Team:AUC TURKEY/Project/Mechanism

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-
 
-
<div class=WordSection1>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Overview</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The most
 
-
appropriate scale to deducing the qualitative chance in reporter systems relies
 
-
on visual <span class=GramE>data</span>.<a name="_ednref1"></a><a href="#_edn1"
 
-
title=""><span style='mso-bookmark:_ednref1'><span class=MsoEndnoteReference>[i]</span></span><span
 
-
style='mso-bookmark:_ednref1'></span></a><span style='mso-bookmark:_ednref1'></span>The
 
-
reporter system that we designed as an alternative to the current reporter systems
 
-
uses the change factor in the current reporter systems as the response. <span
 
-
class=GramE>Instead of observing change through the synthesis of color, the
 
-
system is built around the observation of change through breaking down dye; the
 
-
dye degradation plays a key role in the system, therefore for the system to
 
-
function there is the requirement of using specific dye in experiments
 
-
alongside the standard lab equipment. </span>The bacteria will degrade the
 
-
necessary dye to report the response.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Color-Based
 
-
Reporter System</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The dye that
 
-
was designated and the enzyme that was to show activity in accordance to it was
 
-
one of our concerns. The enzyme-substrate action in this novel system carried
 
-
great importance and had to be designed with utmost care.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Peroxidases,
 
-
which actively take part in the breakdown of lignin-based compounds thus
 
-
contributing to the maintenance of the continuity of the existence of white rot
 
-
fungi that we based our bleaching enzymes <span class=GramE>on ,were</span>
 
-
enzymes that we took into our prospect. We elected lignin peroxidase, an enzyme
 
-
actively used by white rot fungi to continue their <span class=GramE>life , as</span>
 
-
the enzyme to be implemented into our system. To increase the variance and the
 
-
richness in future application, we chose a secondary enzyme. The secondary
 
-
enzyme was the horseradish peroxidase as it had a very strong structure and
 
-
high activity.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%'>Lignin
 
-
peroxidase:</span></b><span style='font-size:12.0pt;line-height:115%'> Lignin
 
-
is highly resistant to biodegradation and only higher fungi are capable of
 
-
degrading the polymer via an oxidative <span class=GramE>process.Lignin</span>
 
-
is found to be degraded by an enzyme lignin peroxidases produced by some fungi
 
-
like Phanerochaete chrysosporium.The mechanism by which lignin peroxidase (Lip)
 
-
interacts with the lignin polymer which involves Veratryl alcohol (Valc), a
 
-
secondary metabolite of white rot fungi, acts as a cofactor for the enzyme.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>In
 
-
enzymology, a lignin peroxidase (EC 1.11.1.14) is an enzyme that catalyzes the
 
-
chemical reaction</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol
 
-
+ H2O2&nbsp;&nbsp; 3,4-dimethoxybenzaldehyde +
 
-
1-(3,4-dimethoxyphenyl)ethane-1,2-diol + H2O </span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Thus, the
 
-
two substrates of this enzyme are 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol
 
-
and H2O2, whereas its 3 products are 3,4-dimethoxybenzaldehyde,
 
-
1-(3,4-dimethoxyphenyl)ethane-1,2-diol, and H2O. </span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>This enzyme
 
-
belongs to the family of oxidoreductases, specifically those acting on a
 
-
peroxide as acceptor (peroxidases) and can be included in the broad category of
 
-
ligninases. The systematic name of this enzyme class is
 
-
1,2-bis(3,4-dimethoxyphenyl)propane-1,3-<span class=GramE>diol:hydrogen</span>-peroxide
 
-
oxidoreductase. Other names in common use include diarylpropane oxygenase,
 
-
ligninase I,diarylpropane peroxidase, LiP, <span class=GramE>diarylpropane:oxygen</span>,hydrogen-peroxide
 
-
oxidoreductase (C-C-bond-cleaving). It employs one cofactor, heme.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>LiP
 
-
catalyzes the H2O2-dependent oxidation of a variety of lignin model compounds
 
-
in the following multistep reaction sequence:</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>LiP(Fe+3)P +
 
-
H2O2 à LiP-I(Fe+4 – O)P’ + H2O</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>LiP-I(Fe+4 –
 
-
O)P’ + R à LiP-II(Fe+4 – O)P + R’</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>LiP-II(Fe+4
 
-
– O)P + R + 2(H+) à LiP(Fe+3)P + R’ + H2O </span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Horseradish
 
-
peroxidase: The enzyme horseradish peroxidase (HRP), found in the roots of
 
-
plant horseradish, is used extensively in biochemistry applications primarily
 
-
for its ability to amplify a weak signal and increase detectability of a target
 
-
molecule. It is a metalloenzyme with many isoforms and the most studied type is
 
-
C.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The
 
-
structure of the enzyme was first solved by X-ray crystallography in 1997 and
 
-
has since has been solved several times with various substrates. It is an all
 
-
alpha-helical protein which binds heme as a cofactor.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Alone, the
 
-
HRP enzyme, or conjugates thereof, is of little value; its presence must be
 
-
made visible using a substrate that, when oxidized by HRP using hydrogen
 
-
peroxide as the oxidizing agent, yields a characteristic change that is
 
-
detectable by spectrophotometric methods.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Numerous
 
-
substrates for the horseradish peroxidase enzyme have been described and
 
-
commercialized to exploit the desirable features of HRP. These substrates fall
 
-
into several distinct categories. HRP catalyzes the conversion of chromogenic
 
-
substrates (e.g<span class=GramE>.,</span> TMB, DAB, ABTS) into coloured
 
-
products, and produces light when acting on chemiluminescentsubstrates (e.g.
 
-
ECL).</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Horseradish
 
-
peroxidase is a 44,173.9-dalton glycoprotein with 6 lysine residues which can
 
-
be conjugated to a labeled molecule. It produces a coloured, fluorimetric, or
 
-
luminescent derivative of the labeled molecule when incubated with a proper
 
-
substrate, allowing it to be detected and quantified. HRP is often used in
 
-
conjugates (molecules that have been joined genetically or chemically) to
 
-
determine the presence of a molecular target. For example, an antibody
 
-
conjugated to HRP may be used to detect a small amount of a specific protein in
 
-
a western blot. Here, the antibody provides the specificity to locate the
 
-
protein of interest, and the HRP enzyme, in the presence of a substrate,
 
-
produces a detectable <span class=GramE>signal.Horseradish</span> peroxidase is
 
-
also commonly used in techniques such as ELISA and Immunohistochemistry due to
 
-
its monomeric nature and the ease with which it produces coloured products.
 
-
Peroxidase, a heme-containing oxidoreductase, is a commercially important
 
-
enzyme which catalyses the reductive cleavage of hydrogen peroxide by an
 
-
electron donor.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Horseradish
 
-
peroxidase is ideal in many respects for these applications because it is
 
-
smaller, more stable, and less expensive than other popular alternatives such
 
-
as alkaline phosphatase. It also has a high turnover rate that allows
 
-
generation of strong signals in a relatively short time span.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Moreover,
 
-
&quot;In recent years the technique of marking neurons with the enzyme
 
-
horseradish peroxidase has become a major tool. In its brief history, this
 
-
method has probably been used by more neurobiologists than have used the Golgi
 
-
stain since its discovery in 1870.&quot;</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%'>Design</span></b></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>In order to verify
 
-
that the horseradish peroxidase and lignin peroxidase enzymes, which were not
 
-
transformated and synthesized in bacteria in the past, worked; we decided to
 
-
use a constitutive promoter. We chose the constitutive promoter as J23100, one
 
-
of the strongest.&nbsp; We wanted to be certain that our protein is surely
 
-
produced due to the J23100 constitutive promoter that is 35 bp and coming after
 
-
the prefix of 22 base pairs. <span class=GramE>The exhibition of our results in
 
-
Western Blotting through the addition of a 6 histidin long his-tag at the end
 
-
of the horseradish peroxidase C and lignin peroxidase 1 enzyme sequences, which
 
-
contain BamH-I restriction cites that are followed by our ‘AAAGAGGAGAAA’
 
-
sequenced RBS, was added to our lab plans. </span>This would in turn give us
 
-
the safest experimental procedure to validate the presence of the proteins
 
-
syntesized.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The accruity
 
-
of our design was to be tested through getting the dye to react with the
 
-
culture of bacteria containing enzymes that were to be rapidly synthesized
 
-
through the constitutive promoter. The changes ranging from the visually
 
-
observable changes in the color concentration to the shifts in the wavelenght
 
-
absorbance which can only be detected through Varioskan approve the validity of
 
-
our project. The degradation of the specified dyes by the lignin peroxidase and
 
-
horsereadish peroxidase, enzymes we selected to breakdown these dyes, is enough
 
-
to complete the rudimentary part of our project. The addition of the enzymes as
 
-
a composite at the end of another part would enable the production of the
 
-
protein in the sequence as well as the the enzymes enabling the response
 
-
through an accelerated breakdown process.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Aside of the
 
-
affirmation of the synthesis of the enzymes with the Western Blott results, to
 
-
confirm the functionality of the proteins carries great importance. We came to
 
-
the conclusion that working with several methods to verify the results would be
 
-
more professional and certain:</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>-The
 
-
confirmation of the enzyme activity can be <span class=GramE>done</span>
 
-
through collecting the data acquired through the observation of the interaction
 
-
between the interaction of the specified dyes and DegradEcolor bacteria. For
 
-
this feat to be accomplished, the selection of a dye that both lignin
 
-
peroxidase and horseradish peroxidase can degrade in equivalent levels would be
 
-
more reasonable. We chose Methylene blue as the dye to be used as it was
 
-
degraded by the two enzymes in similar amounts during trials. The trials were
 
-
consisting of the observation of the changes in the absorbance and color
 
-
through the reactions between methylene blue and the two enzymes. The
 
-
degradation of the dye plays a keyrole in the determination of the enzyme
 
-
activity<span class=GramE>..</span></span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>-HRP
 
-
activity was assayed using 2,4-dichlorophenol and 4-aminoantipyrine as the
 
-
substrates, substrates used to assay the activity of enzymes. LiP activity was
 
-
assayed using veratryl alcohol as the substrate. </span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>-While
 
-
examining the general properties of the two designated enzymes, we found out
 
-
that the horseradish peroxidase enzyme had the ability to determine the
 
-
presence of a molecular target. If we are to recall the Western blott procedure
 
-
we see the following:</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The proteins
 
-
in the lysate that were planted in the jel first run and transferred to the
 
-
membrane afterwards. After being left to interact with the primary antibodies
 
-
causing the immuglobins to bind with the specific binding site located on the <span
 
-
class=GramE>protein.In</span> the case of contamination or the absence of
 
-
protein synthesis, no binding will be observed. After the completion of the
 
-
binding of the primary antibodies, the secondary antibody binding process
 
-
begins. While the secondary antibodies bind to the primary antibodies, they
 
-
bring with them the horseradish peroxidase enzymes that are attached to them.
 
-
The enhanced chemiluminescence solution does emission under the Western
 
-
blotting device. The luminol in the enhanced chemiluminescence solution is
 
-
oxidised by hydrogen peroxide, however this reaction can only occur in the
 
-
presence of the horseradish peroxidase; as explained, if the proteins are
 
-
correctly synthesized the horseradish peroxidase will cause oxygenation to take
 
-
place causing emission. The same effect can be acquired through the horseradish
 
-
peroxidase that is synthesized by DegradEcolor. In thıs case, the functionality
 
-
of the enzyme could be proven after seeing emission from the interaction
 
-
between the enhanced chemiluminescence solution and DegradEcolor or lysate
 
-
prepared from DegradEcolor. As horseradish peroxidase was able to catalise the
 
-
reaction of hydrogen peroxide, lignin peroxidase, another peroxidase enzyme,
 
-
would most likely be able to have the same effect. We are expecting to see
 
-
emission from the bacteria or lysate prepared from the bacteria that produce
 
-
lignin peroxidase.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Dye
 
-
Degradation</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Methylene blue,
 
-
the dye which the horseradish peroxidase and lignin peroxidase exhibited
 
-
equivalent levels of degradation on, will show that DegradEcolor produced the
 
-
functional proteins. Addition of the horseradish peroxidase or lignin
 
-
peroxidase enzyme sequence to the composite part would make the part include a
 
-
reporter system. If the part is coded and the enzyme is translated, the enzyme
 
-
will be synthesized and change in methylene blue will be observed. Many
 
-
deductions can be obtained with the results of the methylene blue degradation
 
-
including the following:</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>-The
 
-
bleeching of the dye color, which can be understood through qualitative
 
-
observation, allowsus to reach certain conclusions. The bleeching of the color
 
-
primarily indicates that the enzymes were synthesized. therefore no
 
-
contamination took place. Apart from the synthesis factor, the conclusion
 
-
that&nbsp; the conformational structure is functional can be reached. This will
 
-
in turn provide insight that the other desired proteins will also be
 
-
synthesized. The system will also enable the ability to evaluate the efficiency
 
-
of the system through the gradient of color concentration.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>-The changes
 
-
in absorbance will ease the acquirement of the certain results. The absorbance <span
 
-
class=GramE>data</span> can be used to prepare a professional and highly
 
-
efficient scale for examination and use. The prepared scales can be used for
 
-
comparison between the future experiments and the current experiments. It would
 
-
be hard and even erronous to make judgement on strains that do not have high
 
-
protein synthesis but the comparison between the acquired absorbance values and
 
-
the scales not only&nbsp; removes the risk factor but also gives the
 
-
opportunity of making precise judgement in the absence of visual <span
 
-
class=GramE>data</span>.</span></p>
 
-
 
-
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mso-position-vertical-relative:line;mso-width-percent:0;mso-height-percent:0;
 
-
mso-width-relative:page;mso-height-relative:page' o:allowoverlap="f">
 
-
<v:imagedata src="https://static.igem.org/mediawiki/2014hs/e/e3/Ekran_Al%C4%B1nt%C4%B1s%C4%B1.PNG"/>
 
-
<w:wrap type="square" anchory="line"/>
 
-
</v:shape><![endif]--><![if !vml]><img width=776 height=162
 
-
src="https://static.igem.org/mediawiki/2014hs/e/e3/Ekran_Al%C4%B1nt%C4%B1s%C4%B1.PNG"
 
-
align=left hspace=12
 
-
alt="https://static.igem.org/mediawiki/2014hs/e/e3/Ekran_Al%C4%B1nt%C4%B1s%C4%B1.PNG"
 
-
v:shapes="Resim_x0020_2"><![endif]></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'><o:p>&nbsp;</o:p></span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'><o:p>&nbsp;</o:p></span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'><o:p>&nbsp;</o:p></span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'><o:p>&nbsp;</o:p></span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>Advanced
 
-
System</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>The main
 
-
principle of our advanced system that has brought a new dimension to reporter
 
-
systems lies in the variance in the activity levels of the lignin peroxidase
 
-
and horseradish peroxidase enzymes. The enzymes to have effect on one specific
 
-
dye at the same time would not bring us any experimental gain. For this reason,
 
-
the advanced system contains two different dyes alongside the two enzymes. The
 
-
system is built around the inability of one enzyme in degrading the one dye
 
-
while the other can, while the opposite is true for the other dye. Experimental
 
-
systems containing a complex unison of enzymes and dyes can be constructed.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>To further
 
-
enhance our project, we formed such a complex system. The bacteria were given
 
-
two parts, one containing horseradish peroxidase while the other contains
 
-
lignin peroxidase. The dyes that were selected were Methyl green and Azure-b.
 
-
While methyl green is, as the name implies, green colored, azure-b has a color
 
-
in between pink and purple. Horseradish peroxidase can effectively degrade
 
-
methyl green but lacks the ability to effectively degrade azure-b meanwhile
 
-
lignin peroxidase is active in the degradation of azure-b and lackluster in
 
-
degrading methyl green.</span></p>
 
-
 
-
<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%'>If parts
 
-
starting off with different inducible promoters were transformed to the same
 
-
bacteria, different <span class=GramE>data</span> from different conditions
 
-
could be acquired. Think of a system in which the bacteria have inducible
 
-
promoters that are oxygen sensitive and the other carbon dioxide sensitive. If
 
-
methyl green and azure-b was to be added to cause interaction with the bacteria,
 
-
the varying levels of oxygen and carbon dioxide would therefore result in
 
-
different levels of enzymatic activity. Let’s say that the oxygen inducible
 
-
bacteria contain genes that code for horseradish peroxidase and the carbon
 
-
dioxide inducible bacteria contain genes that code for lignin peroxidase. <span
 
-
class=GramE>The variation in the level of oxygen and carbon dioxide would
 
-
change the rate of specific enzyme activity hence leading to a difference in
 
-
the degradation levels of methyl green and azure-b. This would change the color
 
-
of the resultant substrate thus allowing the identification of the activity of
 
-
the inducible promoters. </span>In this way, scales could be prepared for many
 
-
different types of inducible promoters for countless possibilities.</span></p>
 
-
 
-
<div>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt'><span
 
-
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
 
-
mso-fareast-font-family:"Times New Roman"'><br clear=all style='mso-special-character:
 
-
line-break'>
 
-
<o:p></o:p></span></p>
 
-
 
-
<div class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt'><span
 
-
style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
 
-
mso-fareast-font-family:"Times New Roman"'>
 
-
 
-
<hr size=1 width="33%" align=left>
 
-
 
-
</span></div>
 
-
 
-
<div id=edn1>
 
-
 
-
<p class=MsoEndnoteText><a name="_edn1"></a><a href="#_ednref1" title=""><span
 
-
style='mso-bookmark:_edn1'><span class=MsoEndnoteReference>[i]</span></span><span
 
-
style='mso-bookmark:_edn1'></span></a><span style='mso-bookmark:_edn1'></span> <sup><span
 
-
style='color:#252525'>K.E.L. Eriksson, R.A. Blanchette and P. Ander (1990).
 
-
&quot;Microbial and Enzymatic Degradation of Wood and Wood Components,&quot;. <i>Springer-Verlag</i></span></sup></p>
 
-
 
-
<p class=MsoEndnoteText><sup>[i]&nbsp; </sup><sup><span style='font-size:9.0pt;
 
-
color:#333333'>Veitch, Nigel C<span class=GramE>.,</span> <i>Horseradish peroxidase:
 
-
a modern view of a classic enzyme</i>, Phytochemistry, 65, <b>2004</b>,
 
-
249-259, 23-May-2010</span></sup></p>
 
-
 
-
<p class=MsoNormal style='line-height:normal'><sup>[i]</sup><sup><span
 
-
style='font-size:10.0pt'> Ann B. Orth,&nbsp; Daniel J. Royse, Ming Tien
 
-
“Ubiquity of Lignin-Degrading Peroxidases among Various Wood-Degrading Fungi,”
 
-
Applied and Environmental Microbiology (1993):4017-4023</span></sup></p>
 
-
 
-
<h1 style='margin-bottom:5.0pt;line-height:150%'><sup><span style='mso-fareast-font-family:
 
-
"Times New Roman"'>[i]</span></sup><span style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/0168644594900760"><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
color:#316C9D;text-decoration:none;text-underline:none'>Annele Hatakka</span></a></span><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
mso-fareast-font-family:"Times New Roman"'>, “</span><span style='font-size:
 
-
8.0pt;line-height:150%;font-family:"Arial","sans-serif";mso-fareast-font-family:
 
-
"Times New Roman";color:#5C5C5C'>Lignin-modifying enzymes from selected
 
-
white-rot fungi: production and role from in lignin degradation,” </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/journal/01686445"><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
color:#2E2E2E;background:#F9FBFC;text-decoration:none;text-underline:none'>FEMS
 
-
Microbiology Reviews</span></a></span><span style='font-size:8.0pt;line-height:
 
-
150%;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";
 
-
color:#5C5C5C'> (1994):125-135</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h1>
 
-
 
-
<p class=MsoNormal style='line-height:normal'><sup>[i]</sup><span
 
-
style='font-size:8.0pt'> <span style='color:#252525'>Renganathan V, Miki K,
 
-
Gold MH (1985). &quot;Multiple molecular forms of diarylpropane oxygenase, an
 
-
H2O2-requiring, lignin-degrading enzyme from Phanerochaete chrysosporium&quot;.
 
-
<i>Arch. Biochem. Biophys.</i> <b>241</b> (1): 304–14. </span></span><a
 
-
href="http://en.wikipedia.org/wiki/Digital_object_identifier"><span
 
-
style='font-size:8.0pt;color:#0B0080;text-decoration:none;text-underline:none'>doi</span></a><span
 
-
style='font-size:8.0pt;color:#252525'>:</span><a
 
-
href="http://dx.doi.org/10.1016%2F0003-9861%2885%2990387-X"><span
 
-
style='font-size:8.0pt;color:#663366;text-decoration:none;text-underline:none'>10.1016/0003-9861(85)90387-X</span></a><span
 
-
style='font-size:8.0pt;color:#252525'>. </span><a
 
-
href="http://en.wikipedia.org/wiki/PubMed_Identifier"><span style='font-size:
 
-
8.0pt;color:#0B0080;text-decoration:none;text-underline:none'>PMID</span></a><span
 
-
style='font-size:8.0pt;color:#252525'> </span><a
 
-
href="http://www.ncbi.nlm.nih.gov/pubmed/4026322"><span style='font-size:8.0pt;
 
-
color:#663366;text-decoration:none;text-underline:none'>4026322</span></a></p>
 
-
 
-
<p class=MsoEndnoteText><span class=GramE><sup>[i]</sup><a
 
-
href="http://www.jbc.org/search?author1=Susana+Camarero&amp;sortspec=date&amp;submit=Submit"><b><span
 
-
style='font-size:8.0pt;color:#333333;text-decoration:none;text-underline:none'>Susana
 
-
Camarero</span></b></a><b><span style='font-size:8.0pt;color:#403838'>, </span></b><a
 
-
href="http://www.jbc.org/search?author1=Sovan+Sarkar&amp;sortspec=date&amp;submit=Submit"><b><span
 
-
style='font-size:8.0pt;color:#333333;text-decoration:none;text-underline:none'>Sovan
 
-
Sarkar</span></b></a><b><span style='font-size:8.0pt;color:#403838'>, </span></b><a
 
-
href="http://www.jbc.org/search?author1=Francisco+Javier+Ruiz-Due%C3%B1as&amp;sortspec=date&amp;submit=Submit"><b><span
 
-
style='font-size:8.0pt;color:#333333;text-decoration:none;text-underline:none'>Francisco
 
-
Javier Ruiz-Dueñas</span></b></a><b><span style='font-size:8.0pt;color:#403838'>,</span></b><a
 
-
href="http://www.jbc.org/search?author1=Mar%C4%B1%CC%81a+Jes%C3%BAs+Mart%C4%B1%CC%81nez&amp;sortspec=date&amp;submit=Submit"><b><span
 
-
style='font-size:8.0pt;color:#333333;text-decoration:none;text-underline:none'>Marı&#769;a
 
-
Jesús Martı&#769;nez</span></b></a><b><span style='font-size:8.0pt;color:#403838'>
 
-
and </span></b><a
 
-
href="http://www.jbc.org/search?author1=%C3%81ngel+T.+Mart%C4%B1%CC%81nez&amp;sortspec=date&amp;submit=Submit"><b><span
 
-
style='font-size:8.0pt;color:#333333;text-decoration:none;text-underline:none'>Ángel
 
-
T. Martı&#769;nez “</span></b></a><span style='font-size:8.0pt'>Description of
 
-
a Versatile Peroxidase Involved in the Natural Degradation of Lignin That Has
 
-
Both Manganese Peroxidase and Lignin Peroxidase Substrate Interaction Sites,” <span
 
-
style='color:#403838'>Centro de Investigaciones Biológicas, Consejo Superior de
 
-
Investigaciones Cientı&#769;ficas, Velázquez 144, E-28006 Madrid, Spain, last
 
-
accessed 06.21.2014, </span></span><a
 
-
href="http://www.jbc.org/content/274/15/10324.short"><span style='font-size:
 
-
8.0pt'>http://www.jbc.org/content/274/15/10324.short</span></a></span></p>
 
-
 
-
<p class=MsoNormal style='line-height:normal'><sup>[i]</sup><span
 
-
style='font-size:10.0pt'> Jean Luc Wertz and Olivier Bedue, Lignocellulosic
 
-
Biorefineries (Lausanne: EPFL Press, 2013), 278-286</span></p>
 
-
 
-
<h1 style='margin-bottom:5.0pt;line-height:150%'><sup><span style='mso-fareast-font-family:
 
-
"Times New Roman"'>[i]</span></sup><span style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656"><span
 
-
style='font-size:10.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>Wolfgang Blodig</span></a><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656#A1"><sup><span
 
-
style='font-size:12.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>a</span></sup></a></span><sup><span style='font-size:12.0pt;
 
-
line-height:150%;mso-fareast-font-family:"Times New Roman";color:#2E2E2E'>, </span></sup><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656#FN1"><sup><span
 
-
style='font-size:12.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>1</span></sup></a></span><span style='font-size:10.0pt;
 
-
line-height:150%;mso-fareast-font-family:"Times New Roman";color:#2E2E2E'>, </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656"><span
 
-
style='font-size:10.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>Andrew T. Smith</span></a><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656#A2"><sup><span
 
-
style='font-size:12.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>b</span></sup></a></span><span style='font-size:10.0pt;
 
-
line-height:150%;mso-fareast-font-family:"Times New Roman";color:#2E2E2E'>, </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656"><span
 
-
style='font-size:10.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>Kaspar Winterhalter</span></a><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656#A1"><sup><span
 
-
style='font-size:12.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>a</span></sup></a></span><span style='font-size:10.0pt;
 
-
line-height:150%;mso-fareast-font-family:"Times New Roman";color:#2E2E2E'>, </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656"><span
 
-
style='font-size:10.0pt;line-height:150%;color:#316C9D;text-decoration:none;
 
-
text-underline:none'>Klaus Piontek “</span></a><a
 
-
href="http://www.sciencedirect.com/science/article/pii/S0003986199913656"><b><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
color:#5C5C5C;text-decoration:none;text-underline:none'>Evidence from
 
-
Spin-Trapping for a Transient Radical on Tryptophan Residue 171 of Lignin
 
-
Peroxidase,” </span></b></a><a
 
-
href="http://www.sciencedirect.com/science/journal/00039861"><b><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
color:#2E2E2E;background:#F9FBFC'>Archives of Biochemistry and Biophysic</span></b></a></span><span
 
-
style='font-size:8.0pt;line-height:150%;mso-fareast-font-family:"Times New Roman"'>s</span><b><span
 
-
style='font-size:8.0pt;line-height:150%;font-family:"Arial","sans-serif";
 
-
mso-fareast-font-family:"Times New Roman"'> (1999):86-92</span></b><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h1>
 
-
 
-
<h1 style='margin-top:5.0pt;margin-right:0cm;margin-bottom:11.0pt;margin-left:
 
-
0cm;line-height:120%'><sup><span style='mso-fareast-font-family:"Times New Roman"'>[i]</span></sup><span
 
-
style='font-size:8.0pt;line-height:120%;mso-fareast-font-family:"Times New Roman"'>
 
-
</span><span style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://link.springer.com/search?facet-author=%22M.+Yadav%22"><span
 
-
style='font-size:8.0pt;line-height:120%;color:#333333;text-decoration:none;
 
-
text-underline:none'>M. Yadav</span></a></span><span style='font-size:8.0pt;
 
-
line-height:120%;mso-fareast-font-family:"Times New Roman";color:#333333'>, </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://link.springer.com/search?facet-author=%22P.+Yadav%22"><span
 
-
style='font-size:8.0pt;line-height:120%;color:#333333;text-decoration:none;
 
-
text-underline:none'>P. Yadav</span></a></span><span style='font-size:8.0pt;
 
-
line-height:120%;mso-fareast-font-family:"Times New Roman";color:#333333'>, </span><span
 
-
style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://link.springer.com/search?facet-author=%22K.+D.+S.+Yadav%22"><span
 
-
style='font-size:8.0pt;line-height:120%;color:#333333;text-decoration:none;
 
-
text-underline:none'>K. D. S. Yadav</span></a></span><span style='font-size:
 
-
8.0pt;line-height:120%;mso-fareast-font-family:"Times New Roman"'>. “</span><span
 
-
style='font-size:8.0pt;line-height:120%;font-family:"Georgia","serif";
 
-
mso-fareast-font-family:"Times New Roman";color:#333333'>Purification,
 
-
characterization, and coal depolymerizing activity of lignin peroxidase from <i>Gloeophyllum
 
-
sepiarium</i>,” </span><span style='mso-fareast-font-family:"Times New Roman"'><a
 
-
href="http://link.springer.com/journal/10541"><span style='font-size:8.0pt;
 
-
line-height:120%;font-family:"Arial","sans-serif";color:#333333;text-decoration:
 
-
none;text-underline:none'>Biochemistry (Moscow)</span></a></span><span
 
-
style='font-size:8.0pt;line-height:120%;mso-fareast-font-family:"Times New Roman"'>
 
-
(2009):1125-1131</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h1>
 
-
 
-
<p class=MsoNormal style='line-height:normal'><sup>[i]</sup><sup><span
 
-
style='font-size:10.0pt'> <span style='color:#252525'>&nbsp;</span></span></sup><a
 
-
href="http://en.wikipedia.org/wiki/Protein_Data_Bank"><sup><span
 
-
style='font-size:10.0pt;color:#0B0080;text-decoration:none;text-underline:none'>PDB</span></sup></a><sup><span
 
-
style='font-size:10.0pt;color:#252525'> </span></sup><a
 
-
href="http://www.rcsb.org/pdb/explore/explore.do?structureId=1GWU"><sup><span
 
-
style='font-size:10.0pt;color:#663366;text-decoration:none;text-underline:none'>1GWU</span></sup></a><sup><span
 
-
style='font-size:10.0pt;color:#252525'>; Gajhede M, Schuller DJ, Henriksen A,
 
-
Smith AT, Poulos TL (December 1997). &quot;Crystal structure of horseradish
 
-
peroxidase C at 2.15 A resolution&quot;. <i>Nat. Struct. Biol.</i> <b>4</b>(12):
 
-
1032–8. </span></sup><a
 
-
href="http://en.wikipedia.org/wiki/Digital_object_identifier"><sup><span
 
-
style='font-size:10.0pt;color:#0B0080;text-decoration:none;text-underline:none'>doi</span></sup></a><sup><span
 
-
style='font-size:10.0pt;color:#252525'>:</span></sup><a
 
-
href="http://dx.doi.org/10.1038%2Fnsb1297-1032"><span class=GramE><sup><span
 
-
style='font-size:10.0pt;color:#663366;text-decoration:none;text-underline:none'>10.1038</span></sup></span><sup><span
 
-
style='font-size:10.0pt;color:#663366;text-decoration:none;text-underline:none'>/nsb1297-1032</span></sup></a><sup><span
 
-
style='font-size:10.0pt;color:#252525'>. </span></sup><a
 
-
href="http://en.wikipedia.org/wiki/PubMed_Identifier"><sup><span
 
-
style='font-size:10.0pt;color:#0B0080;text-decoration:none;text-underline:none'>PMID</span></sup></a><sup><span
 
-
style='font-size:10.0pt;color:#252525'> </span></sup><a
 
-
href="http://www.ncbi.nlm.nih.gov/pubmed/9406554"><sup><span style='font-size:
 
-
10.0pt;color:#663366;text-decoration:none;text-underline:none'>9406554</span></sup></a></p>
 
-
 
-
<p class=MsoEndnoteText><sup>[i] <span style='color:#252525'>&nbsp;</span></sup><a
 
-
href="http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb?uniprot=P00433"><sup><span
 
-
style='color:#663366;text-decoration:none;text-underline:none'>&quot;Peroxidase
 
-
C1A Related PDB sequences&quot;</span></sup></a><sup><span style='color:#252525'>.
 
-
<i>UniPDB</i>. European Bioinformatics Institute</span></sup></p>
 
-
 
-
<p class=MsoEndnoteText><sup>[i] <span style='color:#252525'>Veitch NC
 
-
(February 2004). &quot;Horseradish peroxidase: a modern view of a classic
 
-
enzyme&quot;. </span></sup><a
 
-
href="http://en.wikipedia.org/wiki/Phytochemistry_(journal)"><i><sup><span
 
-
style='color:#0B0080;text-decoration:none;text-underline:none'>Phytochemistry</span></sup></i></a><sup><span
 
-
style='color:#252525'> <b>65</b> (3): 249–59. </span></sup><a
 
-
href="http://en.wikipedia.org/wiki/Digital_object_identifier"><sup><span
 
-
style='color:#0B0080;text-decoration:none;text-underline:none'>doi</span></sup></a><sup><span
 
-
style='color:#252525'>:</span></sup><a
 
-
href="http://dx.doi.org/10.1016%2Fj.phytochem.2003.10.022"><span class=GramE><sup><span
 
-
style='color:#663366;text-decoration:none;text-underline:none'>10.1016</span></sup></span><sup><span
 
-
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<h1 style='margin-bottom:2.0pt;line-height:80%'><sup><span style='mso-fareast-font-family:
 
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"Times New Roman"'>[i]</span></sup><sup><span style='font-size:10.0pt;
 
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mso-fareast-font-family:"Times New Roman";color:#282828'>Part:BBa_J23100,” last
 
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</div>
 
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Revision as of 21:42, 18 February 2015