Introduction

http://proteopedia.org/w/Introduction_to_molecular_visualization

This web page gives an overview of the conventions in visualization programs. Read this web page prior to lab and keep open a tab during lab for reference.

Controls you will find useful in these JSmol tutorials and web pages:

Toggle spinning (bottom of image frame) allows you to start/stop spinning of the molecule

Rotate the molecule by holding down the left mouse button and moving the mouse

Zoom the molecule by holding the shift key and left mouse button down and moving the mouse away from you or towards you.

Identify amino acid residue/atom by putting the mouse over the atom of interest. The amino acid residue and specific atom of that residue will be identified in a pop-up and/or a window in the lower left corner. NOTE: in some views there are atoms in front that aren't visible -they are present, but have been rendered invisible in the script.  If that is the case you may misidentify the amino acid.  Be sure it makes sense.  In a specific example you may encounter, the amino acid Val (branched hydrocarbon side chain) is very different in structure from His (5-membered ring structure with 2 N atoms).

Menu  - right-click the mouse with the cursor in the jmol frame.  This will open up the jmol menu.  The menu allows you to select, change color schemes, turn on and off H bonds etc.  For more advanced users you can also open the console which allows you to enter and execute specific script commands.

Visualizing Peptides Tutorial

http://proteopedia.org/wiki/index.php/Peptides

Choose each the selections, starting with the single amino acid (glycine, as drawn), sequentially. 

*NOTE that the images are peptides that are part of a larger structure. The writer of the tutorial selected a small section of a polypeptide chain, hiding some amino acid residues and atoms, and then “building” the more complex tetrapeptide by “unhiding” them. Since the amino acids are within a polypeptide chain, the “carboxyl groups” will only have a single oxygen atom, and amino groups just a single hydrogen atom. The entire complex (pdb structure 1ROG, a small peptide bound to MHC-I) can be viewed in FirstGlance https://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ROG, and the peptide visualized in this tutorial is the nonapeptide, chain B)

For questions that ask you to “identify” a particular structure, raise your hand when ready and point it out to your instructor. If you are doing this on your own, you can check with me in class or office hours, or discuss it with class members in the discussion group. You can also paste screenshots into this document and label them. You can’t directly insert screenshots into discussions on D2L

Peptides and Backbones

1.  Single amino acid representations

Identify the amino group, the carboxyl group, and Ca.

Examine the backbone model of the AlaAlaAla tripeptide.  In this model, oxygen is shown as red, carbon as gray, nitrogen as blue, and hydrogen as white. 

How many peptide bonds are there in a tripeptide?  Identify them. 

Identify the N terminus and C terminus of this tripeptide.

Examine the structure of the LysAlaAla tripetide.

What charge would you expect on the Lys side chain? 

How many bonds does the nitrogen have on this sidechain? 

Identify the N terminus, C terminus and epsilon-amino group of the Lys side chain.

Examine the remaining tripeptide and tetrapeptide sequences.

For the tetrapeptide, how would you classify the isoleucine and threonine side chains? (polar, nonpolar, or charged)

Examine the superimposed spacefill and backbone traces.

What is a backbone trace?  Does it correspond to any actual bonds?

Hemoglobin Tutorial

http://bioinformatics.org/jmol-tutorials/jtat/hemoglobin/contents/contents.htm

2.  Hemoglobin & Heme

 Work sequentially through the views, reading the descriptions for each view, and answer the following questions

The interaction of the 4 hemoglobin polypeptide chains is known as the _________________ structure of the protein.

What atoms of the heme bind to the ferrous iron?

Note that the oxygen molecule binds at an angle to the iron (view 7). Why does it bond at an angle rather than straight on? (Hint: sp2 hybrid orbitals draw the structure of molecular oxygen showing the position of outer shell electron orbitals on the oxygens.)

There are two histidines in the vicinity of the heme.  One called the proximal histidine, is bound to the iron opposite to the oxygen binding site.  The other histidine is called the distal histidine and hydrogen bonds to the oxygen but does not coordinate with the iron. 

Mouse over an atom of the proximal His with the mouse.  The chain (B) and number (92) of the amino acid residue should be displayed in a dialog box. 

What atom of the proximal histidine is coordinating with the heme iron?

What atom of His 63 is H bonding with the oxygen? (Trick Question! The atom isn't shown!)

3. Hemoglobin Secondary Structure

What secondary structure is most abundant in hemoglobin?

What part of the alpha helix forms the H bonds that stabilize this structure?

In view 12, toggle off spinning and rotate the alpha helix displaying the side chains so that you are looking down the end of the helix. 

Describe the positioning of the side chains in relation to the direction of the helix

4.  Amphipathic Alpha helices

What characterizes an amphipathic alpha helix?  

In views 2 and 3, what elements characterize the hydrophilic side of the helix?

What specific examples of amino acid residues do you find on the hydrophobic side?  (mouse over them)

In view 5, the animation slices down the middle of the beta subunit. What types of heme-protein contacts predominate in the pocket that holds heme?

5.  Hydrophobicity, Polarity and Charge

 In these views, you will want to select the button next to Cut below the window with the structure. Use the slider to go from 100% cut (top surface) down to 50% (middle). If you go to 0%, you will be viewing only the amino acids on the far side of the molecule.

Where in the Hb molecule are you most likely to find hydrophilic and hydrophobic amino acids?

What structural feature is found on the surface between Glu/Lys, Asp/Lys, Glu/Arg, and Carboxy terminus/Lys residues?

 6. Regulation of Oxygen Binding

 Skip to the next section.

But! Those of you taking Biochemistry may benefit from this section!

7.  Sickle Hemoglobin

What amino acid substitution is found in sickle Hb?

How does this this substitution cause the formation of sickle Hb polymers?

If the glutamate was instead substituted by lysine, do you think Hb polymers would form?  Why or why not?

HIV-1 Protease Tutorial

https://proteopedia.org/wiki/index.php/Hiv_protease

This tutorial is a Proteopedia web page like the first one for peptides. As you read through the description click on the green links to start an animation illustrating the particular point.  You can toggle the spinning and you can get a larger window if you click “popup” or the + .

In the initial cartoon view….

What secondary structure is most apparent?

Describe the interactions between the N and C termini of the two subunits.   (turn off spin and enlarge the cartoon model to view). What secondary structure is involved?

Saquinavir binds to the active site of the protease.   What class of inhibitor is it (competitive or noncompetitive)?

Describe what occurs to the protein conformation when substrate (or inhibitor) binds to the active site.  How do you suppose this facilitates catalysis?