Visual Molecular Dynamics a First Introduction to Scientific Visualization

Visual Molecular Dynamics A First Introduction to Scientific Visualization

Geoffrey Gray

VMD on CIRCE:

On the lower bottom left of your screen, click on the window start-up menu. In the search box type “mstsc”. Click on “mstsc.exe”. On hostname type “circe.rc.usf.edu” Enter your login name and password at the prompts; this will open a new window. In this window on the menu bar select “Applications” (top left). Select “System Tools” at the bottom of the drag down menu. Select “Terminal”. In the terminal, type “module load apps/vmd/1.9”. Next type “vmd”; this will launch the program.

Usage:

During a simulation, a tremendous amount of data is generated. In general this is good, as it provides researchers with a large number of options for analysis. However, if you are unable to express this data in a meaningful way, then it is useless. One of the ways that computational scientists may try to interpret the results of their simulations is via the use of visualization software. There are many freely available programs available on the internet. Today we will use one of the most popular, Visual Molecular Dynamics (VMD) VMD allows the user to look at the crystal structure of a sample, or to watch a simulation by looking multiple frames (snapshots) of their simulation. We will look at these molecular “movies” in some of the later exercises. Right now, we will just look at single crystal structures. You might wonder where we could obtain a crystal structure of a protein. These structures are obtained experimentally and then downloaded as files to a large database known as the Protein Database (PDB). These PDB files are a common format for expressing molecular structures. In order to download our first file, go to the following website url: http://www.rcsb.org/pdb/home/home.do

Today we will look at two different structures. First, type in the code 4OC7, a crystal structure of the retinoid X-receptor (RXR). It binds to DNA, regulating gene expression. The genes regulated by the RXR are involved in apoptosis (regulated cell death). Numerous diseases (such as cancer) occur when cell death fails to occur. Thus, by promoting the binding of the RXR to the gene, apoptosis is promoted, which had many therapeutic benefits.

First load in the 4OC7 structure by going to File > New Molecule > Browse > Load.

Take a moment to look at the resulting crystal structure. Because it was obtained by X-ray crystal diffraction, the hydrogens do not show up. Why is this?

Now that we have a crystal loaded, we can change the representation mode to display it in a way that may be more insightful to us. First let's change the representation by going to Graphics > Representations > Drawing Method > Licorice.

Notice this is very crowded, and it is difficult to really see the system in a helpful way. Thankfully, the makers of VMD have provided a variety of display options. Following the same procedure as before, change the drawing method to New Cartoon. This is a very pleasing way to display large proteins and gives structural information that otherwise is not available in methods that draw molecules as lines (e.g. lines, licorice, cpk, etc.). You will notice three different types of structures, twisting, flattened arrows, and coiled loops. These represent the secondary structure of α-helices, β-sheets, and loops. If you do not see them, that is okay, we can also change the coloring methods for the structure. To do this, under Representations, go to Coloring Method > Secondary Structure.

You will now see several different types of colors corresponding to four different structural elements. Purple corresponding to alpha helices, yellow for beta-sheets, white for turns, and cyan for regions. Notice how much more information we get from this representation, as opposed to the lines or the licorice. We now have experimental data on the structural features of our protein.

Now that we have our protein expressed in a way that makes some sense to us, we can express individual portions of the protein differently. If any of your noticed, the protein was bound to a ligand. This ligand is not shown by New Cartoon, because it does not fall into any of the structural categories we have previously looked at. However, we can choose to show it in a different representation and include it in our image. Under Representations, press Create Rep. This will add a second representation, which we may then modify without disturbing the original. Highlight this second representation and in the Selected Atoms space type “not protein”. Once this is done, go to Drawing Method and choose Licorice, and then go to Coloring Method and choose Name. Now, compounds that are not proteins may be seen in conjunction with proteins. The selection option is a very powerful tool, and may be used to define a number of specific features. For example, create another representation by hitting Create Rep. Next type “resname ARG” as the selection. Now, consider if we wished to look at potential contacts between the ligand and the protein. To do this, we may select all atoms within a specified distance of the ligand (given in Å). Notice now how we have reduced the overwhelming image to only a few pertinent pieces of data.

Load an MD Trajectory:

In VMD perform the following:

File > New Molecule. Browse > /shares/mri_workshop/visualization/md/conf.gro Load Browse > /shares/mri_workshop/visualization/md/md.trr Load

This should load a trajectory for analysis. You should now see a “movie” playing on the screen. This shows the movement of the system through time. Once the movie has stopped, we can now perform analysis. First let’s align the trajectory.

Extensions > Analysis > RMSD Trajectory In the lower right hand corner, hit “Add Active”. In the upper right corner hit “Align”, followed by “RMSD” (located directly to the left of “Align”).

This will produce values for the RMSD next to the structure. Additionally it will align the trajectory, meaning that the overall structure will not rotate or translate (making it much easier to analyze). Now let’s perform some analysis. Following the previous example, select the protein and show as “New Cartoon”. Now, make a New Representation and show it as HBonds. This shows the hydrogen bonds formed in a system. Change the ColorID to red and the Line Thickness to 8. What do you see throughout the trajectory? Are any hydrogen bonds broken? Are any new hydrogen bonds formed?

While the methods used here are by no means quantitative, they give us unparalleled insight into what is occurring in our simulation and what sort of analysis we might perform. The techniques used today in VMD are in no way comprehensive. There are many more visualization schemes available. In addition, VMD can perform many basic calculations, and is easily modifiable to incorporate more complex calculations that a user may wish to perform. Despite the relatively few possibilities of this program that were used today, hopefully you now have a flavor of what VMD is capable.

Exercises:

1. One of the most studied proteins is Hemoglobin. Hemoglobin is known to exist in two states, R (relaxed) and T (tense). Both of these have been resolved in crystallographic studies. Download the files 1BBB and 1BZ0 (that’s a zero NOT and O), which are for the R state and the T state, respectively. Visualize both of these proteins separately and identify their subunits. How can we represent these structures in a useful way? How many subunits does Hemoglobin have? How could we identify them?

2. As previously mentioned, VMD can perform a number of numerical calculations. Here we will perform a simple overlay followed by an RMSD analysis. Load both of the structures and select Extensions > Analysis > RMSD Calculator. Change the selection to “protein” and click the Align button. This performs and overlay of the two structures, minimizing the RMSD between the two structures.Once they are aligned, click RMSD. What is the RMSD? Is this a lot?

3. In addition to RMSD, we can also calculate a Ramachandran Plot. Go to Extensions > Analysis > Ramachandran Plot. You will already see a standard plot for comparison obtained from a survey of many crystal structures (blue and green splotches). Go to molecule selection and look at both. How do the R and T states if Hemoglobin differ? How are they the same?

4. We can also click on the individual points to show the name and residue number of the amino acid, along with its ϕ and ψ angles. Which ones fall in the standard values? Which ones are outside of the standard values?

5. Now that you have identified the residues that are outside of the standard values, show these explicitly for both R and T state. How do they compare to each other? Why do you think these might be different?

6. In addition to a 2-dimensional display, the Ramachandran Plot may also be shown in 3- dimensions. Click on the Create 3-d Histogram. Does this show you anything that the 2- dimensional plot does not? Now show this plot for the other protein. Does comparing these plots give us additional information? Hint: to show the next protein, change your Molecule Selection and click on Create 3-d Histogram again.

VMD - quick guide:

Download VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

User guide: http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html

To load in pdb file: File → New Molecule → Browse Click "Load" to load the file

• Be sure to use the "Orthographic" projection: a more natural way to display the protein, by selecting: Display → Orthographic

• To get rid of the axis: select Display → Axes → Off

To rotate: press "r" and move mouse

To translate: press "t" and move mouse

To recenter: press "c" and use mouse to select new center of rotation

To make bigger/smaller: press "s" (scale) and move mouse

To measure distances: press 2 and select 2 atoms with the mouse. The distance is reported on screen and also on the terminal screen. Units: Å (= 10-10 m).

To measure angles: press 3 and select 3 atoms with the mouse. The angle is reported on screen and also on the terminal screen. Units: degree.

To measure dihedral angles: press 4 and select 4 atoms with the mouse. The dihedral is reported on screen and also on the terminal screen. Units: degree.

To delete labels (from calculating distances, for example): Select Graphics → Labels, then select "Atoms" and click Delete, "Bonds" and click delete, etc.

To delete molecule: Select the molecule in the "VMD Main" window, and select Molecule → Delete Molecule

To change representation: Select Graphics → Representations...

Coloring method will change color

Use Drawing Method → New Cartoon to show secondary structure Use Drawing Method → CPK to show ball and stick Use Drawing Method → Licorice to show fat bonds etc.

Use "Create Rep" to show part several representations at the same time

Use "Selected Atoms" to show part of system. Note that this is case-sensitive. Examples: chain A protein backbone hydrophobic acidic resname TYR type CA resid 1 to 4

You can use "and"/"or" to combine statements; use () when doing so. Examples: (chain A) and (resid 1 to 4) backbone and ((resid 10 to 15) or (resid 20 to 25)) (resname TYR) and (type CA)

Typing of multiple names is interpreted as "or": Examples: chain A B C resid 10 11 15 resname HIS PHE

You can use "not" in your selection statements. Examples: not backbone (not hydrophobic) and (resid 20 to 30) chain A and (not (resid 30 to 35))

All possible selection statements are shown under the caption "Selections"

Use "Delete Rep" to delete a representation

To hide a representation: double click the representation to hide it, double click it again to make it reappear