DNA, RNA, Proteins. MCB-100. University of California, Berkeley.

John Kuriyan

The PYMOL scripts in this section illustrate the structures of DNA, RNA and Proteins.

Download the folder containing PYMOL scripts and structure data (ZIP compressed file)


There are three folders. To run the demos, move to one of the folders, and issue the following command:

On a PC:

To start the demo, click on the file named start.pml in the folder.

On a Mac OSX computer: open a terminal window, move to the folder, and issue the command:

> pymol start.pml


To jump to illustrations of each of the demos, click on the links below:

STRUCTURE OF DNA

STRUCTURE OF RNA

STRUCTURE OF A PROTEIN

 

Structure Coordinates used in these demos:

 


DNA

To see the DNA demos, move to the "bDNA" folder.

In this folder, the Pymol script "start.pml" shows the structure of B-form DNA, as deduced by James Watson and Francis Crick. The bonds between atoms are shown as sticks. Carbon atoms in one strand are colored green, and are cyan in the other strand. Nitrogens are blue, oxygens red, phosphorus is purple and hydrogens are white.


To run the next demo, type 1 in the window, at the PYMO> prompt. (This actually runs the Pymol script "run1.pml"). This shows the sugar-phosphate backbone of the two strands of DNA in red and yellow.


To run the next demo, type 2 (or @run2.pml) at the PYMOL> prompt.
This shows all of the atoms in the two strands of DNA as spheres, with red for one strand and yellow for the other.


To run the next demo, type 3 (or @run3.pml) at the PYMOL> prompt. The four nucleic acid bases are color coded as indicated below.


To run the next demo, type 4 (or @run4.pml) at the PYMOL> prompt. This now shows two sets of base pairs: (T:A, top and C:G, bottom).


To see the demos of A-form DNA, move to the "aform_DNA" folder.

In this folder, the Pymol script "start.pml" shows the structure of A-form DNA, Carbon atoms in one strand are colored cyan, and are yellow in the other strand. Nitrogens are blue, oxygens red, phosphorus is orange and hydrogens are blue.


To run the next demo, type 5 at the PYMOL> prompt. This now shows the major and minor grooves.


RNA

To run the RNA demos, move to the folder named "RNA".

In this folder, start.pml shows the structure of a particular RNA molecule. In contrast to DNA, which has an essentially uniform shape and double helical structure, different RNA molecules can adopt different kinds of specific three-dimensional folded structures. This particular RNA molecule is part of a ribozyme, a class of RNA molecules that catalyze chemical reactions. The function of this kind of RNA molecule is not to store information, as is the case with DNA, but rather to form a molecular machine. This particular structure was determined by the group of Tom Cech, building on earlier work of Jamie Cate and Jennifer Doudna. REFERENCE


To run the next demo, type 1 (or @run1.pml) at the PYMOL> prompt. This now shows the sugar-phosphate backbone of the RNA molecule as a purple tube. If you look carefully, you will see that the molecule consists of a single chain which wraps around on itself. This ability of RNA to fold back on itself to form complex structures, including double helical segments, distinguishes it from DNA, in which the double helical structure is formed by two different molecules.

 


To run the next demo, type 2 (or @run2.pml) at the PYMOL> prompt. This shows the 4 different bases of RNA (A, U, C, G) in different colors, as indicated below. Note that not all bases are paired, and that the nature of the pairings is not always that seen in Watson-Crick DNA.


To run the next demo, type 3 (or @run3.pml) at the PYMOL> prompt. This shows three consecutive sets of base pairs in the RNA molecule. Note that one of the pairs (between Guanine and Uracil, which replaces Thymine in RNA) does not correspond to a Watson-Crick pairing. Such base pairs occur commonly in RNA, due to its irregular three-dimensional structure. Hydrogen bonds between the bases are indicated in yellow.


PROTEIN

To run the protein demos, move to the folder named "proteins".

In this folder, start.pml shows the structure of a particular protein molecule. This particular protein is an enzyme known as a KINASE, which transfers a phosphate group from ATP to another protein. This particular structure was determined by the group of Susan Taylor. REFERENCE

"start.pml" shows the structure of the protein molecule, with all the chemical bonds shown as sticks. Hydrogen atoms are not shown, because there are so many of them that they would overwhelm the structure. Carbon atoms are green, nitrogens are blue, oxygens are red and sulfur atoms (there are very few of these) are orange.


To run the next demo, type 1 (or @run1.pml) at the PYMOL> prompt. The polypeptide backbone of the protein has been colored red, and the sidechains are yellow. You can begin to see that the molecule is formed from one chain that folds back on itself.


To run the next demo, type 2 (or @run2.pml) at the PYMOL> prompt. The polypeptide backbone is illustrated as a red ribbon. Strands of beta-sheets are shown as arrows, and alpha-helices are shown as spirals. You can now clearly see how the single protein chain folds up to form this structure.


To run the next demo, type 3 (or @run3.pml) at the PYMOL> prompt. The surface of the protein molecule is shown in orange. Note the nooks and crannies on the surface, which have specific shapes. This protein kinase molecule binds ATP, which is shown in colored spheres, with carbon green, nitrogen blue, oxygen red and phosphorus in purple. The specific interactions between proteins and small molecules, such as ATP, or macromolecules, such as DNA and other proteins, are critical to life functions. This specificity is ensured by the three-dimensional shapes of the folded protein molecules.


To run the next demo, type 4 (or @run4.pml) at the PYMOL> prompt. This shows a snapshot in the action of the protein kinase, when it grabs another protein and transfers phosphate to it. The backbone of the second protein is shown as a green ribbon. Complementarity in shape and chemical properties between the proteins dictates the nature of their interaction.

 

Protein Databank Coordinates

The following coordinates from the protein databank were used to create these demos. They are included in the downloadable zip file.


P4-P6 Tetrahymena Ribozyme RCSB PDB Code: 1HR2

Reference:

Juneau K, Podell E, Harrington DJ, Cech TR.
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
Structure (Camb). 2001 Mar 7;9(3):221-31.


Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA.
RNA tertiary structure mediation by adenosine platforms.
Science. 1996 Sep 20;273(5282):1696-9.

 


Protein Kinase Structure complexed to ATP. RCSB PDB Code 1ATP.

Zheng J, Knighton DR, ten Eyck LF, Karlsson R, Xuong N, Taylor SS, Sowadski JM.
Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor.
Biochemistry. 1993 Mar 9;32(9):2154-61.