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International Journal of Biological & Medical Research
Int J Biol Med Res. 2014; 5(3): 4246-4257
In silico Analysis of Chloroperoxidase and Lignin Peroxidase of Pathogenic Fungus
Macrophomina phaseolina
a b a b
Yeasmeen Ali , Mohd Omar Faruk Sikder , Lolo Wal Marzan , Farjana Sharmenb, Md Mursalin Khan ,
a
Md Amzad Hosain , *
a
Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong- 4331.
b
Bioinformatician, Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka- 1207.
A R T I C L E I N F O A B S T R A C T
Keywords:
Motif
Botryosphaeriaceae
Physicochemical property
Active site
Secondary structure.
Original Article
Macrophomina phaseolina is a destructive fungus that affects more than 500 plant species
throughout the world. Lignin degradation of the host plant is crucial step for the pathogenesis
of this fungus. Chloroperoxidase and lignin peroxidase are two important enzymes for lignin
degradation. To develop an effective antagonist against this fungus, understanding these
proteins is necessary. In this study, we have reported physico-chemical characteristics,
phylogenic relationship, secondary structure, 3-D structure, motifs of 7 chloroperoxidase and
3 lignin peroxidase proteins. Moreover, pockets as well as conserved residues in the motif
sequence were identified as the target for site-directed mutagenesis of chloroperoxidase and
lignin peroxidase. This mutagenesis or designing target ligands against these proteins may
stoptheligninolyticactivityofM.phaseolina,whichwouldsaveeconomicallyimportantplants.
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1. Introduction
Copyright 2010 BioMedSciDirect Publications IJBMR - All rights reserved.ISSN: 0976:6685.c
Macrophomina phaseolina is a Botryosphaeriaceae fungus that
belongs to phylum ascomycota. It is one of the most devastating soil
and seed borne pathogens infecting more than 500 plant species
[1]. The plant species includes jute [2], cotton [3], maize [4], pulses
[5], sunflower [6] etc. This fungus under favorable environmental
conditions can cause diseases like charcoal rot, stem rot, damping
off, seedling blight, collar rot, and root rot in various important
crops[7].
Disease development is considered to be associated with
several factors such as heat stress, soil water deficit, physiological
stress or coarse soil texture [8]. Due to having sclerotia [thick-
walled resistant hyphal mat] in soil and plant debris, it is difficult to
control M. phaseolina [9]. This pathogen is widely distributed
throughout the world especially in tropical and subtropical
countries [10]. In Bangladesh, due to pathogenicity of this fungus
onlyjutefiberproductionrateisreducedby30%[11].
In 2012, the genome sequence as well as gene prediction of M.
phaseolina was accomplished. The genome size was about 49 Mb
and about 14,249 protein-coding genes were predicted [11]. It
possessesligninolyticactivity,whichistheresultofcombinationof
different enzymatic system such as slaccases, lignin peroxidases,
galactoseoxidases,chloroperoxidases,haloperoxidases,andheme
peroxidases. Lignin peroxidase [Lip] is an extracellur enzyme [12],
which with the help of a cofactor, Veratryl alcohol interacts with
lignin polymer. Likewise, chloroperoxidase [CPO] is also an
extraxellur enzyme that requires heme or vanadium as a cofactor
[13]. This enzyme acts on lignin by oxidization of Cl− to
hypochlorous acid [HOCl] or a similarly reactive chlorine
electrophile[14]. However, the mechanism is not still well
understood.
Our study is to analyze the chloroperoxidase and lignin
peroxidase of M. phaseolina, which will help to understand the
pathogenesis of this devastating fungus. We have analyzed 7
chloroperoxidase and 3 lignin peroxidase enzymes and found
different important investigations such as physic-chemical
characteristics, functional motifs, 3D structure of these proteins.
We also showed the active site pockets, different amino acids that
could be structurally and functionally critical as well as
Copyright 2010 BioMedSciDirect Publications. All rights reserved.c
* Corresponding Author : Yeasmeen Ali
Lecturer, Department of Genetic Engineering and Biotechnology,
University of Chittagong, Chittagong- 4331.
E-mail: hossainamzad1971@yahoo.com

2. 4247
Yeasmeen Ali et.al Int J Biol Med Res. 2014; 5(3): 4246-4257
phylogeneticrelationshipamongtheseperoxidases.Allofthese
findings would decipher an effective way to block the activity of
chloroperoxidase and lignin peroxidase of M. phaseolina to protect
differenteconomicallyimportantcropspecies.
MATERIALSANDMETHODS:
Retrieval of Macrophomina phaseolina chloroperoxidase and
ligninperoxidaseproteinsequences:
Protein sequences of M. phaseolina were retrieved from NCBI
protein database in FASTA format. 7 chloroperoxidase and 3 lignin
peroxidase protein sequences were selected for analysis.
[http://www.ncbi.nlm.nih.gov/].
Physico-chemicalcharacterization:
Different properties including number of amino acids,
molecular weight, theoretical isoelectric point [pI], amino acid
composition [%], number of positively [Arg + Lys] and negatively
charged [Asp + Glu] residues, extinction co-efficient, instability
index, aliphatic index and Grand Average of Hydropathicity
[GRAVY] were calculated using ExPASy's ProtParam tool [15]
[http://expasy.org/tools/protparam.html]. The crystallization
tendency of the proteins was determined by using the CRYSTALP2
W E B S E R V E R [ 1 6 ] [ h t t p : / / b i o m i n e -
ws.ece.ualberta.ca/CRYSTALP2.html] that accepts protein
sequences in the FASTA format. The CRYSTALP2 is a kernel-based
method that uses the composition and collocation of amino acids,
hydrophobicity and isoelectric point of the given sequences to
estimatethecrystallizationpropensityoftheproteins.
Characterizationofsecondarystructure:
Secondary structure prediction was performed by SOPMA [17]
[Self-Optimized Prediction Method with Alignment,
http://npsapbil.ibcp.fr/cgibin/npsa_automat.pl?page=/NPSA/np
sa_sopma.html] tool The input protein sequences were given in
FASTA format. The number of conformational states was adjusted
to four in order to predict Helix, Sheet, Coil and Turn while other
parameters were set as default. By using this software, Alpha helix
[Hh], 310 helix, [Gg], Pi helix [Ii], Beta bridge [Bb], Extended strand
[Ee], Beta turn [Tt], Bend region [Ss], Random coil [Cc], Ambigous
states,andotherstateswerepredicted.
Protein3Dstructureprediction:
The 3D structures of chloroperoxidases and lignin peroxidases
were predicted using the 3D-JIGSAW [version 3] comparative
m o d e l i n g s e r v e r [ 1 8 ] [ h t t p : / /
bmm.cancerresearchuk.org/~3djigsaw/], which accepts
sequences in FASTA format. This program constructs 3D models for
given protein sequences based on the known homologous proteins
structure. It uses HMM for searching homologous templates in
sequencedatabases[PFAM+PDB+nr]andsplitsthequerysequence
into domains. The good templates with maximum coverage of the
queries are then used for modeling and the generated models are
representedasPDBfileformat.
Detectionofmotif:
The motif scan tool [19, 20] [http://myhits.isb-sib.ch/cgi-
bin/motif_scan] was used to identify the motifs and their locations
in the sequence of Lignin peroxidase and chloroperoxidase. These
protein sequences were given as input data [FASTA format] and
scannedagainst'PROSITEPatterns'.Theselectedmotifswerethen
visualized by using Swiss- Pdb Viewer V4.1.0 [21]. Locations,
nature, match score and match details of the motifs were analyzed.
It was aimed to find out the conserved regions of these motifs. At
this point of view, multiple sequence alignment [MSA] of these
motifs was performed using EBI Clustal Omega [22].
[https://www.ebi.ac.uk/Tools/msa/clustalo/]. As expected, a
number of conserved regions were found and their length,
conservedaminoacidswereanalyzed.
Activesiteprediction:
Active site analysis was performed using Computed Atlas of
Surface Topography of Protein [CASTp]. CASTp for automatically
locating and measuring protein pockets and cavities, is based on
precise computational geometry methods, including alpha shape
and discrete flow theory. CASTp identifies and measures pockets
and pocket mouth openings, as well as cavities. The program
specifies the atoms lining pockets, pocket openings, and buried
cavities; the volume and area of pockets and cavities; and the area
and circumference of mouth openings. Most frequently, the largest
pocket/cavity has been the active site, but there are a number of
instructive exceptions [23]. Ligand volume and binding site
volume are somewhat correlated, but the ligand seldom occupies
the entire site. Auxiliary pockets near the active site have been
suggested as additional binding surface for designed ligands [24].
Analysis of active sites is important for the modeled protein as a
precursor to further work on its docking studies, and to shape the
processofmakingagridbeforedocking.
PredictionofEvolutionaryrelationship:
Evolutionary tree among these 10 lignin degrading protein
sequences were aligned using multiple sequence alignment tool
C l u s t a l o m e g a [ 2 5 ] [ h t t p s : / / w w w. e b i . a c . u k
/Tools/services/web_clustalw2/toolform.ebi] , followed by
construction of evolutionary tree using the protein sequences in
FASTA format as input data The alignment parameters were tuned
finely to find out the best alignment and Neighbor Joining [NJ]
methodwasselectedtoconstructthetree.
RESULTS:
Physico-chemicalcharacterization:
Isoelectric point [pI] is a pH in which net charge of protein is
zero. pI of lignin peroxidase 2 and 3 were observed to lie in the
acidic range, while the rest of the proteins occur in alkaline range.
From the study of instability index, it was found that all
peroxidases are stable [except Chloroperoxidase 7], as instability
index value less than 40 indicates stability of a protein

3. sequences and ranked them according to the scores of
ramachandran plot. For each of the proteins, the top ranked 3D
model was selected from the given models [supplementary file, fig
1]. The 3D models generated by 3D JIGSAW were then used further
forthemotifdetectionandpocketfindings.
MotifIdentification:
Chloroperoxidase and lignin peroxidase are found in M.
phaseolina as well as many other fungi, posing a major role in lignin
degradation [11, 31]. Motifs for chloroperoxidase and lignin
peroxidase were identified using Motif scan tool [Fig 1,
Supplementary file, table 4]. If we look into the conserved regions
[Fig 2], a number of residues are revealed which are already known
to have important role in catalysis. These conserverd regions are
predominated by cysteine, proline, aspartate, asparagines,
histidine,alanineandglycine.
Activesiteanalysis:
The active sites of chloroperoxidase and lignin peroxidase were
predicted [fig 3]. Further, in this study, we have also reported the
best active site area of the experimental enzymes as well as the
number of amino acids involved in it; showed the number of
pockets,withtheirareaandvolume[Supplementaryfile,fig2].
In case of the lignin peroxidase, the volume of the pockets is
quite similar and average is 2157 ų. There are some variations in
the area of pockets; for lignin peroxidase 2, it is 1100.9 Å2
[Supplementary file, table 5]. On the other hand, for lignin
peroxidase 3, it is highest 1857.8 Å2. For lignin peroxidase 1, the
area is between the two others-1542.7 Å2. But from the
visualizationwecanseeasimilarpocketstructures.
In the analysis of the chloroperoxidases we find similar pocket
sizes and structures too. For the chloroperoxidase 2,
chloroperoxidase 3, chloroperoxidase 4, chloroperoxidase 5 and
chloroperoxidase 6, the average pocket area is 2301.7 Å2 and
average pocket volume is 3428.6 Å3. Among these, the highest area
showedbychloroperoxidase4thatis3072.7Å2andvolumeis5042
Å3. There are two chloroperoxidases show major variations; those
are chloroperoxidase 1 and chloroperoxidase 7. For
chloroperoxidase1,areais697.6Å2andvolumeis907.5Å3.Incase
of chloroperoxidase 7, we identified paramount variation; it is
totally different from other chloroperoxidases regarding the area
[208.4 Å2], volume [203.8 Å3] and pocket. From the visualization,
we can see a similar pocket structure among the chloroperoxidases
otherthanthechloroperoxidase7.
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[Supplementary file, Table 1]. Additionally, Aliphatic index [AI]
refers to the relative volume of a protein occupied by its aliphatic
side chains. The higher the Aliphatic index of proteins, the more
thermally stable the proteins. Aliphatic index of chloroperoxidase
1 [100.11] and 5 [90.84] classifies them as most thermostable,
closely followed by other chloroperoxidases [chloroperoxidase 3,
4, 6 and lignin peroxidase 9]. Grand average of hydropathicity
index [GRAVY] indicates the interaction of the proteins in water.
Chloroperoxidase 1 [0.099] and lignin peroxidase 1 [0.022] are
hydrophobic [due to positive GRAVY values]. GRAVY values of
otherperoxidaseswereobservedwithinawiderangeof-0.055to-
0.54[hydrophilic].
The amino acid composition of each peroxidase sequence was
calculated by using ExPASY's ProtParam tool [supplementary file,
Table 2]. High percentage of alanine [above 9.9] and serine [above
8.5] was found in all three lignin peroxidases compared to other
amino acid. In all chloroperoxidase [except chloroperoxidase 7],
leucine content was found significant. Again, chloroperoxidase 2, 4
and 5 have a glycine content above 8.9. Moreover, a good
percentage of serine was found in chloroperoxidase 3 [9.6] and 7
[9.2]andalsochloroperoxidase7isprolinerich[10.0%].
There are some properties of the proteins such as isoelectric
point, hydrophobicity, and the frequency of certain collocated di
and tripeptides that are pivotal indicators of crystallization [16].
The CRYSTALP2 accounts all such characteristics of given
sequences for estimating the confidence of crystallization.The
higher the confidence, the more probable that protein is
crystallizableandviceversa.Amongthe7chloroperoxidasesand3
lignin peroxidases, chloroperoxidase 5 showed the highest
confidence of crystalizaiton that was 0.61 which was followed by
chloroperoxidase 2 [0.565] and chloroperoxidase 6 [0.523],
respectively [supplementary file, table 1]. In contrast, lignin
peroxidase 3 represented the least confidence of crystallization
[0.221]. Each of the the remaining chloroperoxidases exhibited
higher confidence of crystallization than that of remaining lignin
peroxidases. From the CRYSTALP2 result, it can be assumed that
chloroperoxidases are more likely to be crystallized than lignin
peroxidases. Among all chloroperoxidase, chloroperoxidase 5
representsmaximumpropensityforcrystallization.
Characterizationofsecondarystructure:
SOPMA analysis of secondary structure of chloroperoxidase
andligninperoxidaseproteinsequencesresultsthepredominance
of random coil which is followed by alpha helix, extended strand,
andbetasheet,respectively[supplementaryfile,table3].Incaseof
Chloroperoxidase 1, Lignin Peroxidase 1, it was found that alpha
helixexceedtherandomcoil.
Protein3Dstructure:
The 3D structure of protein is very crucial for comprehending
the protein functions, their sub-cellular localization as well as
protein-protein interactions. Based on homology modeling, 3D-
JIGSAWresultsshowedfive3Dmodelsforeachofthegiven
Yeasmeen Ali et.al Int J Biol Med Res. 2014; 5(3): 4246-4257

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Fig 1: Motifs in Chloroperoxidase and Lignin peroxidase. Insets show most common amino acids in motifs.
Yeasmeen Ali et.al Int J Biol Med Res. 2014; 5(3): 4246-4257

5. 4250
Fig 2: Conserved regions in chloroperoxidase [top] and lignin peroxidases [bottom] motifs using boxshade.
Activesiteanalysis:
The active sites of chloroperoxidase and lignin peroxidase
were predicted [fig 3]. Further, in this study, we have also reported
the best active site area of the experimental enzymes as well as the
number of amino acids involved in it; showed the number of
pockets,withtheirareaandvolume[Supplementaryfile,fig2].
In case of the lignin peroxidase, the volume of the pockets is
quite similar and average is 2157 ų. There are some variations in
the area of pockets; for lignin peroxidase 2, it is 1100.9 Å2
[Supplementary file, table 5]. On the other hand, for lignin
peroxidase 3, it is highest 1857.8 Å2. For lignin peroxidase 1, the
area is between the two others-1542.7 Å2. But from the
visualizationwecanseeasimilarpocketstructures.
In the analysis of the chloroperoxidases we find similar pocket
sizes and structures too. For the chloroperoxidase 2,
chloroperoxidase 3, chloroperoxidase 4, chloroperoxidase 5 and
chloroperoxidase 6, the average pocket area is 2301.7 Å2 and
averagepocketvolumeis3428.6Å3.Amongthese,thehighestarea
showedbychloroperoxidase4thatis3072.7Å2andvolumeis
5042 Å3. There are two chloroperoxidases show major
variations; those are chloroperoxidase 1 and chloroperoxidase 7.
Forchloroperoxidase1,areais697.6Å2andvolumeis907.5Å3.In
caseofchloroperoxidase7,weidentifiedparamountvariation;itis
totally different from other chloroperoxidases regarding the area
[208.4 Å2], volume [203.8 Å3] and pocket. From the visualization,
we can see a similar pocket structure among the
chloroperoxidasesotherthanthechloroperoxidase7.
Fig 3: Pockets [active site] of the enzymes
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Evolutionaryrelationship:
Phylogenetic tree shows evolutionary relationship among all the ten proteins. There are two major clades on the tree. All
chloroperoxidases [except chloroperoxidase 1] reside in a common clade whereas, three lignin peroxidases reside in another tree.
Chloroperoxidase1seemstobetheoutgroupofthetree.
Table 1: Physico-chemical parameters of chloroperoxidase and lignin peroxidase:
Fig 4: Phylogenetic relationship among chloroperoxidases and lignin peroxidases
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Table 2: Composition of amino acid of chloroperoxidase and lignin peroxidase (in %):
Table 3: Secondary structure prediction of chloroeroxidase and lignin peroxidase (in %):
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Table 4: Identification of motifs:
Table 5: Active site Prediction
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10. Fig 2: Pockets (active site) in motif of chloroperoxidase and lognin peroxidase.
Yeasmeen Ali et.al Int J Biol Med Res. 2014; 5(3): 4246-4257
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11. DISCUSSION:
Instability index and aliphatic index indicate the relative
thermostability of the proteins, whereas GRAVY values show
hydrophilic nature of most of them. lignin peroxidases have high
percentage of alanine and serine. On the other hand,
chloroperoxidases are predominated by leucine, glycine, proline
and serine. These amino acids have important role in protein
structure. Serine is small in size and hence reasonably common to
occur within the tight turns on the protein surface or within the
interior of a protein. Serine side-chain hydroxyl oxygen can form a
hydrogen bond with the protein backbone [26]. Leucine is a
hydrophobic amino acid as it has a branched hydrocarbon side
chains usually buried in folded proteins. The hydrophobic effect
accounts for stabilization of water-soluble proteins [24]. High
percentage of glycine may be responsible for the stability of triple
helicalstructure,sinceincorporationoflargeaminoacidscancause
steric hindrance [27]. Increased proportion of proline residues is
significant not only to act as structural disruptor of the secondary
structuralelementsbutalsotopointoutwardandstabilizethehelix
[28].
From the CRYSTALP2 result, it is clear that chloroperoxidases
are more likely to be crystallized than lignin peroxidases. Among all
chloroperoxidase, chloroperoxidase 5 represents maximum
propensity for crystallization. The knowledge of crystallization
tendency of protein has a great importance in structural biology
that provides valuable insight into the structure-function
relationship of the proteins [16]. Moreover, crystallographic
knowledge of proteins has immense roles in pharmaceutical,
biotechnological and chemical industries for rational drug
designing, protein engineering and other applications. [29].
Secondarystructureanalysisshowedpredominanceofrandomcoil
over other structures. Large number of random coil gives the
protein more flexibility and self-assembly [30]. Protein 3D models
were created using homology modeling that were validated by
Ramachandranplot.
Motif scan tool was used as motif finder in these proteins.
Conserved regions of these motifs are important zone to mitigate
their activities. It is possible to inactivate these proteins by
designing ligands against these conserved sites in 3D protein
structure. Moreover, any type of site directed mutagenesis can be
performedintheseregionstoinactivatetheseproteins.Todoso,we
have to acquire a deep knowledge on it. cysteine, proline, aspartate,
asparagines, histidine, alanine and glycine are major amino acid
that not only have structural role but also important in catalytic
function. Cysteine is important for disulfide linkage as well as for
metal binding [32]. Another important residue is proline. It is
unable to adopt a normal helical conformation because it
introduces kinks into alpha helices. Aspartate and asparagine are
frequently involved in protein active sites. Because of their negative
charge, they can interact with positively charged non-protein
atoms. Since Aspartate has a shorter side-chain, it is slightly more
rigid within protein structures. Thus, it has a slightly stronger
preferencetobeinvolvedinproteinactivesites[26].Histidineisthe
most common amino acid in protein active sites. They
efficiently bind metal ions, often acting together with cysteines.
Alanineplaysimportantroleinsubstraterecognitionorspecificity,
particularly in interactions with non-reactive atoms such as
carbon.TheuniquenessofGlycine[HasRgroup]alsomeansthatit
can play a distinct functional role, such as using its sidechain-less
backbonetobindtophosphates[26].
Predicted active sites were of similar structure in same protein
family. Volume, area and charge density of active sites were
satisfactory. All of the chloroperoxidase proteins [except
chloroperoxidase 1] share a common ancestral point [marked by
arrow, Fig 4] after being diverged from root of the tree. Fungal
lignin peroxidase 1 and 3 are more closely related than lignin
peroxidase 2. Chloroperoxidase 1 seems to be the outgroup of the
tree. Probably this protein has acquired a lot of change in its
sequenceovertimewithoutlosingitscatalyticactivity.
CONCLUSION:
A number of plants for example crop, fiber or other
commercially valuable species are infected by Macrophomina
phaseolina fungus and causes a great lose throughout the world.
For the pathogenesis of this fungus, different genes are involved.
Among these genes, chloroperoxidase and lignin peroxidase are
two important genes that are required for a crucial step that is
lignin degradation. In present study, we have analyzed physico-
chemical characteristics, secondary and tertiary structure as well
as motifs in 7 chloroperoxidase and 3 lignin peroxidase. During
this analysis, we found amino acids like cysteine, aspertate,
asparagine, proline, histidine and glycine, which play vital role
both structurally and functionally. Moreover, we have searched the
active sites in these 10 proteins and found highest pocket area for
chloroperoxidase 4 and lignin peroxidase 3. Study of evolutionary
relationship reveals that all of the proteins shared a common
ancestor. All of these findings help us to understand the characters
of these proteins. This will facilitate to design a potent target
against chloroperoxidase and lignin peroxidase and protect the
fungalsusceptiblecropspecies.
CONFLICTOFINTERESTS
The authors declare that there is no conflict of interests
regardingthepublicationofthispaper.
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