Next, you will analyze the structure of a ribonucleic acid (RNA). Ribonucleic acids differ from deoxyribonucleic acids both structurally and functionally. Structural differences between RNA and DNA include different sugar moieties (ribose versus deoxyribose), one different nucleobase (uracil in RNA versus thymine in DNA), and differences in helical structure. In particular, RNA forms double-helices only rarely; however many viruses contain a double-stranded RNA genome. When you examine the structure of this RNA molecule, observe above-described differences. To examine the RNA molecule, close the DNA molecule and open an RNA molecule following instructions below:
In the 'Edit' menu, select 'Clear All'
In the 'File' menu, select 'Open'
Select file tRNA.pdb in the ../MOL directory, and hit OK to open the file.
Ribonucleic acids carry out many functions in the living organisms. Many RNA molecules are involved in protein synthesis at ribosomes. Traditional classification of RNA molecules is based on their function in protein synthesis. The three main classes of RNA are:
In addition to these three roles, a number of minor functional RNA types can be distinguished:
The microRNA and related non-coding RNA molecules have recently gained interest due to their possible involvement in diseases ranging from cancer to autism. Small RNA molecules are effective in laboratory studies of protein function by allowing scientists to specifically lower the concentration of a given protein via a process called RNA interference. Some RNA molecules, called ribozymes, catalyze biochemical reactions. Furthermore, one can artificially create ribozymes as specific catalysts; an RNA molecule catalyzing a stereospecific Diels-Alder reaction has been reported (Angew. Chem. Int. Ed. 39, 4576-4579 (2000)).
This RNA structure was determined by the X-ray diffraction and contains several Mg++ ions and water molecules. The Mg++ ions are visible as small purple dots, and the water molecules are visible as small red dots at the position of oxygen atoms. Hydrogen atoms are typically invisible in X-ray structures of macromolecules. Some of these water molecules are solvating Mg++ cations or polar groups in the RNA; some of the water molecules were just added to fill a position with increased electron density during model building. You can examine the location of waters and Mg ions using PyMOL (next section); they are (incorrectly) not visible in the version of SYBYL you are using. If they were visible, you could change the representation of Mg++ ions to small spheres and undisplay the waters to reduce the clutter.
In the 'View' menu, select 'Display Style->Mixed Rendering ...'
Click 'Atom Types ...' and, select 'Mg', hit OK, and again OK
Select 'Spacefill for Representation and hit 'OK'
In the 'View' menu, select 'Undisplay Atoms ... '
Click 'Sets' and, select 'Water', hit OK, and again OK
One of the computers in the Laboratory of Computational Chemistry and Biochemistry is equipped with a 3D visualization systems. This system consists of stereoscopic visualization eyewear, infrared emitter, a graphics card capable of providing a sync signal, and high-speed monitor. Go over to the 3D-capable computer when instructed by your TA to learn how stereoscopic vision helps in perceiving protein structures. Rotate the molecule with the mouse to better perceive to depth of the 3D model. Fold your glasses so that the battery will not drain.
Assignments (RNA):SYBYL provides a built-in image capture tool. Another way of saving images is to use a screen capture program. On Linux, hitting the Print Screen button while holding down the Alt key creates an image of the active window, and prompts you to save it. To take a picture of an area of the screen with SYBYL's image capture tool, follow steps below:
Edit the image by adding your name. This can be done with many image-editing programs, we will use a program called 'display'. It is a part of a suite of free programs developed by John Cristy who at the time worked at DuPont. The program with manuals is available from http://www.imagemagick.org.
While your cursor is on the image, click the left mouse button, and select Image Edit-> Annotate from the menu. Pick a good-looking font by selecting Browser under Font Name menu. Fonts such as adobe-helvetica-bold-r-normal will look good on images. The default color is black, which will not work well on your dark background. So select a better color from the Font Color menu. Type your name on the black area and hit Apply.
Edit the image by labeling the anticodon region in the molecule. If you do not know where the anticodon region is, review the early pages of the tutorial. You may label the anticodon region by drawing a circle or ellipse around it using the Image Edit-> Draw from the menu.
Save your work as a PNG file. To save the file, go to File -> Save. You may replace the original image; hit Save, and exit (File -> Quit) the ImageMagick program. There are several image formats with their strengths and weaknesses. You may have heard good things about JPEG, which is good for photographs that contain millions of colors. However, JPEG is not suitable for storing computer-generated images of molecules because it's lossy compression degrades the quality of such images. PNG (Portable Network Graphics) is one of the best formats for storing computer-generated images.
Start a new Unix Shell and verify that you have the image in your directory by typing:
ls -l
You should see the PNG file that you just saved in this folder. E-mail the image to your instructor (kalju@chem.ucsb.edu) using your favorite e-mail account. You may click on the "Send Mail" icon to connect to U-Mail. Note that you may not see your file in the upload window. If this happens, hit the Filter button first and replace the "*.html" label with "*".
The structure and function of this RNA molecule are further described in a JMol-based tutorial from University of Maryland. A good account about catalytic RNA molecules is given by the 1989 Nobel Prize winner Thomas Cech. His Nobel Lecture is available at http://www.nobel.se/chemistry/laureates/1989/cech-lecture.pdf as a PDF document.