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MARY ELLEN WILTROUT: Hi.

This is Mary Ellen Wiltrout, one of the course coordinators for 700X.

In this video I hope to help you use the molecule-viewing software.

This tool will allow you to explore a protein in the 700X

problem sets and exams.

This program can show a protein and one of several views, each of which

highlights different features of these large molecules.

Note, it may take a minute for the Protein View to load when you start.

We'll start with a combination of two views, Space Fill and Dots.

Here we have six amino acids shown in Space Fill view.

As you can see, atoms are shown as solid spheres taking up,

approximately, the space that they fill in a real molecule.

Remember that one protein molecule is microscopic and that you're seeing a

magnified view.

Here individual atoms are colored by their element--

gray, carbon atoms, red, oxygen atoms, blue, nitrogen atoms, yellow, sulphur

atoms, orange, phosphorus atoms, and white, hydrogen atoms.

Sometimes if noted a specific problem may use a view but alternative

coloring of atoms, like all purple.

In all views you can rotate the protein to get a better look at all

sides by clicking, holding, and dragging the mouse or clicking and

holding with one finger and dragging a second finger on a trackpad.

You can also zoom in by holding the Shift key while dragging the mouse or

by just moving two fingers across a trackpad.

In all views you can identify the atom that you're looking at by leaving the

cursor over that atom.

In a few seconds, an idea label will pop up with

information about that atom.

It is important to understand how to interpret the

label to answer questions.

The first three letters in brackets indicate the amino acid that this atom

is part of.

In this case, you see LYS, which is the three-letter

abbreviation for Lysine.

The number immediately following the amino-acid abbreviation tells you the

position of this amino acid in the proteins primary sequence.

Amino acids in a protein are numbered based on their primary sequence

starting with one at the amino terminus or N terminus.

In this case, Lysine a the 13th amino acid from the N

terminus of the protein.

The shorthand for this is LYS 13.

The very last number is the number of this particular atom.

Each atom in the protein has a unique number.

In this case, the nitrogen atom is number 97.

Altogether, atom number 97 is a nitrogen atom in Lysine 13.

Space Fill view is good for determining if

particular atoms are touching.

Another view is called Dots.

As you can see, the amino acids not in Space Fill are shown as clouds of

colored dots.

As with other views, you can leave the mouse over an atom to see the

information label.

In Dots view you have to be careful.

If you put the mouse over a dot you will get the information for the

nearly invisible dotted atom.

This can be confusing when you want the information from an atom shown in

Space Fill covered by other amino acids shown in Dots.

How could you determine if an amino acid is on the surface or interior of

the protein?

Dots view lets you see inside a protein to determine where certain

amino acids, shown in Space Fill, are located.

You can clearly see many of the atoms of this amino acid without dots on

them even as you rotate in zoom.

Therefore, this amino acid is on the surface of the protein.

Likewise, no matter how much you rotate or zoom, you cannot see the

atoms of this amino acid without dots on them.

This amino acid is located inside the protein.

Another view is called Cartoon.

As you can see, the protein is represented as a simplified cartoon of

the major secondary structure features of the protein's backbone.

Different shapes and colors indicate the different types

of secondary structure.

Alpha helices are shown as pink or purple spirals.

Beta strands that make up beta sheets are shown as yellow arrows.

Random coil is shown as white cords.

You can still use the cursor to identify amino acids

at particular locations.

Here, phenylalanine is in an alpha helix.

The last view to discuss is called Ball and Stick View.

Here, the atoms are shown as balls connected by sticks that show the

covalent bonds that connect them.

The rest of the protein is shown as gray cartoon.

How could you determine which atoms are involved in a non-covalent

interaction between amino acids and a protein or between a

protein and its substrate?

You can use the Ball and Stick View.

Note that this program only shows covalent bonds.

You will need to infer the presence of any non-covalent interactions based on

the structures involved.

You will determine if two atoms are close enough to interact.

You can then use the pop up to identify the atoms involved.

Note that sometimes the protein will load with the wrong view, like All

Space Fill.

Take note to how the problem describes what view you should see.

If the wrong view is shown reload the page and the

correct view should appear.

Researchers use this program to study how proteins function or interact with

other proteins or molecules.

Now it's your turn.

Give protein viewing a try.

We hope you have fun.