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Chapter 56. Tutorial 02
56.1. HYDROPHOBIC Molecular Interaction Field
Go from the your working directory in the Tutorial02 directory:
cd Tutorial02
To begin with we have supplied the same Protein Data Bank file called PDB.pdb on the Tutorial02 directory. The files PDB.kout and grid.in are also supplied in this directory. You therefore do not have to worry about format conversions.
The goal of this tutorial is to produce a Grid kont file containing Molecular Interaction Field for the hydrophobic probe called DRY. If you want more information about the DRY probe click here.
Use your favourite page editor to change the grid.in command file. The grid.in file looks like this:
: : Command File for Programme GRID : : : : Assign Channel Numbers and Output File names : : --------------------------------------------- : LONT 6 LONT PDB.lont KONT 20 KONT PDB.kont : : Assign Channel Numbers and Input File names : : -------------------------------------------- :INPT 10 INPT PDB.kout : : Provide Control Parameters : : --------------------------- : CLER 5.000 DEEP 5.000 DPRO 4.000 DWAT 80.000 EACH 5.000 EMAX 5.000 FARH 5.000 FARR 8.000 ALMD 0.000 KWIK 1 LEAU 0 LENG 20 LEVL 1 LIST -2 MOVE 0 NETA 0 NPLA 2 NUMB 1 VALU 0.000 OH2 IEND First trial with GRID cage round a water molecule. 0 1 : :Record the name of the executable Programme and the name of :the Default Directory as comment lines starting with a colon : : :PROG: /usr/people/GRID/grid :DEFA : |
One must replace the water probe (OH2 line) with another probe with hydrophobic characteristics. Thus, the name DRY should be used for the probe, and the line saying OH2 should be replaced by a line saying DRY. The next thing is to give a title to your computation. You can substitute the old title with a new one like this: "Second trial with bigger CAGE and the DRY probe"
Save the new grid.in file and start the computation using the UNIX command:
Grid < grid.in & (or use the full path /your_grid_directory/grid < grid.in &)
You are now studying a complete protein, and your GRID map will be not restricted to a part of the protein structure like in the previous tutorial. However, the computation over the whole protein will not take more than about eight minutes on a modern processor.
56.1.1. OUTPUT FROM GRID TO GRAPHICS
Begin to use Gview by typing gview with the name of the new grid kont file:
Gview PDB.kont
The Molecular Interaction Field produced by DRY probe will be reported on the screen. This contour level has been automatically selected by the Gview program. To change the energy levels, select:
Edit->Field style
Move the cursor of the interaction energy levels up to -0.5 and then press Exit on the dialogue box. Move the image pressing the left button of the mouse and moving the mouse at the same time.
To import the macromolecule structure together with the DRY MIF, use the commands:
File->Open and select the PDB.kout structures reported on the new dialog. Then press Open.
The PDB.kout structure will be reported on the 3Dplot. Experimental water molecules are represented with red crosses. For more information about Gview setting click here.
Graphic visualisation shows there are 143 water molecules around the PDB structure, and, as expected, the hydrophobic contours of the DRY probe almost always define regions which are not occupied by those waters.
Only one water (O1134) is within the DRY region, and four reasons can be proposed to explain this result: the DRY probe can be incorrect at that position; the experimental results could be incorrect for that water molecule; the water molecule observed by the crystallographer could be something else, like NH4+ ion that has exactly the same number of electrons to diffract X-rays like a water molecule; finally another possibility is that the water is really at that place, but because the position is favoured by a polar side-chain from the next protein molecule in the crystal. Of course without the mentioned structure GRID cannot take into account this effect.
The most negative energy occurs at grid point number 44,45,51. These are the indices defining the grid point, and not the actual xyz coordinates which are 14.500, 10.000 and 33.000 Angstrom. You can find this information using this command:
cat PDB.lont
The strong hydrophobic interaction in this region is mainly due to the interaction of the hydrophobic probe with three residues, such as Trp64, Trp109 and Val99.
It is interesting to note that very close to this highly hydrophobic region there are four water molecules strongly linked to each other by hydrogen bonds. These water molecules are the O1172, O1072, O1073 and O1074 located close to the triptophan residue 109. To find more information about this region, edit the file PDB.lont and look for Z=51. In this table the water molecules are marked with a '*' symbol, to highlight that they were not considered as part of the Target protein during the computation.
The figure below reports the GRID map produced around these supposed water molecules, using a ON probe in grid.in command file. This probe refers to the oxygen's atom of a nitro group. When the energy is contoured at -5.0 kcal, then two of the three oxygens are inside the grid contour. Try to reproduce yourself the view of the figure below.
You have now completed your second Tutorial. Well done!! We look forwards to hearing from you if we can help in any way.
Please, continue with Tutorial 03.
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