11. Assignment For RasMol Tutorial

Revised November 1, 1997.

Introduction

It is a requirement of CHY 361 at the University of Southern Maine (fall, 1997) that you demonstrate your ability to use RasMol. To satisfy this requirement, you will explore another protein. You will prepare some scripts, test them, save them to a floppy disk, and turn them in for evaluation. Finally, you will write a brief description of the protein, its interaction with the hetero group, and some of its structural features.
NOTE: You must test scripts immediately after preparing them and before moving them to another location on your hard disk or a floppy disk. Scripts as written by RasMol are not portable. After you move them, they must be modified in order to work properly. I can modify them in order to grade them. If you are interested in how to make scripts portable for your own use, click here.
Obtain a PDB file name from your instructor. Each student will work with a different file. All assigned proteins contain a hetero group -- a cofactor, prosthetic group, or inhibitor. Obtain your file from the Protein Data Bank using Netscape.

Using what you have learned from this tutorial, make the scripts named and described in the following list. All your scripts will be named xxxx#.spt, where xxxxdenotes the PDB file code for your protein, and # is a one-digit number (example: 3b5c2.spt).

Click here for 1997 assignments.

TEACHERS: Click here for a list of appropriate PDB files for this assignment.

Script List

Once you have constructed the required view, use rotation, translation, and zooming to produce clear, informative views in which the features requested are clearly displayed. Then save the script.

If your protein contains two or more identical chains, restrict all views to one chain and its associated hetero group. If there are hetero groups in addition to the one listed in the table of assigned files, do not include them with any of the requested views. Include only the hetero group listed in the table. Finally, do not leave water molecules on display in any of your completed views.

Here are the scripts you should make:

xxxx1.spt
Backbone display of the protein, colored by structure; spacefill display of hetero group(s), colored CPK.

xxxx2.spt
Closeup of the hetero group(s) alone, in ball & stick display, with shadows and specular reflections, colored CPK.

xxxx3.spt
Closeup of hetero-group binding, showing hetero group and all protein atoms within 6.5 Å of it; sticks display of hetero, colored CPK; and wireframe display of the surrounding protein, colored CPK. If any of the hetero atoms disappear in sticks display (this often happens with metal ions), select them individually and display them in ball & stick. In addition, use distance monitors to display hydrogen bonds or salt bridges between hetero atoms and protein atoms. Find as many such interactions as you can. Arrange the view so that the interactions and distance labels are in clear view.

CRITERIA FOR IDENTIFYING HYDROGEN BONDS AND SALT LINKS: Remember that hydrogen bonds involve two electronegative atoms that share one hydrogen atom. In proteins, hydrogen bonds involve mostly N and O, but never C. A thiol sulfur of cysteine can form a weak hydrogen bond with N or O, but not with another S. Hydrogen atoms are not visible in electron density maps from protein crystallography, so they are not shown in protein models. Therefore, we must infer the presence of a hydrogen bond when we find a pair of appropriate atoms within about 2.8 angstroms of each other. In addition to chemical criteria (one atom must be of a type that is normally protonated, one atom must be N or O, and the other must be N, O, or S) and distance criteria (2.8 ± 0.5 angstroms), the atoms must satisfy geometric criteria for hydrogen bonding. The hydrogen is involved with a bonding orbital on one atom, and with a nonbonding orbital on the other, so a line extending from one hydrogen-bonded atom to another must make either a tetrahedral or trigonal angle with the other covalent bonds at both atoms. Salt bridges, or electrostatic interactions, must involve atoms of opposite charge. The atoms can be in almost any orientation to each other, at distances near the van der Waals contact distance of about 3 Å.
xxxx4.spt
Same atoms as xxxx3.spt but all in spacefill display, with carbons (only) of hetero group colored green, and all other atoms, including non-carbon atoms of the hetero group, in CPK colors. Arrange this picture conveniently for slabbing through the structure to show the fit of the hetero group into the protein.

xxxx5.spt
Ball & stick display of one prominent element of secondary structure: either a pleated sheet of least three strands, or one alpha helix of at least 8 residues. Main chain atoms colored CPK. Side chains colored as follows: polar green, positive blue, negative red, hydrophobic yellow. Mainchain H-bonds displayed. Note whether the sheet or helix in your display appears to be amphipathic -- that is, having one side hydrophilic and one side hydrophobic. Then note whether the sheet or helix is buried within the protein, or on its surface. In your written description of the protein (see below), comment on the distribution of nonpolar and polar groups and tell how they fit the location (surface or buried) of the sheet or helix in the protein.

Immediately test-run each of your scripts as follows:

RasMol > script xxxx#.spt < return >

After a delay of a few seconds, you should see the script you created. If you need to modify the script, give it a slightly different name when you write it, like xxxx#.spt#. Due to a bug in RasMol, it sometimes quits when you write a file with the same name as an existing file. Delete unwanted files and rename the corrected versions with the assigned names when you have all scripts working to your satisfaction.

Please see the NOTE above about portability of scripts. Because you may not be able to view your scripts later, you may want to study them carefully now, and make some notes for use in the written description of your protein. Once you end your working session, you will not be able to view them again unless you make them portable.

Description of the Protein

To complete this assignment, write a brief description (no more than one page, double-spaced) of your assigned protein, referring to the views saved in your scripts. In the first paragraph, give the name and source of the protein, and then describe its function. If it is an enzyme, give the reaction that it promotes, drawing molecular structures of substrate(s) and product(s).

In the second paragraph, describe the structure, including a) the number of chains and number of residues in each; and b) major secondary structural elements, and the residue numbers that they encompass. In this paragraph, be sure to carry out the instructions for xxxx5.spt.

In the third paragraph, describe the binding of the hetero group to the protein, referring to the appropriate scripts.

Model your written description after the introductory description of any protein (for example myoglobin) in a biochemistry textbook. Write this description with a word processor, print it, and also save it on the desktop with your scripts. Your word processor program allows you to save the description in various formats. The following formats are acceptable: ClarisWorks, Microsoft Word, RTF, ASCII text, or text.

Here are some sources of information about your protein and its hetero group:

When you have completed your scripts and description, copy 1) your PDB file, 2) written description file, and 3) all scripts to a floppy disk. Provide the disk and the printed description to your instructor by the deadline given in the syllabus. This assignment counts as one exam. (Late disks: grade reduction of one-half letter grade plus one half letter grade for each 24 hours late -- no exceptions.)

Protein Assignments

For the RasMol Tutorial

Name

PDB Code

Hetero Group
Student 2pia FMN
Student 1zin AP5A (ATP-analog inhibitor)
Student 1hmy S-adenosylmethionine
Student 2cts Coenzyme A
Student 1trk Thiamine Pyrophosphate
Student 1aaw Pyridoxal Phosphate
Student 1lid Oleic Acid
Student 1avd Biotin
Student 1ayl ATP
Student 1bmt Vitamin B12
Student 1hpc Lipoic Acid
Student 1crb Retinol
Student 1dhf Folic Acid
Student 1fx1 FMN
Student 1bdo Biotin
Student 1all Phycocyanbilin
Student 1ajv Sulfamide Inhibitor AHA006
Student 1lhc Peptide-analog inhibitor
Student 1dr1 NADP
Student 1ldg NAD

12. Useful Web Sites for Molecular Modelers

HOME