Pol ε has a unique base substitution error specificity that has been useful for inferring its role in replication of the leading strand template.