Difference between revisions of "Team:Peking/Model/GelPoint"

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<p>Our SpyTag/SpyCatcher network surely belongs to the category of three-dimensional networks, which requires at least one kind of the reactant possess a functionality more than 2. We attempt to anticipate the gel point specific for the TDP with reaction extent p through Flory’s Theory.</p>
 
<p>Our SpyTag/SpyCatcher network surely belongs to the category of three-dimensional networks, which requires at least one kind of the reactant possess a functionality more than 2. We attempt to anticipate the gel point specific for the TDP with reaction extent p through Flory’s Theory.</p>
 
<p>For a more direct route from initial experimental parameter configuration to its prediction, the linkage between the initial solution state and final reaction extent (when it reaches equilibrium) may be established. A simple way to do this, with enough qualitative credibility, is to use the concentrations of the functional groups A and B, together with the equilibrium constant K of the condensation reaction between A and B:</p>
 
<p>For a more direct route from initial experimental parameter configuration to its prediction, the linkage between the initial solution state and final reaction extent (when it reaches equilibrium) may be established. A simple way to do this, with enough qualitative credibility, is to use the concentrations of the functional groups A and B, together with the equilibrium constant K of the condensation reaction between A and B:</p>
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<p style="text-align:center;"><img style="width:  %;" src="https://static.igem.org/mediawiki/2016/0/08/T--Peking--images_mdy_fig2.png" alt=""/></p>
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<p>It is worth noting that the intramolecular reactions would lead to the formation of “loop”, which decreases the degree of crosslinking and the strength of polymers. That’s to say, the effective part of crosslinking is the intermolecular reaction of the functional groups on monomers (Figure 2).</p>
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<figure>
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    <p style="text-align:center;"><img style="width:%;" src="https://static.igem.org/mediawiki/2016/e/e3/T--Peking--images_mdy_fig3.png" alt=""/></p>
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    <figcaption style="text-align:justify;">
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        <p>Fig. 2. Intramolecular and intermolecular reaction. A: Intramolecular reaction leads to the formation of “loop” and decrease the degree of crosslinking. B: Intermolecular reaction will increase the degree of crosslinking and result in gelation.</p>
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    </figcaption>
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</figure>
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<p>In Flory’s description, a branched oligomer becomes a crosslinking polymer when the reactive extent reaches the gel point <i>P<sub>c</sub></i>. </p>
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<p>In Flory-Stockmayer Theory, the formula used to calculate the gel point <i>P<sub>c</sub></i> is well described. We have therefore derived the formula to calculate the <i>P<sub>c</sub></i> for our own case,
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<p style="text-align:center;"><img style="width:  %;" src="https://static.igem.org/mediawiki/2016/6/69/T--Peking--images_mdy_fig4.png" alt=""/></p>
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<p>Where the parameters are:</p>
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<p><i>P<sub>c</sub></i>: The gel point, at which the gel forms.
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</p>
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<p><i>N<sub>A</sub></i>: The amount of monomers containing functional groups A.
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</p>
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<p><i>N<sub>B</sub></i>: The amount of monomers containing functional groups B.
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</p>
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<p><i>f<sub>A</sub></i>: Functionality of monomers containing A, e.g. when the system contains equivalent amounts of A-A and A-A-A, then.
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</p>
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<p><i>f<sub>B</sub></i>: Functionality of monomers containing B.
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</p>
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<p>The deduction of formula (2) is contained in Supplementary Information- Calculation of the Gel Point.</p>
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<p>Assume that the total number of A and B is constant, then the differences of the propensities towards different kinds of configurations can easily be compared via their respective gel points. Hereby a tetrad SpyTag-SUP and double SpyCatcher reaction is a different configuration from a triple SpyTag-SUP and triple SpyCatcher reaction. </p>
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<p>We define <i>θ</i> as the fraction of SpyTag-SUP in the mixture of SpyTag and SpyCatcher,</p>
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<p style="text-align:center;"><img style="width:  %;" src="https://static.igem.org/mediawiki/2016/8/8f/T--Peking--images_mdy_fig5.png" alt=""/></p>
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<p>Then the relation between <i>P<sub>c</sub></i> and <i>θ</i> is,</p>
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<p style="text-align:center;"><img style="width:  %;" src="https://static.igem.org/mediawiki/2016/d/d2/T--Peking--images_mdy_fig6.png" alt=""/></p>
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<p>Which can be described in figure 3,
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</p>
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<figure>
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    <p style="text-align:center;"><img style="width:%;" src="https://static.igem.org/mediawiki/2016/8/83/T--Peking--images_mdy_fig7.png" alt=""/></p>
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    <figcaption style="text-align:justify;">
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        <p>Fig. 3.  Theoretical gel points for a number of monomer configurations. The horizontal axis represents the amount (or molar concentration) of nA-SUP over the amount (or molar concentration) of all monomers, <b><i>θ</i></b>, while the vertical axis represents the gel point, <b><i>P<sub>c</sub></i></b>.</p>
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    </figcaption>
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</figure>
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<p>High <i>P<sub>c</sub></i> means low probability of gelation, thus low degree of crosslinking, during the reaction process. As we have mentioned, this will not be easy to form a polymer network with high degree of crosslinking and lead to poor mechanical strength and a small contact area with solution. We thus choose triple, tetrad, and sextuple SpyTag-SUP (3/4/6A-SUP) and triple SpyCatcher (3B) as basic crosslinking monomers.</p>
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                                <h3>References:</h3>
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                                <p>[1] Zakeri, B., et al., Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. <i>Proceedings of the National Academy of Sciences</i>, <b>2012. 109(12)</b>: p. E690-E697.</p>
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                                <p>[2] Lu, Z. et al. A protein engineered to bind uranyl selectively and with femtomolar affinity. <i>Nature chemistry 1856</i>, <b>236-241</b> (2014).</p>
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                                <p>[3] Sau-Ching, W. et al. Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction. <i>Proteins 77</i>, <b>404-412</b> (2009).</p>
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Revision as of 09:34, 18 October 2016

Gel Point Model

Model of Gel Point.

Calculate the Gel Point

For some definitions, a polymer is a large molecule, or macromolecule, composed of many repeated subunits. Polymerization is a process of reacting monomer molecules together in a chemical reaction to form polymer chains or three-dimensional networks.

A condensation reaction, is a chemical reaction in which two molecules or moieties, often functional groups, combine to form a larger molecule, together with the loss of a small molecule. And in polymer science, the condensation reaction between monomers are called condensation polymerization. The condensation polymerization comprises 2 kinds of reactions - linear polymerization (LP) and three-dimensional polymerization (TDP). The difference between these two reaction types is that the former can lead to the formation of one-dimensional polymers, while the latter to the three-dimensional crosslinking networks (Figure 1). It is well-known that crosslinking network formed by TDP possess a larger contact area and higher mechanical strength. We thus decide to use monomers containing more than 3 functional groups, i.e., the poly-branching monomer Af (f>=3, where A stands for “functional group”, or “functionality”).

Fig. 1. Common kinds of polymerization. A: Linear Polymerization, B: Three-dimensional Polymerization. Functional groups a and b can react with each other. M can neither react with a nor b.

Gelation, reflecting a certain reaction extent polymerization would perform, is a common phenomenon of TDP, during which the physical properties like the degree of crosslinking, the viscosity and the “rigidity” of polymers increase a lot. Although the gel could collapse and be dissolved, what we really want to do in our project is to avoid gelation and increase the degree of crosslinking as much as possible.

Our SpyTag/SpyCatcher network surely belongs to the category of three-dimensional networks, which requires at least one kind of the reactant possess a functionality more than 2. We attempt to anticipate the gel point specific for the TDP with reaction extent p through Flory’s Theory.

For a more direct route from initial experimental parameter configuration to its prediction, the linkage between the initial solution state and final reaction extent (when it reaches equilibrium) may be established. A simple way to do this, with enough qualitative credibility, is to use the concentrations of the functional groups A and B, together with the equilibrium constant K of the condensation reaction between A and B:

It is worth noting that the intramolecular reactions would lead to the formation of “loop”, which decreases the degree of crosslinking and the strength of polymers. That’s to say, the effective part of crosslinking is the intermolecular reaction of the functional groups on monomers (Figure 2).

Fig. 2. Intramolecular and intermolecular reaction. A: Intramolecular reaction leads to the formation of “loop” and decrease the degree of crosslinking. B: Intermolecular reaction will increase the degree of crosslinking and result in gelation.

In Flory’s description, a branched oligomer becomes a crosslinking polymer when the reactive extent reaches the gel point Pc.

In Flory-Stockmayer Theory, the formula used to calculate the gel point Pc is well described. We have therefore derived the formula to calculate the Pc for our own case,

Where the parameters are:

Pc: The gel point, at which the gel forms.

NA: The amount of monomers containing functional groups A.

NB: The amount of monomers containing functional groups B.

fA: Functionality of monomers containing A, e.g. when the system contains equivalent amounts of A-A and A-A-A, then.

fB: Functionality of monomers containing B.

The deduction of formula (2) is contained in Supplementary Information- Calculation of the Gel Point.

Assume that the total number of A and B is constant, then the differences of the propensities towards different kinds of configurations can easily be compared via their respective gel points. Hereby a tetrad SpyTag-SUP and double SpyCatcher reaction is a different configuration from a triple SpyTag-SUP and triple SpyCatcher reaction.

We define θ as the fraction of SpyTag-SUP in the mixture of SpyTag and SpyCatcher,

Then the relation between Pc and θ is,

Which can be described in figure 3,

Fig. 3. Theoretical gel points for a number of monomer configurations. The horizontal axis represents the amount (or molar concentration) of nA-SUP over the amount (or molar concentration) of all monomers, θ, while the vertical axis represents the gel point, Pc.

High Pc means low probability of gelation, thus low degree of crosslinking, during the reaction process. As we have mentioned, this will not be easy to form a polymer network with high degree of crosslinking and lead to poor mechanical strength and a small contact area with solution. We thus choose triple, tetrad, and sextuple SpyTag-SUP (3/4/6A-SUP) and triple SpyCatcher (3B) as basic crosslinking monomers.

References:

[1] Zakeri, B., et al., Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proceedings of the National Academy of Sciences, 2012. 109(12): p. E690-E697.

[2] Lu, Z. et al. A protein engineered to bind uranyl selectively and with femtomolar affinity. Nature chemistry 1856, 236-241 (2014).

[3] Sau-Ching, W. et al. Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction. Proteins 77, 404-412 (2009).

Supplementary Information