Difference between revisions of "Team:Queens Canada/Molecular Dynamic Simulations"

 
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<p>Although the nuclear receptors share large homologous segments, their individual sequences can produce large differences in structure in 3D space.  
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<h2 style="width:70%;margin-left:15%">Molecular Dynamic Simulations</h2>
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<p style="width:70%;margin-left:15%;font-size:18px">Although the nuclear receptors share large homologous segments, their individual sequences can produce large differences in structure in 3D space.  
 
Therefore, to create a glucocorticoid biosensor adapted from the existing estrogen receptor- based intein splicing construct developed by Buskirk et al.  
 
Therefore, to create a glucocorticoid biosensor adapted from the existing estrogen receptor- based intein splicing construct developed by Buskirk et al.  
 
2004, we knew that we could gain valuable insight by determining the appropriate length and flexibility of our linkers between the glucocorticoid  
 
2004, we knew that we could gain valuable insight by determining the appropriate length and flexibility of our linkers between the glucocorticoid  
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images we submitted to the Queen’s University Cluster Computer.</p>
 
images we submitted to the Queen’s University Cluster Computer.</p>
  
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<figcaption>The molecular dynamics were run at a temperature of 298K with a total duration of 100 ns (or 0.1 microseconds). The system included a box of  
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<figcaption style="width:70%;margin-left:15%">The molecular dynamics were run at a temperature of 298K with a total duration of 100 ns (or 0.1 microseconds). The system included a box of  
 
water around the protein (i.e. it used explicit solvent) and NaCl was added to neutralize charges and to give a concentration of 100 mM NaCl. Both the  
 
water around the protein (i.e. it used explicit solvent) and NaCl was added to neutralize charges and to give a concentration of 100 mM NaCl. Both the  
 
ions and solvent water molecules were removed for clarity in the movie.</figcaption>
 
ions and solvent water molecules were removed for clarity in the movie.</figcaption>
  
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<figcaption>RMSD Cartoon at Time = 0 seconds</figcaption>
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        <img src="https://static.igem.org/mediawiki/2018/f/f7/T--Queens_Canada--RMSDcartoon0.png" alt='RMSD0'/>
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<p>The molecular dynamics simulation performed consist of the N-terminal of the RecA intein (shown in blue), and the C-terminal of the RecA intein  
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        <figcaption>RMSD Cartoon at Time = 0 seconds</figcaption>
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(shown in red), separated by an N-terminal linker with the sequence GPGGSG, the Ligand Binding domain of the Glucocorticoid Receptor bound to the  
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    </figure>
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agonist Dexamethasone, and then a C-Terminal linker with the sequence GGSGAS. The two halves of the trans-intein and are not immediately associated  
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    <p style="width:70%;margin-left:15%;font-size:18px">The molecular dynamics simulation performed consist of the N-terminal of the RecA intein (shown in blue), and the C-terminal of the RecA intein  
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with each other and therefore not able to splice.</p>
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    (shown in red), separated by an N-terminal linker with the sequence GPGGSG, the Ligand Binding domain of the Glucocorticoid Receptor bound to the  
 +
    agonist Dexamethasone, and then a C-Terminal linker with the sequence GGSGAS. The two halves of the trans-intein and are not immediately associated  
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    with each other and therefore not able to splice.</p>
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<figcaption>RMSD Cartoon at Time = 10 nanoseconds</figcaption>
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        <img src="https://static.igem.org/mediawiki/2018/9/9c/T--Queens_Canada--RMSDcartoon10ns.png" alt='RMSD10ns'/>
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        <figcaption>RMSD Cartoon at Time = 100 nanoseconds</figcaption>
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<p>After 10 nanoseconds of simulation, it can be seen that the linkers are of sufficient length such that the N terminal of the intein, shown in blue  
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    </figure>
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and the C terminal of the intein shown in red, may form a favorable interaction.</p>
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    <p style="width:70%;margin-left:15%;font-size:18px">After 100 nanoseconds of simulation, it can be seen that the linkers are of sufficient length such that the N terminal of the intein, shown in blue  
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    and the C terminal of the intein shown in red, may form a favorable interaction.</p>
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<p>Therefore, from the above media it can be seen that the N-terminal linker GPGGSG, and C-Terminal linker GGSGAS, which were originally adapted from  
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<p style="width:70%;margin-left:15%;font-size:18px">Therefore, from the above media it can be seen that the N-terminal linker GPGGSG, and C-Terminal linker GGSGAS, which were originally adapted from  
 
Buskirk et al. 2004, are sufficient in length and flexibility to form a favourable interaction, and therefore are in close enough proximity to perform  
 
Buskirk et al. 2004, are sufficient in length and flexibility to form a favourable interaction, and therefore are in close enough proximity to perform  
 
an intein splicing event for an agonist-bound glucocorticoid receptor ligand binding domain.</p>
 
an intein splicing event for an agonist-bound glucocorticoid receptor ligand binding domain.</p>
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Latest revision as of 19:10, 17 October 2018

Molecular Dynamic Simulations

Although the nuclear receptors share large homologous segments, their individual sequences can produce large differences in structure in 3D space. Therefore, to create a glucocorticoid biosensor adapted from the existing estrogen receptor- based intein splicing construct developed by Buskirk et al. 2004, we knew that we could gain valuable insight by determining the appropriate length and flexibility of our linkers between the glucocorticoid receptor and the intein. We have achieved this through modeling with PyMol and performing molecular dynamic simulations of the root-mean-square deviation of atomic position. Dr. Campbell of the Department of Biomedical and Molecular Sciences has kindly agreed to run the simulations based on PyMol images we submitted to the Queen’s University Cluster Computer.


The molecular dynamics were run at a temperature of 298K with a total duration of 100 ns (or 0.1 microseconds). The system included a box of water around the protein (i.e. it used explicit solvent) and NaCl was added to neutralize charges and to give a concentration of 100 mM NaCl. Both the ions and solvent water molecules were removed for clarity in the movie.
RMSD0
RMSD Cartoon at Time = 0 seconds

The molecular dynamics simulation performed consist of the N-terminal of the RecA intein (shown in blue), and the C-terminal of the RecA intein (shown in red), separated by an N-terminal linker with the sequence GPGGSG, the Ligand Binding domain of the Glucocorticoid Receptor bound to the agonist Dexamethasone, and then a C-Terminal linker with the sequence GGSGAS. The two halves of the trans-intein and are not immediately associated with each other and therefore not able to splice.

RMSD10ns
RMSD Cartoon at Time = 100 nanoseconds

After 100 nanoseconds of simulation, it can be seen that the linkers are of sufficient length such that the N terminal of the intein, shown in blue and the C terminal of the intein shown in red, may form a favorable interaction.

Therefore, from the above media it can be seen that the N-terminal linker GPGGSG, and C-Terminal linker GGSGAS, which were originally adapted from Buskirk et al. 2004, are sufficient in length and flexibility to form a favourable interaction, and therefore are in close enough proximity to perform an intein splicing event for an agonist-bound glucocorticoid receptor ligand binding domain.