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Shahin Gavanji, Hamidi Abdul Aziz, Behrouz Larki, Amin Mojiri
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International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013 Available online at http://www.ijsrpub.com/ijsres
ISSN: 2322-4983; ©2013 IJSRPUB
50
Full Length Research Paper
Computational Prediction and Analysis of Interaction of Silver Nitrate with
Chitinase Enzyme
Shahin Gavanji1*, Hamidi Abdul Aziz
2, Behrouz Larki
1, Amin Mojiri
2
1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
2School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang, Malaysia
*Corresponding Author: [email protected]
Received 28 February 2013; Accepted 22 March 2013
Abstract. Silver nitrate is an inorganic compound with chemical formula AgNO3. Silver or silver ions have long been used in
many areas due to their strong antimicrobial activity against pathogenic microbes such as bacteria, yeast, fungi and algae.
Trichoderma spp. are considered as biocontrol and growth promoting agents for many crop plants due to their antagonistic
properties against plant pathogens. We, in this study, checked the possible interaction between silver nitrate and Chitinase
enzyme. We used Molegro virtual docker (MVD). The results obtained from docking showed us that the best pose which is
derived from MolDock score for Chitinase was -49.1418 with reranking score equal to -58. 1719. It is concluded that silver
nitrate and Chitinase have interaction. Obtained results showed that silver nitrate can be attached to Chitinase in Trichoderma
fungi cells leading to deactivation the enzymes.
Key words: Chitinase- Molecular mechanism-Silver nitrate-bioinformatics.
1. INTRODUCTION
Trichoderma viride is a filamentous Ascomycota.
Agricultural and orchard soil, which contain huge
quantities of plant roots are the best places to live for
these organisms (Samuels et al., 1999). Persoon
almost 200 years ago described the genus
Trichoderma that consists of anamorphic fungi
isolated primarily from soil and decomposing organic
matter. Isolates of Trichoderma are ubiquitous and
their isolation and culture are very easy. These
isolates can grow quickly on a wide range of
substrates and produce metabolites with demonstrable
antibiotic activity or mycoparasitic against a wide
range of pathogens. Because of these properties,
Trichoderma species have been used in biological
control of fungi including plant pathogens (Inbar and
Chet, 1992; Lumsden and Locke, 1989). Through
nutrient competition and rhizosphere competence,
mycoparasitism, enzyme, metabolism of germination
stimulants and induced defense responses in plants,
Trichoderma spp can control root foliar pathogens
(Howell, 2003; Zimand et al., 1996).
Jin and Custis (2011) also showed that
Trichoderma strains induce changes in the microbial
composition on roots, enhance nutrient uptake,
stabilize soil nutrients, promote root development, and
increase root hair formation. Since mycoparasitic and
antibiotic properties were demonstrated in 1932 and
1934 by Weindling, there have been biotechnological
applications of these fungi as biocontrol agents (Chet,
1987; Haran et al., 1996; Schirmbock et al., 1994).
Most species of the genus grow rapidly in artificial
culture and produce large numbers of small green or
white conidia from conidiogenous cells of widely
branched conidiophores which al low a relatively easy
identification of Trichoderma as a genus (Rifai,
1969). Research is in progress on multifunctional
materials containing silver nanoparticles (SNPs) in
reactive or nonreactive polymer networks for
applications as biocidal products and drug supports
(Gaidau et al., 2009).
Silver nitrate is an inorganic compound with
chemical formula AgNO3. Silver salts have antiseptic
properties. Until the development and common
adoption of antibiotics, dilute solutions of AgNO3 is
used to be dropped into newborn babies' eyes at birth
to prevent contraction of gonorrhea from the mother.
Eye infections and blindness of newborns was
reduced by this method, but incorrect dosage could
cause blindness in extreme cases. This protection was
used by Credé in 1881 for the first time (Credé, 1881).
The antimicrobial properties of silver were first
detected thousands of years ago when silver
containers have been used to store water for
preservation. Its disinfection property has been
scientifically studied for over a century. Before a
disinfectant can be efficiently used as a water
disinfectant, its inactivation kinetics must be
recognized. Kinetics generally depend on both the
dosage of disinfectant and the time of application.
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
51
It is important to understand the kinetics so that the
minimum dosage of disinfectant can be applied for the
minimum amount of time while still effectively
inactivating any pathogens in the water. In recent
years, research has focused mostly on generated silver
ions or colloidal silver electrolytically. In addition,
silver tends to adsorb to glassware, which can lead not
only to a decrease in the silver concentration within a
given experiment but also to a release of the silver in
subsequent experiments unless measures further than
general glassware washing are taken for the removal
of silver from the glassware surface (Chambers et al.,
1962). Therefore studies must both minimize the
external factors affecting the concentration and to
measure the changes in concentration that take place
throughout the experiment. Chambers, Proctor and
Kabler established the importance of using an
effective neutralizer solution which is made of a
mixture of sodium thioglycolate and sodium
thiosulfate, rather than sodium thiosulfate alone,
which though it is effective in neutralizing other
disinfectants does not satisfactorily stop the
bactericidal action of silver nitrate. The researchers
tested the effect of pH on the kinetics, finding that a
higher pH increased the bactericidal action (Chambers
et al., 1962; Gavanji et al., 2011; Gavanji et al., 2012).
Wuhrmann and Zobrist added that at a higher
temperature, inactivation occurs faster (Wuhrmann
and Zobrist 1958). Elemental silver and silver salts
have been used as antimicrobial agents for a long time
(Gavanji et al., 2012). Silver or silver ions have long
been used in many areas due to their strong
antimicrobial activity against pathogenic microbes
such as bacteria, yeast, fungi and algae (Gavanji et al.,
2013). It may be used for controlling different plant
pathogens in a relatively safer way compared to
synthetic fungicides (Park et al., 2006). Until now,
limited studies have provided pieces of evidence of
the applicability of silver for controlling plant diseases
(Park et al., 2006).
Silver ions are very reactive, which are known to
cause the inhibition of microbial respiration and
metabolism as well as physical damage (Gavanji et
al., 2013; Bragg and Rannie, 1974; Thurman and
Gerba, 1989). Ionic silver has some disadvantages
such as its high reactivity which made it unstable and
thus easily oxidized or reduced into a metal depending
on the surrounding environment. In addition, ionic
silver causes discoloration by itself or allows other
materials to cause undesirable coloration and it does
not continuously exert antimicrobial activity. Also,
silver in the form of a metal or oxide, which is stable
in the environment, is applied in a relatively increased
amount due to its low antimicrobial activity (Park et
al., 2006). In recent years, the use of silver as a
biocide in the form of micro crystals or nanoparticles
has grown significantly, as these preparations are
useful against many resistant populations and
‘biofilms’ aggregates of microorganisms that grow on
the surfaces of bodies of water and inside water pipes
(Silver, 2003; Panyala et al., 2008; Gaidau et al.,
2009). Generally, the antimicrobial mechanism of
chemical agents depends on the specific binding with
surface and metabolism of agents into the
microorganism. Furthermore, it has been suggested
that silver ions penetrate into bacterial DNA once
entering the cell, which prevents further proliferation
of the pathogen (Woo et al., 2009).
The aim of present study was to study
bioinformatic interaction of silver nitrate and
Chitinase enzyme to determine harmful effect of
silver nitrate on the enzyme. Chitin is an example of
highly basic polysaccharides. Their unique properties
include polyxylate formation, ability to form films,
chelate metal ions and optical structural
characteristics. Like cellulose, it naturally functions as
structural polysaccharide, but differs from cellulose in
the properties. Chitin is extremely hydrophobic and is
insoluble in water. It is soluble in
hexafluoroisopropanol, hexafluoroacetone,
chloroalcohol in conjugation with aqueous solutions
of minerals acid and dimethylacetamide containing
5% lithium chloride. The nitrogen content in chitin
differs between 5 to 8% depending on the extent of
deacetylation (Yalpani et al., 1992). Acetic anhydride
can entirely acetylate chitin. Linear aliphatic N-acetyl
groups above propionyl, let rapid acetylation of
hydroxyl groups. Highly benzoylated chitin is soluble
in benzyl alcohol, dimethyl sulfoxide, formic acid and
dichloroacetic acid. The N-hexanol, N-decanoyl and
N-dodecanoyl derivatives have been obtained in
metthanesulfonic acid. Chitin is the most widespread
amino polysaccharide in nature and is estimated
annually to be produced almost as much as cellulose.
It is mostly found in antraphode exoskeletons, fungal
cell walls or nematode eggshells. However,
derivatives of chitin oligomers have also been
implicated as morphogenetic factors between
leguminous plants and rhizobium and even in
vertebrates, where they may be important during early
stages of embryogenesis (Merzendorfer and Zimoch,
2003).
Chitin is largely composed of alternating N-
acetylglucosamine residues, which where linked by β-
(1-4) glycosidic bonds. Since hydrolysis of chitin by
chitinase treatment leads to release of glucosamine in
addition to N- acetylglucosamine, it was concluded
that it might be the significant portion of polymer.
Chitin polymer tends to form microfibrils (also
referred as rod or crystallites) of ~3 nm in diameter
that are stabilized by hydrogen bonds formed between
the amine and carbonyl groups. Chitin micro fibrils of
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
52
peritropic matrices may exceed 0.5μm in length and
frequently associate in bundles containing parallel
groups of 10 or more single microfibrils. X- ray
diffraction analysis suggested that chitin is a
polymeric substance that occurs in three different
crystalline modifications, termed α, β and γ. They
mainly differ in the degree of hydration, in size of the
unit cell and in the number of chitin chains per unit
cell. In the α form, all chains display an anti-parallel
orientation. In the β form the chains are set in a
parallel manner and in the γ form sets of two parallel
strands alternate with single anti parallel strands. The
anti parallel arrangement of chitin molecules in α
form allows tight packaging into chitin microfibrils,
consisting ~20 single chitin chains that are stabilized
by a high number of hydrogen bonds which are
formed between the molecules. This arrangement may
contribute significantly to the physicochemical
properties of cuticle such as strength and stability
(Merzendorfer and Zimoch, 2003).
In contrast, the packaging tightness and numbers of
inter-chain hydrogen bonds of the β and γ chains are
reduced, leading to an increase in the number of
hydrogen bonds with water. The high degree of
hydration and reduced packaging tightness resulted in
more flexible and soft chitinous structures, as are
found in peritropic matrices.
Fig. 1: Mechanism of Chitinases action (www.sigmaaldrich.com)
Chitinases are enzymes that catalyze the
degradation of chitin. They have been detected in
many organisms, including bacteria, fungi, plants,
invertebrates and vertebrates (Rogalski et al., 1997;
Felse and Panda, 2000). Chitinases are generally
classified into endo- and exochitinases. The
endochitinase activity is defined as the random
cleavage at internal points in the chitin chain. The
exochitinase activity is defined as the progressive
action starting at the non-reducing end of chitin with
the release of chitobiose or N-acetylglucosamine units
(figure 1). Chitobiosidase and N-acetyl-b-
glucosaminidase are considered as exochitinases
(Felse and Panda, 2000). The combination of endo-
and exochitinases results in a synergistic increase in
the chitinolytic activity (Bolar et al., 2001). In another
research the role of silver nanoparticles on growth rate
of two biocontrol agent species of Trichoderma viride
and T. harzianum was investigated by measuring the
diameter of colonies of fungi (Gavanji et al., 2012.).
So we, in this study, checked the possible interaction
between silver nitrate and Chitinase enzyme.
2. MATERIALS AND METHODS
2.1. Preparing 3 dimensional structures of silver
nitrate and Catalase and Nitrat reductase:
In the first step, amino acid sequences of Chitinase
enzyme with accession number of B6E5Q4 were
taken from NCBI website (www.ncbi.nlm.nih.gov/)
(Figure2). Then the Chitinase enzyme with the
number of 1D2K was obtained from Protein Data
Bank website (www.rcsb.com). In the next step,
Silver Nitrate with AgNo3 molecular formula
(number 22878) was provided from ChemSpider
website (www.chemispider.com) (figure3).
MLGFLGKSVALLAALQATLTSATPVSTNDVSVEKRASGYTNAVYFTNWGIYGRNFQPQDLVASDITHVIYSFMNFQADGTVVSGDAYAD
YQKHYSDDSWNDVGNNAYGCAKQLFKLKKANRNLKVMLSIGGWTWSTNFPSAASTDANRKNFAKTAITFMRDWGFDGIDVDWEYPAD
DTQATNMVLLLKEIRSQLDAYAAQYAPGYHFLLSIAAPAGPEHYSALHMADLGQVLDYVNLMAYDYAGSWSSYSGHDANLFANPSNPN
FSPYNTDQATKAYINGGVPASKIVLGMPIYGRSFESTNGIGQTYNGIGSGSWENGIWDYKVLPKAGATVQYDSVAQAYYSYDSSSKELISF
DTPDMVSKKVSYLKNLGLGGSMFWEASADKTGSDSLIGTSHRALGSLDSTQNLLSYPNSQYDNIRSGLN
Fig. 2: Amino acid sequence of Chitinase (Trichoderma harzianum-Hypocrea lixii)
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
53
2.2. Molecular docking study
Molegro virtual docker (MVD) 2011.4.3.0 is used for
computer simulated docking study. Before initiation
the docking operation, protein and ligand structures
were prepared using MVD. For this purpose, charges
assigned to the model of protein and ligands structures
and flexible torsions in ligands were detected by this
software (Gavanji et al., 2013).
Fig. 3: A: Structure of silver nitrate. B and C: structure of Chitinase enzyme.
3. RESULTS AND DISCUSSION
3.1. Chitinase Structure Analysis
The Chitinase consists of 424 amino acids, and its
molecular weight is 46293 Da. The red parts in figure
4 show the hydrophobic regions and the blue parts
show the negative charge (figure 4).
3.2. Finding ligand binding sites:
3DLigand Site server (http://www.sbg.bio.ic.ac.uk)
was used for prediction of potentially binding sites of
model. In the server output TRP, PHE, TRP, THR,
ASP, TRP, GLU TRP were predicted as present in
binding site(table 1). The position and the percentage
of each amino acides is shown in table 4. Also as an
alternative approach, MVD is used for finding cavities
of model. For this purpose, probe size was 1.2, max
number of ray checks was 16, minimum number of
ray hits was 12 and Grid Resolution was 0.8. Five
cavities were found by MVD (figure 5).
Fig. 4: The hydrophobic regions and negative charge.
3.3. Finding ligand binding sites with Site Hound-
web server:
Site Hound-web identified ligand binding sites by
computing interactions between a chemical probe and
a protein structure. By using web server, 10 regions
with different levels of energy had been recognized
(figure 9). The regions are divided into A to J (table
2). The highest energy is related to ligand bound to
enzyme at A position which is equal to -11112.50 and
the lowest one at A position is predicted to be -465.75
(table 2 and 3).
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
54
Table 1: ligand binding sites by computing interactions with 3D Ligand Site server.
Fig. 5: Cavities of Chitinase predicted model. MVD used for cavity detection. Detecting parameters: probe size 1.2, max
number of ray checks was 16, minimum number of ray hits 12 and Grid Resolution 0.8
Table 2: ligand binding sites by computing interactions with Site Hound-web server.
Bioinformatic checking of ligand bound to amino
acids showed that the best position for interaction
between ligand and amino acids is A position in
which the ligand (X:66,Y:21, Z39) is bounded to
amino acids existed in this position(Figure6 and 7).
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
55
Table 3: Amino acides involved in interaction with different groups.
Fig. 6: features of ligand bound to amino acides presented in A position.
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
56
Fig. 7: Features of ligand bound to amino acides presented in A position.
3.4. Molecular docking study with Molegro virtual
docker (MVD):
MolDock score (Thomsen and Christensen, 2006)
with a grid resolution of 0.30 Â was used as scoring
function for docking (Figure 8). Internal electrostatic
interaction and hydrogen bond between ligand and
protein were permitted. MolDock SE was used as the
docking algorithm and ten runs for ligands were
carried out. After docking, energy minimization and
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
57
optimization of hydrogen bonds were performed. The
energy threshold was 100.00 and similar poses were
ignored. Docking results are evaluated based on
MolDock and reranking score. Rerank score is
estimated for interaction. For the defined docking
radius in Catalase-peroxidase and Nitrate reductase
enzyme, the best pose which is derived from
MolDock score for Chitinase enzyme was -49.1418
with Reranking score equal to -58.1719 (Table 4).
Table 4: Binding energy level of top five poses of silver nitrate to Chitinase.
Fig. 8: interaction of silver nitrate with Chitinase enzyme
The microscopic study of interaction between T.
harzianum and Rhizoctonia solani showed that as the
result of T. harzianum activity, the cell wall of fungi
will be affected. Studies showed that at the very
beginning of Mycoparasitic activity of fungi, the
Myceliums of Trichoderma hoop around the
Myceliums of the host and then penetrate into it and
make changes in its cell wall and finally disturb the
cytoplasm structure. With regard to purification and
study the extracellular enzymes through
Mycoparasitic activity of T. harzianum, it was
revealed that the major part of changes in cell wall of
the host are the result of direct action of Hydrolytic
enzymes of Trichoderma (Artigues and Vavet, 1984;
Elad et al., 1985) which are glucanase, protease and
Chitinase(Ridout et al., 1988) that by their synergistic
activitis cause disturbance in cell wall(Haran et al.,
1996; Elad et al., 1985; Lorito et al., 1994). Indeed,
the presence of Chitinase enzymes is very effective in
biocontrol activitis. In different species of
Trichoderma, there have been some exo and endo
chitinases by which the glycosidic bounds will be
broken leading to destruction of cell wall (Haran et
al., 1996).
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
58
Fig. 9: Ligand bound to amino acides presented in A, B, C, D, E and F position.
Studies about chitinase enzymes in T. harzianum
showed that there have been some types of the
enzymes existed in the fungi. The experiments
revealed four enzymes in the fungi which are
CHIT52, CHIT42, CHIT33 and CHIT31 respectively
(Haran et al., 1995). The studies suggested that
CHIT52, with molecullar weight of 52 kDa, is very
sensitive to heat. The appropriate temperature and pH
for enzyme activity are 40 °C and 4 respectively.
Studies about the effect of metal ions on enzyme
activity reported that the metals show no considerable
role in chitinase enzymes activity (Harman et al.,
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
59
1993, Ulhoa and Peberdy, 1992). Experiments on the
effect of different chitinases on the cell wall of host
fungi showed that each of these enzymes affects the
cell wall exclusively. In a study about the direct effect
of CHIT42, CHIT33 and CHIT31 on the cell wall of
Botrytis cinerae revealed that only CHIT42 enzyme
can have Hydrolytic affect and two other enzymes
(CHIT33 and CHIT31) increase the hydrolize effect
of CHIT42 and they cannot make any destruction to
the cell wall by themselves (De la Cruz et al., 1993;
De Marco et al., 2000). Although some kinds of
chitinase enzymes have been purified in different
species of Trichoderma, but study about their features
at the level of DNA is basically refered to 3
endochitinases CHIT31, CHIT33 and CHIT42(Limon
et al., 1995; Zeilinger et al., 1999).
Although the antimicrobial properties of silver
have been known for centuries, recently we have only
begun to understand the mechanisms by which silver
inhibits bacterial growth. It is proposed that silver
atoms bind to thiol groups (-SH) in enzymes and as a
result cause the deactivation of enzymes. Silver forms
stable S-Ag bonds with thiol-containing compounds in
the cell membrane that are involved in transmembrane
energy production and ion transportation (Klueh et al.,
2000). It is also believed that silver can join in
catalytic oxidation reactions that result in the
construction of disulfide bonds (R-S-S-R). Silver
performs this process via catalyzing the reaction
between oxygen molecules in the cell and hydrogen
atoms of thiol groups so that water is subsequently
released as a product and two thiol groups become
covalently bonded to one another through a disulfide
bond (Davies and Etris, 1997).
The silver-catalyzed formation of disulfide bonds
could possibly modify the shape of cellular enzymes
and consequently affect their function. However, these
effective biocidal properties have the potential to
adversely affect beneficial bacteria in the environment
especially those existed in the soil and water.
Exploration is increasing into the potential toxic
mechanisms and long-standing effects by which these
nanomaterials could cause environmental dangers
throughout broad production and use. Extensively
used nanoparticles, such as silver nanoparticles will
most likely enter the environment and may produce a
physiological response in certain organisms, possibly
altering their fitness and finally might affect their
populations or community densities. Although there
have been studies discovering the toxicity of metal
NPs and despite their widespread application,
currently there is inadequate toxicity data necessary to
fill the gap for the ‘‘source pathway receptor-impact’’
framework necessary for correct risk measurement of
Ag NPs (Laban et al., 2010). These results suggest the
possibility using of silver nanoparticles to eliminate
phytopathogens. Several parameters will require
estimation proceeding to practical application,
including phytotoxicity and antimicrobial effects in
situ and development of systems for delivering
particles into host tissues that have been colonized by
phytopathogens.
It is believed that nanometer-sized silver particles
have different physical and chemical properties from
their macro scale counterparts which alter their
interaction with biological structures. Research has
been focused on antibacterial material containing
various natural and. Among them, silver or silver ions
have long been known to have potential inhibitory and
bactericidal effects as well as a broad spectrum of
antimicrobial activities (Kandile et al., 2010). Because
of its antimicrobial properties, silver has also been
used in filters to purify drinking water and to clean
swimming pool water (Wijnhoven et al., 2009). The
nanosilver products make broad claims concerning the
power of their nanosilver components such as:
elimination of 99% of bacteria, rendering material
permanently and killing approximately 650 kinds of
harmful germs and it was 2 to 5 times faster than other
forms of silver (Gavanji et al., 2013). Some studies
have reported that the positive charge on the Ag ion is
necessarily essential for its antimicrobial activity
through the electrostatic attraction between negative
charged cell membrane of microorganism and positive
charged nanoparticles.
4. CONCLUSION
Based on obtained results using Bioinformatic
softwares, it is clear that silver nitrate can cause
harmful effect to Chitinase enzyme leading to
deactivation of the enzyme. Hence, it is suggested to
use silver nitrate with care in environment.
REFERENCES
Artigues M, Vavet P (1984). Activites (1-3)
glucanisque et chitinisque de quelques
champignons, en relation avec leur aptitude a
detruire les sclerotes de Corticum rolfsii dans la
terre sterile. Soil Biology and Biochemistry, 16:
527-538.
Benn TM, Westerhoff P (2008). Nanoparticle silver
released into water from commercially
available sock fabrics. Environmental Science
& Technology, 42(11): 4133-4139.
Bolar JP, Norelli JL, Harman GE, Brown SK,
Aldwinckle HS (2001).Synergistic activity of
endochitinase and exochitinase from
Trichoderma atroviride (T. harzianum) against
the pathogenic fungus (Venturia inaequalis) in
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
60
transgenic apple plants.Transgenic Research,10:
33-543.
Bragg PD, Rannie DJ (1974). The effect of silver ions
on the respiratory chain of Escherichia coli.
Canadian journal of microbiology, 20:883-889.
Cecil WC, Proctor MC, Kabler WP (1962).
Bactericidal Effect of Low Concentrations of
Silver. Journal of the American Water Works
Association, 54: 208-216.
Chet I (1987). Innovative approaches to plant disease
control. John Wiley and Sons, New York, N.Y.
p.137– 160.
Faunce T, Watal A (2010). Nanosilver and global
public health: international regulatory issues.
Nanomedicine, 5(4): 617-632.
Credé CSE (1881). Die Verhürtung der
Augenentzündung der Neugeborenen. Archiv
für Gynaekologie 17 (1): 50–53.
Davies, RL, Etris SF (1997). The Development and
Functions of Silver in Water Purification and
Disease Control. Catalysis Today, 36: 107–114.
De la Cruz J, Rey M, Lora JM, Hidalgo-Gallego A,
Dominguez F, Pintor-Toro JA, Liobell A,
Benitez T (1993). Carbon source control on
beta-glucanases, chitobiase and chitinase from
Trichoderma harzianum. Archives of
Microbiology, 159: 316-322.
De Marco JL, Lima LHC, De Sousa MV, Felix CR
(2000). A Trichoderma harzianum chitinase
destroys the cell wall of the phytopathoge
Crinipellis perniciosa , the causal agent of
witches' broom disease of cocoa. World journal
of Microbiology and Biotechnology, 16: 383-
386.
Elad Y, Lifshitz R, Baker R (1985). Enzymatic
activity of the mycoparasite Pythium nunn
during interaction with host and non-host fungi.
Physiological Plant Pathology, 27: 131-148.
Felse P A, Panda T (2000). Production of microbial
chitinases: A revisit. Bioprocess Engineering,
23:127-1344.
Gaidau C, Petica A, Ciobanu C, Martinescu T (2009).
Investigations on antimicrobial activity of
collagen and keratin based materials doped with
silver nanoparticles. Biotechnology Letters,
14(5):4665-4672.
Gavanji S, Abdul Aziz H, Larki B, Mojiri A ( 2013).
Bioinformatics Prediction of Interaction of
Silver Nitrate and Nano Silver on Catalase and
Nitrat Reductase. International Journal of
Scientific Research in Environmental Sciences,
1(2):26-35.
Gavanji, S, Larki, B, Mehrasa M (2013). A review of
Effects of Molecular mechanism of Silver
Nanoparticles on Some microorganism and
Eukaryotic Cells. Technical Journal of
Engineering and Applied Sciences, 3(1):48-58.
Gavanji S, Shams M, Shafagh N, jalali Zand A, Larki
B, Doost Mohammadi M, Taraghian AH,
niknezhad SV (2012). Destructive Effect of
Silver Nanoparticles on Biocontrol Agent Fungi
Trichoderma viride and T. harzianum. Caspian
Journal of Applied Sciences Research, 1(12):
83-90.
Gavanji S, Asgari MJ, Vaezi R, Larki B (2011).
Antifungal effect of the extract of propolis on
the growth of three species of Epidermophyton
flucosum, Trichophyton violaseum and
Trichophyton tonsurans in laboratory
environment. African Journal of Pharmacy and
Pharmacology, 5(24): 2642-2646.
Gavanji S, Larki B, jalali Zand A, Mohammadi E,
Mehrasa M, Taraghian AM (2012).
Comparative effects of propolis of honey bee
on pathogenic bacteria. African Journal of
Pharmacy and Pharmacology, 6(32): 2408-
2412.
Haran S, Shickler H, Chet I (1996). Molecular
mechanisms of lytic enzymes involved in the
biocontrol activity of Trichoderma harzianum.
Microbiology, 142: 2321-2331.
Haran S, Shickler H, Oppenheim A, Chet I (1995).
New components of the chitinolytic system of
Trichoderma harzianum. Mycological
Research, 99: 441-446.
Harman GE, Hayes CK, Lorito M, Broadway RM, Di
Pietro A, Peterbauer C, Tronsmo A (1993).
Chitinolytic enzymes of Trichoderma
harzianum: purification of chitobiosidase and
endochitinase. Phytopathology, 83: 313-318.
Howell CR (2003). Mechanisms employed by
Trichoderma species in the biological control of
plant diseases: the history and evolution of
current concepts. Plant disease, 87: 4-10.
Inbar J, Chet I (1992). Bionomics of fungi cell wall
recognition by use of lectin-coated nylon fibres.
Journal of Bacteriology, 174: 1055-1059.
Jin X, Custis D (2011). Microencapsulating aerial
conidia of Trichoderma harzianum through
spray drying at elevated temperatures.
Biological Control, 56: 202–208.
Kandile NG, Zaky HT, Mohamed MI, Mohamed HM
(2010). Silver Nanoparticles Effect on
Antimicrobial and Antifungal Activity of New
Heterocycles. Bull. Korean Chemical Society,
31(12):3530-3538.
Klueh U, Wagner V, Kelly S, Johnson A, Bryers JD
(2000). Efficacy of Silver-Coated Fabric to
Prevent Bacterial Colonization and Subsequent
Device-Based Biofilm Formation. Journal of
Gavanji et al.
Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme
61
Biomedical Materials Research, 53(6): 621-
631.
Laban G, Nies LF, Turco RF, Bickham JW,
Sepu´lveda MS (2010). The effects of silver
nanoparticles on fathead minnow (Pimephales
promelas) embryos. Ecotoxicology, 19: 185–
195.
Limon MC, Lora JM , Garcia I, Cruz J, Liobell A,
Benitez T, PintorToro JA (1995). Primary
structure and expression pattern of the 33-kDa
chitinase gene from the mycoparasitic fungus
Trichoderma harzianum. Current Genetics, 28:
478-483.
Lorito M, Harman CK, Di Pietro A, Woo SL, Harman
GE (1994). Purification, characterization and
synergistic activity of a gulacan 1,3-beta
glucosidase and an N- acetylglucosaminidase
from Trichoderma harzianum. Phytopathology,
84: 398-405.
Lumsden RD, Locke JC (1989). Biological control of
damping-off caused by Pythium ultimum and
Rhizoctonia solani in soiless mix.
Phytopathology, 79:361-366.
Merzendorfer H, Zimoch H (2003). Chitin metabolism
in insects: structure, function and regulation of
chitin synthases and chitinases. Journal of
Experimental Biology, 206: 4393–4412.
Panyala NR, Mandez EMP, Havel J (2008). Silver or
silver nanoparticles: a hazardous threat to the
environment and human health. Journal of
Applied Biomedicine, 6:117-129.
Park HJ, Kim SH, Kim HJ, Choi SH (2006). A New
Composition of Nanosized Silica-Silver for
Control of Various Plant Diseases. plant
pathology, 22(3):295-302.
Ridout CJ, Coley-Smith JR (1988). Fractionation of
extracellular enzymes from a mycoparasitic
strain of Trichoderma harzianum. Enzyme and
Microbial Technology, 10:180-187
Rifai MA ( 1969). A revision of the genus
Trichoderma. Mycology, 116: 1– 56.
Rogalski J, Krasowska B, Glowiak G, Wojcik W,
Targonski Z (1997). Purification and ...
produced by Trichoderma viride F-19. Acta
Microbiologica Polonica, 46: 363-375.
Samuels GJ, Lieckfeldt E, Nirenberg HI (1999).
Trichoderma asprellum a new species with
warted conidia and redescription of T. viride.
Sydowia, 51: 71-88.
Schirmbock M, LoritoYL, Wang CK, Hayes I, Scala
F, Harman Ge, Kubicek CP (1994). Parallel
formation and synergism of hydrolytic enzymes
and peptaibol antibiotics, molecular
mechanisms involved in the antagonistic action
of Trichoderma harzianum against
phytopathogenic fungi. Applied and
Environmental Microbiology, 60:4364– 4370.
Silver S (2003). Bacterial silver resistance:molecular
biology and uses and misuses of silver
compounds. Fems microbiology reviews, 27:
341-353.
Thurman KG, Gerba CHP (1989). The molecular
mechanisms of copper and silver ion
disinfection of bacteria and viruses. Critical
Reviews in Environmental Control, 18:295-
315.
Ulhoa CJ, Peberdy JF (1992). Purification and some
properties of the extracellular chitinase
produced by Trichoderma harzianum. Enzyme
and Microbial Technology, 14: 236-240.
Wijnhoven SWP, Peijnenburg WJGM, Herberts CA,
Hagens WI, Oomen AG, Heugens EHW,
Roszek B, Bisschops J, Gosens I, Van De D,
Dekkers S, De Jong WH, Van Zijverden M,
Sips AJ, Geertsma RE (2009). Nano-silver a
review of available data and knowledge gaps in
human and environmental risk assessment.
Nanotoxicology, 3(2): 109-138.
Woo KS, Kim KS, Lamsal Kabir, Kim YJ, Kim SB,
Mooyoung J, Sim SJ, Kim HS, Chang SJ, Kim
JK, Lee YS (2009). An In Vitro Study of the
Anti fungal Effect of Silver Nanoparticles on
Oak Wilt Pathogen Raffaelea sp. Journal of
Microbiology and Biotechnology, 19(8): 760–
764.
Wuhrmann VK, Zobrist F (1958). Untersuchengen
uber die bakterizide Wirkung von Silvber in
Wasser. Schweizerische Zeitschrift fur
Hydrologie, 20:218-255.
Yalpani M, Johnson F, Robinson LE (1992). Chitin,
Chitosan: Sources, Chemistry, Biochemistry,
Physical Properties and Applications, Elsevier,
Amsterdam.
Zimand G, Elad Y, Chet I (1996). Effect of
Trichoderma harzianum on Botrytis cinerea
pathogenicity.
Zeilinger S, Galhaup C, Payer K, Woo SL, Mach RL,
Fekete C, Lorito M, Kubicek CP (1999).
Chitinase gene expression during mycoparasitic
interaction of Trichoderma harzianum with its
host. Fungal Genetics and Biology, 26:131-140.
International Journal of Scientific Research in Environmental Sciences (IJSRES), 1(4), pp. 50-62, 2013
62
Shahin Gavanji graduated in Biotechnology at MSc at the Department of Biotechnology, Faculty of
Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran. He has over 10 international
medals in invention. Shahin Gavanji's research has focused on Pharmacy and Pharmacology, Nano
Biotechnology, Bioinformatics, Biotechnology - Medical Biotechnology. He is editor in chief of
International Journal of Scientific Research in Inventions and New Ideas.
Dr Aziz is a Professor in environmental engineering at the School of Civil Engineering, Universiti Sains
Malaysia. Dr. Aziz received his Ph.D in civil engineering (environmental engineering) from University of
Strathclyde, Scotland in 1992. He has published over 200 refereed articles in professional
journals/proceedings and currently sits as the Editorial Board Member for 8 International journals. Dr
Aziz's research has focused on alleviating problems associated with water pollution issues from industrial
wastewater discharge and solid waste management via landfilling, especially on leachate pollution. He
also interests in biodegradation and bioremediation of oil spills.
Behrouz Larki is MSc student at Isfahan (Khorasgan) Branch, Islamic Azad University. Behrouz Larki 's
research has focused on Biology, Pharmacy, Linguistic and Translation. He is managing editor of
International Journal of Scientific Research in Inventions and New Ideas.
Amin Mojiri is a PhD candidate in Environmental Engineering, School of Civil Engineering, Universiti
Sains Malaysia (USM), Pulau Pinang. He is fellowship holder and research assistant at the School of Civil
Engineering (USM). He has more than 18 articles in the international journals. He is editor and reviewer of
some international journals. His area of specialization is waste management, waste recycling, wastewater
treatment, wastewater recycling, and soil pollutions.