BIOL3611

Overview of the Jmol assignment
This assignment serves as preparation for the lab assignments that use Jmol. It was
modified from EXERCISE 17: DNA from “Studying Protein and Nucleic Acid
Structure with Jmol. For use with Berg, Tymoczko, Gatto, and Stryer,
Biochemistry, 8th Edition. By Jeffrey A. Cohlberg. Revised May 2015”.
Objectives of the Jmol assignment
• Determine whether your laptop (or comparable device) can run Jmol for use in
the dry labs (and wet lab 4A), or whether you will need to make alternate
arrangements.
• Investigate selected aspects of DNA structure in 3D.
• Become familiar with selected features and commands in Jmol. (Many others, of
course, will be introduced in the dry labs that follow.)
• Become familiar with the submission style and requirements for Jmol-based dry
labs. For example, since at this time well over 450 students are taking this lab
per year, it’s important that your image submissions look distinctive from those
of your classmates in a variety of ways. One of the things that you will do will be
to include your student ID card in your image (or a different form of ID is fine if
you’ve lost that ID card…), but also the imperfections inherent in taking a photo
(the distinctive angle, possible reflections or other imperfections, etc.) are very
desirable in making your submission unique from the rest, and screenshots are
not accepted. The extra time required to complete this step is factored into the
2hrs and 50min allotted for each dry lab that uses Jmol, and is also factored in
to the amount of credit allotted for this assignment. (As a reminder, dry labs are
designed so that the entire procedure, plus the assignment preparation and its
submission, can be completed during the allotted 2hrs and 50min.) If you are
unable to take photos, please contact your instructor.
Preparation for Jmol assignment
If possible, use a laptop that you can bring to lab, since we will be using Jmol (as well as
Excel) in Lab 4A.
Procedure for Jmol assignment
1. Download Jmol
• Running Jmol will require Java version 1.4 or later, so if necessary go to
http://www.java.com/ to download this before downloading Jmol.
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• Now download Jmol. Go to
https://sourceforge.net/projects/jmol/files/Jmol/ and since we had a poor
experience using some commands with version 14.29, please download the
earlier version, 14.28 by clicking on Jmol-14.28.4-binary.zip
• The download will be in a compressed .zip format – either it will expand
automatically or else find the downloaded file and double-click to expand it.
• Jmol is a ‘Java applet’ and does not need to be installed. You will open Jmol
by looking for the file with the ‘Jar’ (=Java archive) extension.
o On a Mac, you can run Jmol by opening the Jmol folder that you
expanded and double-clicking on the file called Jmol.jar
o On a PC, it should also be named Jmol.jar; if you view the details for
each file type then the one to double-click on will be the ‘Executable
Jar File’.
o To our knowledge it is not possible to run Jmol on a Chromebook at
this time. If your only computing option is a Chromebook, please be
sure to see your instructor to discuss alternate options for
completing these assignments.
• Double-click to verify that Jmol opens – it should look like the view shown
below. If you receive an error message indicating that you can’t open the
application since it is from an unknown source, you may need to adjust your
security preferences to allow you to open Jmol. (On a Mac: go to ‘System
Preferences’ then ‘Security and Privacy’ then indicate that you are allowing
the application to be opened.)
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o Troubleshooting:
§ If you receive a red error message that mentions Java, doublecheck that you have the latest version of Java installed.
§ There are reports that in some PC operating systems when
you double-click it appears that nothing happens, and that this
can be fixed by right-clicking on the Jmol.jar file and choosing
the ‘Open Outside’ option.
§ There are reports that on some PC’s it works to double-click
on the ‘batch’ file. If asked about whether to ‘extract’ files,
choose to do that. Or you may need to select the ‘batch’ file
and force it to open using ‘Java’.
§ Microsoft Surface (Windows Pro 10): tech services in Speare
Hall did the following: downloaded WinRAR (stays free
forever, even though there is a prompt that says to pay), then
downloaded latest version of Java, then downloaded Jmol.
Opened Jmol.jar, and set ‘Open with’ to open with WinRAR.
This needs to be done every time; can be made into an
automatic setting.
2. Examine the structure of double-stranded DNA. You will do a few
manipulations of a typical ‘B-form DNA’ structure, and then submit one photo of
your work. The purposes are (1) to gain familiarity with Jmol well before using
it in the lab assignments, and (2) to gain a better appreciation for DNA structure
through manipulations of a 3D structure.
• Please proceed with the following steps:
i. In the top menu in Jmol go to File -> Console to display the Jmol Script
Console. Although Jmol has many options that can be modified using
menus, it is often faster and easier to use the console to type in
commands. Press the return key (‘Enter’) after each command that
you type. And of course spelling must be perfectly correct!
ii. Type set pdbAddHydrogens into the console (and then press return;
always press return after every command in the console). Adding
hydrogens will force Jmol to show hydrogens in the structure (by
calculating where they ‘should’ be), even though hydrogens due to their
tiny size could not actually be resolved in the original structure data due
to technical limitations. It is generally a good idea to do this every time
you open Jmol! You should receive the response ‘pdbAddHydrogens =
true’
iii. In the top menu in Jmol go to File -> Get PDB and enter the identifier
423D, which is for a standard ‘B’ form double-stranded DNA molecule
that appears as the familiar right-handed double-helix. (Double-check
whether you typed this correctly!! There are other DNA files that are
unsuitable for this assignment that have similar 4-character codes!) The
file should load fairly quickly; if you receive a red error message, then
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first try again. If you still get an error message, then visit the site
http://www.rcsb.org/pdb/ that Jmol is trying to get the file from – if for
some reason the website is down temporarily, then you can try again a
bit later. If you have a recurring problem with this step, contact your
lecture instructor; there is a way to permanently get around this
problem.
iv. When your DNA file loads, if you rotate it around (click and hold down as
you move your cursor), you should immediately note the striking
placement of the nitrogenous bases (blue = nitrogen in this standard
‘CPK’ coloring style, red = oxygen, orange = phosphorus, grey = carbon,
white = hydrogen). If you aren’t seeing the atoms colored this way, it
probably means that you were getting error messages while retrieving
the 423D file, and we tried an alternate method to bring your file in –
your DNA probably looks like purple ribbons instead. No problem, you’ll
be back with everyone else soon! And speaking of color, as you probably
know, color-blindness in its various forms is fairly common. If this
describes you, then you should be aware that Jmol offers a lot of control
(of course) that a textbook image doesn’t. Whenever you click on any
atom, the console will tell you exactly what it is, and you can customize
your view in ways that suit you (e.g. all oxygens in the color of your
choice rather than the default red; background in a contrasting color of
your choice, etc., for any assignment or other purpose). You can ask your
instructor for more information about this.
v. Another useful feature of the console is that it displays information
about the file – in this case, it says that there are two molecules (strand A
and strand B of the DNA) and gives the sequence. ‘D’ indicates that the
nucleic acid is ‘deoxy’ (rather than being RNA), and each ‘P’ indicates a
phosphate connecting each nucleoside. If you take a good look at the
sequence, you should be able to tell that this sequence has reverse
complementarity – two identical sequences are able to bind to each
other, and so this is why only one DNA sequence is given rather than
two. (If you’re not sure why, try writing out what the reverse
complement of the given sequence is… you should end up with the same
sequence as what you started with! In other words, this particular
sequence happens to be able to bind to another copy of itself.)
vi. One thing that makes this image a little cluttered is water molecules and
magnesium ions that crystallized along with the DNA. Type delete
water or mg into the console (and then press return, of course) and
these will disappear. This is a mandatory step! The image that you submit
for this assignment will be a ‘pure’ DNA image, uncluttered by solvent
molecules or ions. (Note: the ‘or’ is required; it tells Jmol that you want
to delete all occurrences of either the water or the magnesium.)
vii. Rotate the structure around and try to see the major groove and minor
groove. These two grooves are very difficult to visualize in the textbook,
and so this is one of your best chances, even though this is a short
segment of DNA. A groove is the opposite of a ridge. Imagine a DNA-
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binding protein approaching the DNA – one that is going to specifically
contact and ‘read’ the nitrogenous bases. Most DNA-binding proteins
bind in the major groove, where there is a lot of space (and therefore the
protein can be relatively wide). By contrast, notice that in the minor
groove there is very little space and only an exceptionally skinny protein
would be able to enter and contact the information-containing (i.e.
nitrogenous base) portion of the DNA. Proteins rarely make contact here,
but on the other hand many small molecules that serve as useful DNAbinding dyes do bind to the minor groove. Optionally, there are two
additional files that you can load afterwards to help you visualize this
further.
viii. Before moving on, take a good look at the planarity of the nitrogenous
bases, and how the carbohydrates (deoxyriboses) are absolutely not
coplanar with the bases. This makes sense, because if the bases are the
horizontal ‘rungs of the ladder’ then the sugar-phosphate backbones are
the vertical supports of the ladder. Try to look for examples of the 3’ and
5’ carbon in deoxyribose (recalling that the 1’ carbon is the one attached
to the base; the numbering is reviewed in textbook figure 4.2).
ix. Change the view by typing the command select backbone; spacefill
then rotate the structure around and you should see that this highlights
the major vs. minor groove even more. (Having a semicolon between
commands allows you to connect multiple commands on the same line
instead of pressing return after each one.)
x. We’ll put the base pairs in spacefill instead. Type select dna; spacefill
then select backbone; spacefill off; wireframe 80 – you should now
see a view that is similar in message to textbook Fig. 1.14, showing the
base pairs in the double-stranded DNA stack at the optimal van der
Waals contact distance, helping to stabilize the DNA structure.
xi. Now look at a single base pair by typing restrict 8 or 17 – you can see
that in spacefill view the two bases in this pair are so close together that
the pair appears to be a single molecule.
xii. Type select 8 or 17; spacefill off; wireframe 80 – now you should be
able to see the separation between the bases. (You can use the ‘undo’
button on the console to go back to the spacefill view to compare, and
then the ‘redo’ button to go forward again to the wireframe view.) Again,
if you rotate this structure you should see clearly that the deoxyriboses
are not remotely in the same plane as the nitrogenous bases. Further, if
you rotate carefully, you should be able to see that each deoxyribose is
not fully planar itself – this is also illustrated in textbook Fig. 4.15.
xiii. Now it’s time to take a photo of a DNA view for your assignment
submission. (Screenshots are not accepted.) Type restrict all; select all
and then type in a style (spacefill or cartoon only or wireframe 80
only or wireframe {some other number} only or trace only). Or, if
you’re feeling creative, experiment more with the pop-up menu (rightclick, or two-finger click) to try out some other ‘Style’ and/or ‘Color’
and/or ‘Surfaces’ options. Choose a background color (not black) from
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the very many options available at
http://jmol.sourceforge.net/jscolors/#JavaScript%20colors (and listed
in the appendix of the lab manual), and once you have chosen a
background color that has name ‘X’ then change the background with the
command background X (e.g. changing it to black would have been
background black). Remember, it’s already black, so choose a different
color…!
xiv. Rotate your DNA molecule to a pleasing angle, and take a photo of your
screen that shows three things: (1) your DNA on your chosen
background, definitely without water or magnesium, (2) your console
with at least some of the commands visible, and (3) your propped-up
actual student ID card (not just a typed-in number) in the lower right.
Remember also the final requirement which is (4) a non-black
background. Upload this photo for your response to the ‘Introduction to
Jmol – DNA’ assignment for the lecture portion of the course. Some of
these artful creations may be shown in lecture! (Note: it’s not important
that your submission photo be a beautiful high quality image – we’ll
work on exporting high-quality Jmol images later as part of a dry lab
assignment. Don’t just make a screenshot on your computer – please do
the extra step of taking a photo that shows your ID card, which is what
you’ll also be doing for the other dry labs.) Remembering, you’re
securing a substantial portion of your lecture assignment grade for your
troubles!
3. Examine another DNA structure, this time with a small dye molecule
bound. This is optional, with no associated submission. However, there is
another file that you can quickly look at that will make the major vs. minor
groove more obvious. Jmol will not save your work, so first make sure that you
are finished with the 423D file, and that you have a suitable image of it for your
assignment submission.
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• Then, you’re ready to proceed with the following steps:
i. Go to File -> Get PDB and type in 5T4W
ii. Type delete water
iii. Type select all; spacefill
iv. Type select dap; color violet
v. Great! Rotate your image around enough so that you can see that you
have highlighted a common ‘minor-groove-binding-dye’ called DAPI – it
fluoresces blue/purple, and because of its planar (flat) shape, it fits
snugly into the minor groove. DNA-binding proteins typically do not
have this geometry – they would fit into the major groove.
vi. Now perform a Google image search such as “DAPI cell nucleus image”
and you should see a wide variety of images where researchers are
showing their work with this common nuclear stain. It is one of the most
popular DNA-binding dyes, and as you have now seen in Jmol, it is
specifically a minor-groove-binding molecule. By contrast, most DNAbinding proteins (e.g. TATA-binding protein) tend to be more bulky, and
because of their larger size tend to be described as ‘major-groovebinding-proteins’. Take a look back at your Jmol image to see the wider
(‘major’) groove where those major groove-binding proteins would bind.
Good! No need to submit a Jmol image for this 5T4W structure.
4. Another optional step: are you still having trouble visualizing the major
groove? Take a quick look at the DNA-bound receptor for the thyroid hormone.
Hormone receptors tend to be large, and these particular researchers who
created the ‘2NLL’ file that we’ll get only worked with the DNA-binding region
(‘domain’) of the protein, so the protein portion that actually binds thyroid
hormone won’t be visible, but they beautifully show that this receptor makes
direct contact with DNA’s major (not minor) groove. (Thyroid receptor is in the
large family of hormone receptors that, when hormone-bound, change shape in
a way that allows them to directly bind DNA and influence transcription of
particular target genes.) Look at this receptor-bound target DNA with the
following steps:
i. Go to File -> Get PDB and type in 2NLL
ii. Type delete water
iii. Type select dna; spacefill
iv. Type select protein; color white; spacefill
vii. Spin the structure around and observe it from various angles. (There is
one purple iodine atom – this is part of a modified nitrogenous base that
was added as part of the experiment – we can ignore it.) Can you see that
the protein, in white, is contacting only the wide ‘major groove’, and is
not contacting the thin ‘minor groove’? The protein’s direct contact with
the nitrogenous base chemistry in the major groove is what allows it to
‘read’ sequence so that this thyroid receptor protein ‘knows’ that it is in
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the right place to be directing transcription of appropriate genes
involved in the response that we should initiate when exposed to thyroid
hormone. So we are seeing one part of the following response: ‘Aha!
These genes are involved in the thyroid response! I’m a thyroid hormone
receptor and I’ve just sensed that thyroid hormone is in the environment
(not shown), so I will now activate transcription of appropriate thyroidregulated genes. I can ‘read’ those appropriate sequences by making
direct contact with the nitrogenous bases via the major groove!”
viii. Good job! No need to submit a Jmol image for this part.

 

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