Team:EPF-Lausanne/Results

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<font size="10" color="#007CBC">Results of Modeling</font>
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Modeling_overview" onMouseOver="document.MyImage7.src='https://static.igem.org/mediawiki/2009/8/83/Modeling_overview.jpg';" onMouseOut="document.MyImage7.src='https://static.igem.org/mediawiki/2009/6/6d/Modeling_overview_grey.jpg';">
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Analysis_methods" onMouseOver="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/6/6e/An_meth.png/150px-An_meth.png';" onMouseOut="document.MyImage4.src='https://static.igem.org/mediawiki/2009/thumb/0/09/An_meth_nb.png/150px-An_meth_nb.png';">
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Results" onMouseOver="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/2/2f/Results.jpg/150px-Results.jpg';" onMouseOut="document.MyImage6.src='https://static.igem.org/mediawiki/2009/thumb/2/2f/Results.jpg/150px-Results.jpg';">
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<a href="https://2009.igem.org/Team:EPF-Lausanne/Information_&_references" onMouseOver="document.MyImage5.src='https://static.igem.org/mediawiki/2009/thumb/a/a2/Ref.jpg/150px-Ref.jpg';" onMouseOut="document.MyImage5.src='https://static.igem.org/mediawiki/2009/thumb/2/25/Ref_nb.jpg/150px-Ref_nb.jpg';">
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----
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<font size="12" color="#007CBC">Results of Modeling</font>
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=Fusion of the LOV domain and the trpR DNA-binding domain=
 
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{|class="wikitable" border="0" cellpadding="10" cellspacing="1" style="padding: 1px; background-color:#007CBC; text-align:center"
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The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD. We were then able to visualize the different proteins tried by Sosnick.
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!width="20%" align="left" valign="top" style="background:#ffffff; color:black"|
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The working protein, that we call LovTAP is the result of the fusion at PHE22 of trpR and can be seen on the next video. The general LOV domain is in yellow. Please note the chromophore called Flavin (FMN) in red in the center of LOV2. The trpR dna binding domain is in orange and DNA in gray.
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=<font color="#007CBC"><big> Summary of the main results </big></font>=
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==<font color="#007CBC"> Wild type simulations </font>==
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<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/IdcDuIjT5vM&hl=fr&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/IdcDuIjT5vM&hl=fr&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object>
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First of all, the <i>equilibration</i> (stabilization of temperature, pressure and density) was accurate for both states of LOV2 domain.  
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</center>
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::*For dark state, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/EDS#Evolution_of_Pression.2C_Volume_and_Temperature here]
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The fusion was made in VMD by aligning the alpha helix of both domains on the backbone of 3 residues. The secondary structure is quite strong and conserved, what makes this fusion realistic.
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::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#PVT here]
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<a href="javascript:ReverseDisplay('hs1')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to see an example of code used in VMD for the fusion</a>
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: ''set reference [atomselect 0 "resid 20 to 22 and backbone and chain J"]''
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: ''set compare [atomselect 1 "resid 542 to 544 and backbone"]''
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: ''set trans_mat [measure fit $compare $reference]''
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: ''set all [atomselect 1 "all"]''
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: ''$all move $trans_mat''
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Secondly, we analyzed many important characteristics of the system:
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We also modelized the other fusion tried by Sosnick.
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:1. <i>RMSD</i> was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable.  
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* @MET11
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* @ALA12
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* @GLU13
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*...
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* @PHE22
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*...
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* @LEU25
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<a href="javascript:ReverseDisplay('hs13')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clear here to view the other fusions</a>
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* @MET11: we clearly see the the j-alpha helix is not aligned with the helix of the trpR. It is also much longer than in the LovTAP. As we know that the change in the chromophore induced a change in the the j-alpha helix relatively to the beta-sheet of the LOV, we can imagine the j-alpha helix is not well positioned.
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<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/1LlLiJkuUzc&hl=fr&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/1LlLiJkuUzc&hl=fr&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></center><br>
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* @ALA12: same remarks as for the previous. Furthermore, it is clear that LOV is in interaction with bound DNA.
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::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSD here]
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<br><center><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/FQ-xXnKAYEE&hl=fr&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/FQ-xXnKAYEE&hl=fr&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></center></br>
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=Equilibration of dark state=
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::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSD here]
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We run an equilibration of 80ns on the dark state (2v0u).
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Here is a movie over the trajectory file.
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:2. <i>RMSF</i> was analyzed for residues' side chains. We were able to localize, helped by some <b>differential analysis</b> some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).
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==Validation of the simulation==
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::*For dark state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#RMSF here]
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Here we look at the output to check input parameters.
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The raw data for the equilibration match what we set for the NPT. Pressure and temperature are kept constant using namd dynamic. The volume is quite constant as well.
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::*For light state, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#RMSF here]
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[[Image:2v0ueq.jpg|center]]
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::*For the differential analysis, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Sidechains_involved_in_signal_transmission_from_FMN_to_alpha_helix here]
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Then we computed the evolution of the rmsd compared to the first timestep of equilibration. We see that there is a plateau after ~40ns, which means that our system's energy is reaching a minimum. That's clearly what we expected.
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:3. The <i>angle between the main beta sheet and the J-alpha helix</i> of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.
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[[Image:2v0u_rmsd.jpg‎|center]]
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::*For the differential analysis of the angle, see [https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis#Movement_of_the_alpha_helix here]
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The comparison of the RMSF over the simulation to the beta factor measured during crystallography is a nice validation of our simulation. We get quite similar curves, with some differences at one end of the protein. We see in the movie that this part moves a lot.
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:4. Side chain <i>dihedral angle</i> of the reactive cystein (residue 450) was computed for both state.
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[[Image:2v0u_rmsf.jpg‎|center]]
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==Analysis of the simulation==
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:Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.
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We have organized our analysis on 2 main ideas:
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* Find a structural change in the j-alpha helix based on the simulation using namd.
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* Find residues showing different comportment in dark and light state
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::*Important graphs and explanations, see [https://2009.igem.org/Team:EPF-Lausanne/Results/EDS#CYS450_-_FMN here]
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First, we start by looking at the angle between the beta sheet and the j-alpha helix.
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:These results were expected, because they confirm the in vitro results obtain by [Halavaty et al.], and this confirm once again that our simulation seems to be accurate.
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:In the light state, the cystein is covalently bonded with the cofactor, FMN, so the side chain dihedral angle was far more stable than in the dark state. This result was completely expected because after a covalent bonding with a big set of atom such as the FMN, the cystein's side chain is less free to move.
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<a href="javascript:ReverseDisplay('hs2')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to see the code used in VMD to get angle data</a>
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: ''source [[Media:Fit_angle.txt‎|fit_angle.tcl]]''
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: ''sel_angle_frames 0 "resid 522 to 543 and protein" {1 0 0}''
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: ''sel_sel_angle_frames 0 "resid 522 to 543 and protein" "resid 493 to 498 and protein"''
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We get a quite constant value. It will be more interesting to compare this graph to the light state.
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::*Important graphs and explanations, see [https://2009.igem.org/Team:EPF-Lausanne/Results/ELS#CYS450_-_FMN here]
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[[Image:2v0u_angoli.jpg‎|center]]
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==<font color="#007CBC"> Simulations of non-light activated LOV2 domain with specific mutations </font>==
 +
Based on the cystein's side chain movement analysis, residue mutations near the active site were designed. The goal was to "push" the side chain of the cystein more often in the direction of the FMN with steric interactions.
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The residues 513 seems to be involved in stabilisation of FMN through hydogen bonds. There is a picture of the situation, residue ASN 414 is on the left, GLN513 in the middle and the FMN is in red. All the hydrogen bonds we investigated over the simulation are pictured.
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For a better view of the active site, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#Active_site here]
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[[Image:2v0u_414_513_FMN.jpg|center|400px]]
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Here is a plot of the distance between the 2 hydrogens from sidechain of GLN513 to the oxygen of FMN. HE22 is definitely involved in an hydrogen bond.
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===<font color="#007CBC"><small> I427F </small></font>===
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[[Image:2v0u_dist_513_FMN.jpg|center|750px]]
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Here the isoleucine 427 was replaced by a phenylalanine.
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=Equilibration of light state=
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This mutation gave very interesting results: 
 +
:<i><big>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~57% in the I427F mutant.</big></i>
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After having modified some parameters in the parameter files, here is the movie concerning the light state of the protein  with the FMN:
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::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#ILE427_to_PHE here]
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[[Media:Light_FMN_without_water.mov | Light State]]
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<p align="center">
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So, an <i>important hypothesis</i> appears:
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<font size="5">
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:If the cystein's side chain points more often toward its reacting carbon in the FMN, there is more chances that upon light activation a covalent bond will be made. Moreover, if there is more steric obstruction toward the unbonding this newly formed covalent bond, this covalent bond will be stabilized, and it will finally leads to a general stabilization of the light activated state of the protein.
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'''Light state'''
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<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/r08C7t0p-0k&hl=fr&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always">
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<embed src="http://www.youtube.com/v/r08C7t0p-0k&hl=fr&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="never" allowfullscreen="true" width="425" height="344">
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=Analysis=
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===<font color="#007CBC"><small> L453G </small></font>===
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* <big>Maxwell-Boltzmann Energy Distribution</big>
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Here the leucine 453 was replaced by a glycine in order to let empty space for glycine's side chain to move toward the FMN.
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We obtain the following histogramm!
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[[Image:Maxwell-Boltzmann_Energy_Distribution.jpg|Energy]]
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This mutation gave less interesting results than the first mutation: 
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:<i>It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~31% in the I427F mutant.</i>
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* <big>Temperature</big>
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::*Important result, see [https://2009.igem.org/Team:EPF-Lausanne/Results/Mutations#LEU453_to_GLY here]
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Using EXCEL, we obtain the following graph, which represents the evolution of the temperature in function of time:
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<br>[[Image:Temp(t).png]]
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<br>The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
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So, an <i>important hypothesis</i> appears:
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:In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.
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|}
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* <big>Density</big>
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<br>
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Using EXCEL, we obtain the following graph, which represents the evolution of the density in function of time:
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<center><big><font color="red"><b><i>Click on each title below to access the detailled results.</i></b></font></big></center>
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<br>[[Image:Density.jpg]]
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<br>
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<br>The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
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=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Fusion<font color="#007CBC"> Fusion of the LOV domain and the trpR DNA-binding domain</font>]=
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* <big>Pressure</big>
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The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD, namely the LOV domain and the TrpR DNA-binding domain. It allowed to visualize the different proteins tried by Sosnick. The working protein, that we call LovTAP is the result of the fusion at PHE22 of TrpR.
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Here is a small plot of pressure and temperature in function of time
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[[Image:1st_run.jpg|Run]]
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<br><br>
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=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/EDS <font color="#007CBC">Dark State simulation</font>]=
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This is where we run a long simulation on the dark state system and analyze the output.
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In the analysis, we tried to achieve the following goals:
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* find a structural change in the Jα helix based on the simulation
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* find residues showing different comportment in dark and light state
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* <big>RMSD</big>
 
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<br>We obtain the following picture:
 
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<br>
 
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[[Image:RMSD_CA_per_res.jpg]]
 
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<br>
 
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<p align="center"><big> <b>RMSD of residue within 3 angström of the FMN</b> </big></p>
 
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[[Image:Resid_3A.jpg]]
 
<br><br>
<br><br>
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We can see that the residues that move the most are the residue number: 425, 451, 453
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=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/ELS <font color="#007CBC">Light state simulation</font>]=
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The light state corresponds to the photoactivated state of the LOV domain, and here are gathered results concerning the light state from a 60ns simulation starting after previous equilibration.
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 +
<br> We mainly focused on an analysis of dihedral angles to understand the movement of useful residues.
<br><br>
<br><br>
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<p align="center"><big> <b>RMSD of residue within 6 angström of the FMN</b> </big></p>
 
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[[Image:Resid_6A.jpg]]
 
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<br>
 
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We can see that the residues that move the most are the residue number:  424, 425, 464, 468
 
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<br>
 
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=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Differential_Analysis <font color="#007CBC">Differential Analysis</font>]=
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* <big>RMSD of selected atoms compared to initial position along time</big>
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Now that the two states are well-characterized, we want to confront the two visions of the protein. This part is thus devoted to the comparison of the two states.
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Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.
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<br>[[Image:Rmsd.jpg]]
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<br><br><br>
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Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708
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After a detailed analysis based on both previous simulation, we were able to determine that the stability of the Cystein 450 is highly correlated with the creation of the covalent bound to the FMN.
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<br>[[Image:RMSD_plateau.jpg]]
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<br><br><br>
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FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. <b>We should compute an average value to normalize amplitude</b>. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393
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<br><br>
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<br>[[Image:RMSD_COMPLETE_RUN.jpg]]
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=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Mutations <font color="#007CBC">Mutations</font>]=
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* <big>Salt bridges</big>
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Our final goal is to find a way to make the protein more stable, or to increase its affinity: that's why we imagined some ponctual mutations on some particular residues to do so.
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Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge.
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<br>
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[[Image:Salt_bridge.jpg]]
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We picked the more mobile residues in the beta sheet, closest to the CYS450, and see if they can improve the overall stability. Here is a list of the mutations planned:
 +
* ILE427 mutated in PHE
 +
* LEU453 mutated in GLY
 +
These were partly based on studies made by :
 +
# Zoltowski:'' Mechanism-based tuning of a LOV domain photoreceptor''
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# Christie, ''Steric Interactions Stabilize the Signaling State of the LOV2 Domain of Phototropin 1''
 +
<br> see [https://2009.igem.org/Team:EPF-Lausanne/Information_&_references#LOV2_.26_LOVTAP_references here] for more information.
 +
We ran two other simulations after mutating the LOV domain at these residues and we discovered a much better stability of the cystein due to I427F. In this configuration, the cystein points toward the FMN in 57,2% of the cases, which is almost twice better as in the wild type protein!
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* <big>RMSF</big>
 
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[[Image:2v02_1ns_rmsf.jpg]]
 
<br><br>
<br><br>
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This is a 1 nanosecond NPT run at 300°K. We hope to see a RMSF curve identical to the beta factor. It should only be shifted higher because of the increased temperature. But having a similar tendency would mean our simulation show oscillations similar to what was observed during crystallography. This is really a quite nice validation of our run!
 
 +
=[https://2009.igem.org/wiki/index.php?title=Team:EPF-Lausanne/Results/Validation <font color="#007CBC">Validation of the equilibration</font>] =
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=Differential analysis=
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This part brings together results validating our equilibration. This one is composed of 3 different steps:
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==Some useful distances==
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* first a '''minimization''', where we try to find a minimum of energy. In fact, it is essential to find a stable point on the potential energy surface in order to begin dynamics. At a minimum on the potential energy surface, the net force on each atom vanishes.
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* <big>Bond between Gln497 and Lys533 in dark state</big>
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Constraints are imposed during minimization.
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[[Image:Gln497.JPG‎ |800px|bond1]]
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<br>
 +
To minimize we need a function (provided by the forcefield) and a starting set of coordinates. The magnitude of the first derivative can be used to determine the direction and magnitude of a step (i.e. change in the coordinates) required to approach a minimum configuration. To reach the minimum the structure must be successively updated by changing the coordinates (taking a step) and checking for convergence. Each complete cycle of differentiation and stepping is known as a minimization iteration.
 +
<br><br>
 +
* a second step composed with a '''heating''' of our protein allows to increase the temperature from 5 to 300K.
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<br>
 +
* finally, we do an '''equilibration'''. This equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to false trajectories in protein dynamics.
 +
<br>
 +
The equilibration can itself be divided into 3 phases:
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- an NPT
 +
- an NVT
 +
- again an NPT
 +
<br>
 +
The aim of doing a minimization followed by an equilibration simulation is to generate a trajectory for the system, which will be analysed further.  
 +
<br>
 +
This part gathers together plots confirming that our minimization-heating-equilibration were correct, and that we followed with a good file of trajectories.
-
* <big>Bond between Gln475 and Lys533 in dark state</big>
 
-
[[Image:Gln475.JPG‎|800px|bond2]]
 
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Latest revision as of 23:20, 21 October 2009






                                               




Results of Modeling



Summary of the main results

Wild type simulations

First of all, the equilibration (stabilization of temperature, pressure and density) was accurate for both states of LOV2 domain.

  • For dark state, see here
  • For light state, see here

Secondly, we analyzed many important characteristics of the system:

1. RMSD was analyzed of all residues' alpha carbon, which shows us that the protein was stable and that our simulation was apparently trustable.
  • For dark state, see here
  • For light state, see here
2. RMSF was analyzed for residues' side chains. We were able to localize, helped by some differential analysis some residues that move much more than others, which would mean that these moving residues were possibly implicated in the movement transmission that induces the general conformational change of the protein upon light activation. The movement of these residues were not correlated. And further analysis demonstrate that we were not able to see the conformational change (see below).
  • For dark state, see here
  • For light state, see here
  • For the differential analysis, see here
3. The angle between the main beta sheet and the J-alpha helix of LOV2 domain was computed, and we could not see any periodic main movement neither in the dark nor the light state.
  • For the differential analysis of the angle, see here
4. Side chain dihedral angle of the reactive cystein (residue 450) was computed for both state.
Interestingly, in the dark state we were able to find that the sulfur atom of this cystein point 30% of the time toward the cofactor, FMN (molecule that reacts with the protein upon light activation) and 70% of the time toward the opposite side of the FMN.
  • Important graphs and explanations, see here
These results were expected, because they confirm the in vitro results obtain by [Halavaty et al.], and this confirm once again that our simulation seems to be accurate.
In the light state, the cystein is covalently bonded with the cofactor, FMN, so the side chain dihedral angle was far more stable than in the dark state. This result was completely expected because after a covalent bonding with a big set of atom such as the FMN, the cystein's side chain is less free to move.
  • Important graphs and explanations, see here

Simulations of non-light activated LOV2 domain with specific mutations

Based on the cystein's side chain movement analysis, residue mutations near the active site were designed. The goal was to "push" the side chain of the cystein more often in the direction of the FMN with steric interactions.

For a better view of the active site, see here

I427F

Here the isoleucine 427 was replaced by a phenylalanine.

This mutation gave very interesting results:

It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~57% in the I427F mutant.
  • Important result, see here

So, an important hypothesis appears:

If the cystein's side chain points more often toward its reacting carbon in the FMN, there is more chances that upon light activation a covalent bond will be made. Moreover, if there is more steric obstruction toward the unbonding this newly formed covalent bond, this covalent bond will be stabilized, and it will finally leads to a general stabilization of the light activated state of the protein.

L453G

Here the leucine 453 was replaced by a glycine in order to let empty space for glycine's side chain to move toward the FMN.

This mutation gave less interesting results than the first mutation:

It changed the amount of time the cystein's side chain point toward the FMN from 30% in the wild type to ~31% in the I427F mutant.
  • Important result, see here

So, an important hypothesis appears:

In that case, it seems that the cystein's side chain dosen't move a lot if empty space is available. This hypothesis sounds rational because the cystein in the wild type protein move in a more or less stable way in its available space. So, in increasing only the space available will make move the side chain slightly more but not significantly.


Click on each title below to access the detailled results.


Fusion of the LOV domain and the trpR DNA-binding domain

The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD, namely the LOV domain and the TrpR DNA-binding domain. It allowed to visualize the different proteins tried by Sosnick. The working protein, that we call LovTAP is the result of the fusion at PHE22 of TrpR.



Dark State simulation

This is where we run a long simulation on the dark state system and analyze the output.

In the analysis, we tried to achieve the following goals:

  • find a structural change in the Jα helix based on the simulation
  • find residues showing different comportment in dark and light state



Light state simulation

The light state corresponds to the photoactivated state of the LOV domain, and here are gathered results concerning the light state from a 60ns simulation starting after previous equilibration.


We mainly focused on an analysis of dihedral angles to understand the movement of useful residues.



Differential Analysis

Now that the two states are well-characterized, we want to confront the two visions of the protein. This part is thus devoted to the comparison of the two states.

After a detailed analysis based on both previous simulation, we were able to determine that the stability of the Cystein 450 is highly correlated with the creation of the covalent bound to the FMN.



Mutations

Our final goal is to find a way to make the protein more stable, or to increase its affinity: that's why we imagined some ponctual mutations on some particular residues to do so.
We picked the more mobile residues in the beta sheet, closest to the CYS450, and see if they can improve the overall stability. Here is a list of the mutations planned:

  • ILE427 mutated in PHE
  • LEU453 mutated in GLY

These were partly based on studies made by :

  1. Zoltowski: Mechanism-based tuning of a LOV domain photoreceptor
  2. Christie, Steric Interactions Stabilize the Signaling State of the LOV2 Domain of Phototropin 1


see here for more information.

We ran two other simulations after mutating the LOV domain at these residues and we discovered a much better stability of the cystein due to I427F. In this configuration, the cystein points toward the FMN in 57,2% of the cases, which is almost twice better as in the wild type protein!



Validation of the equilibration

This part brings together results validating our equilibration. This one is composed of 3 different steps:

  • first a minimization, where we try to find a minimum of energy. In fact, it is essential to find a stable point on the potential energy surface in order to begin dynamics. At a minimum on the potential energy surface, the net force on each atom vanishes.

Constraints are imposed during minimization.
To minimize we need a function (provided by the forcefield) and a starting set of coordinates. The magnitude of the first derivative can be used to determine the direction and magnitude of a step (i.e. change in the coordinates) required to approach a minimum configuration. To reach the minimum the structure must be successively updated by changing the coordinates (taking a step) and checking for convergence. Each complete cycle of differentiation and stepping is known as a minimization iteration.

  • a second step composed with a heating of our protein allows to increase the temperature from 5 to 300K.


  • finally, we do an equilibration. This equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to false trajectories in protein dynamics.


The equilibration can itself be divided into 3 phases: - an NPT - an NVT - again an NPT
The aim of doing a minimization followed by an equilibration simulation is to generate a trajectory for the system, which will be analysed further.


This part gathers together plots confirming that our minimization-heating-equilibration were correct, and that we followed with a good file of trajectories.