Download LS1a Fall 2014 Lab 2: Computer Modeling of Proteins with PyMOL

LS1a Fall 2014
Lab 2: Computer Modeling of Proteins with PyMOL
Goals: The objectives of this lab are to provide you with a better understanding of:
1. how to use PyMOL at a basic level.
2. how to translate a two-dimensional chemical structures to a three-dimensional chemical model.
3. how to relate different three-dimensional representations used by scientists to depict biological
polymers.
4. the two types of protein secondary structure: alpha (α)-helices and beta (β)-sheets
5. how the exceptional polarity of peptide bonds contributes to the stability of secondary structure.
6. how the properties of individual amino acids influence the structure of proteins
Required Safety Regulations and Lab Etiquette
 Wear lab coat and safety glasses at all times
 Wearing appropriate clothes that protect the leg, foot, and ankle (e.g., jeans, socks, and sneakers)
 No eating or drinking in lab
[Points can be deducted from your post-lab assignment for not wearing the appropriate clothes, not
wearing the required personal protective equipment, or leaving a mess.]
This laboratory is a computer-based exercise that will help you to become more comfortable with
viewing two- and three-dimensional images of amino acids and proteins using a software program
called PyMOL (it’s also the same software that is used to make a lot of images look at throughout the
course).
You can complete this lab by reading the instructions as you progress through the different exercises.
Once you become comfortable using PyMOL, answer the different questions on the answer sheets
provided in lab as you move along.
Your answer sheet will be due a week from today’s lab, and the PyMOL files you will be using for today’s
lab will be placed online Friday after 4pm if you would like to finish your assignment after section is
over.
Introduction
As you have learned in lecture, some of the most important molecules associated with life are
“polymers.” Polymers are chains composed of many repeating units called “monomers” that are
covalently linked together. You can think of monomers as chemical building blocks. Different types of
polymers are made of different types of monomers. For example, nucleotides are the monomeric
building blocks of the polymer DNA; just as amino acids are the monomeric building blocks of
polypeptides. (The distinction between a “protein” and a “polypeptide” is largely semantics, but
occasionally a protein will consist of multiple polypeptides, as we will see in the case of hemoglobin.)
Figure 1: A polymer is a string of monomers covalently attached together.
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Amino acids are the monomer “building blocks” of proteins; conversely, proteins are strings of amino
acids covalently attached to each other. Different proteins have different amino acid sequences and the
shape and function of a protein depends on the order and arrangement of its amino acid building
blocks.
In order to understand how proteins work, we must first understand what they look like. Using methods
such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy (both of which are
beyond the scope of this course), scientists are able to determine the distinct three-dimensional
arrangement of atoms within macromolecules which are otherwise waaaaaaaay too small to be seen
with even the most powerful microscopes. Scientists can then use this structural information about a
protein to make educated guesses about how the protein works, based on the relative locations of
certain molecular components. This information is vital to improving our understanding of healthy and
diseased cells at a molecular level, and for identifying potential drug targets, as we will see later in the
course using the examples of HIV and Chronic Myeloid Leukemia (“CML”).
III. Procedure
This lab is composed of three sections, each which deals with a different aspect of amino acid and
protein chemistry and structure. The lab questions starting in Section 2 are highlighted with a “►”
symbol in the left margin of the page and should be answered as you work your way through the
different exercises. Answer your questions on the question sheet that is due in section a week from
today.
Section 1.1: Introduction to PyMOL
A) Basic Manipulations
To begin using PyMOL, pair up with a buddy at a computer and do the following:
 Login to the “Students” account using the password “g3n0m3.” Shh, it’s a secret ;)
 Open the “Life Sciences Labs” folder on the bottom.
 Click on the file that says “LS1a_PyMOL_Lab2.zip.” This will automatically decompress the file and
create a “LS1a_PyMOL_Lab2” folder. This folder has all the appropriate files for us.
 Open the “LS1a_PyMOL_Lab2” folder
 Click on the “1_Amino_Acid_Basics” folder and then open the “Amino_Acids.pml” file.
After clicking on “Amino_Acids.pml,” PyMOL will automatically open have loaded up into two windows:
an “external” interface on top, and a larger “viewer” window below it. We’ll be focusing mostly on the
lower “viewer” window, which you can maximize by clicking the green “+” button at the top left corner
of the window.
The atomic structure of the amino acid (L)-valine should appear in the viewing window and look
something like this:
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Change the orientation and zoom of the molecule by clicking on it with your mouse (playing around
with this program is the best way to use it to learn and highly encouraged). The basic mouse controls
are as follows:




Rotate (= left mouse button): To rotate the molecule, click on the left mouse button and move the
mouse left, right, up or down.
Move (= middle button): To “move” an object on the screen, you must click on the object using the
wheel as a button. Make sure to hold the button down as you move the mouse and try to not turn
the wheel. Turning the wheel simply controls the “Z-axis clipping plane” for the viewer. If you rotate
the wheel by accident and clip the image, turn it back in the other direction until the entire
molecule reappears.
Zoom (= right mouse button): Click on the right mouse button and move the mouse up or down in
order to zoom in or out on the molecule. Go easy at first! It doesn’t take much to “lose” the
molecule if you go too far.
Type “reset” in one of the text entry panels if anything ever gets too crazy, or just close and open
the .pml (or .pse) file again.
It takes a little practice to feel comfortable manipulating molecules, but it’s pretty easy once you
remember what each button does. Practice using all three functions; once you have a feel for how to
manipulate the image, move on to the next section. If you ever lose the molecule, just close the
program and click on the “Amino_Acids.pml” file again.
b. Turning the Objects On/Off
On the right side of the viewer window, you will notice a series of rectangular buttons with names in
them, as well as a series of smaller square buttons ([A], [S], [H], [L], and [C]) next to each rectangular
button:
Each of the rectangular buttons controls an “object” in the viewer. By pressing on the button, you can
make the object appear or disappear. For example, clicking on “L_Valine” will make the amino acid
disappear completely; clicking on it again will cause the amino acid to reappear.
You will not be using the small square buttons for today’s lab ([A], [S], [H], [L] or [C]). If you’d like to
learn more about using what they do, you can visit the company’s website at PyMOL.org or a helpful
PyMOL wiki page. (Briefly: “A” stands for “action,” “S” stands for “show,” “H” stands for “hide,” “L”
stands for “label,” and “C” stands for “color.” Clicking on any of them produces a drop-down menu.)
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Section 1.2: Amino Acid Basics
Let’s begin with the basic building block of proteins: the amino acid. There are 20 standard naturally
occurring amino acids that our cells use as the monomers to construct proteins. The one we will begin
with is valine.
First, make sure that the object “Valine” is turned on and all other rectangular buttons are turned off.
The particular representation currently being used to show (L)-valine is called “sticks.” Carbon atoms
are shown in green, oxygen atoms in red, and nitrogen atoms in blue.
The alpha (α)-carbon
These 20 molecules are all called “amino acids” because all 20 of them contain an amino group and a
carboxylic acid group (nifty). A third group, called the side chain (denoted below by “R”), is different for
each of the 20 amino acids (in fact, it is the only difference between each of the 20 natural amino acids).
In amino acids, the carboxylic acid group, the amino group and the side chain group are all connected to
the Cα carbon.
Amino acid
α-carbon (“Cα”)
Carboxylic acid
Amine
Can you identify the Cα carbon in the valine structure shown on the computer? Once you think you have
identified it, do the following:
 Turn off “Valine” and turn on “Ca_Carbon” This will highlight the Cα carbon in yellow.
Hydrogens
Notice that PyMOL does not explicitly show any hydrogen atoms as part of the valine molecule. The
hydrogens are typically implied in all of the 3-D structures you will be viewing (just as they are implied
by many of the 2-D standard line drawings we look at), so it is worthwhile getting used to looking at
molecules this way. (The lack of hydrogens is because most of our molecular structures have been
determined using X-ray crystallography, a technique that can detect carbon, nitrogen, oxygen,
phosphorous, and sulfur, but not hydrogen because hydrogen is too small.)

Turn off “Ca_Carbon” and turn on “Hydrogens”
This gives you a better sense of where the hydrogen atoms are located in the structure. Notice that
three hydrogen atoms are bound to the nitrogen, while no hydrogen atoms are bound to either of the
two carboxyl-group oxygens. This is the way valine would exist in solution at cellular pH (pH
approximately 7.4):
Generic amino acid at physiological pH
Notice that because PyMOL does not include typically hydrogens, it can also not tell you anything about
whether atoms are formally charged.
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Notice that if you rotate the molecule such that the nitrogen is on the left, the carboxyl group is on the
right, and side chain is pointing towards the top, then we can observe the amino acid’s stereochemistry:
the L-configuration of the amino acid describes the side chain pointing out towards towards you as the
hydrogen points away from you:
Figure 2: Stereochemistry of a L-valine, notice how the side chain points “out of the page”
towards you when the molecule is rotated such that the hydrogen points “into the page” away
from you. On the left is the two-dimension line drawings we usually use to represent L-valine, on
the right is a PyMOL image of the same molecule in the same orientation.
Double Bonds
You might also have noticed that double bonds are not distinguished from single bonds in the PyMOL
molecule you are viewing. Again, this will be a common theme for the structures that you will be
viewing in this lab. In certain cases it may indeed be useful to see the double bonds, and PyMOL is
capable of showing them.


Turn off “Hydrogens”
Turn on “Double_Bond”
Here you can see how PyMOL distinguishes single bonds from double bonds using the “sticks”
representation. In this case, a double bond can be seen between the carbon atom and one of the
oxygen atoms of the carboxylic acid group.
Using different representations to show structures
Although the “sticks” representation is useful for viewing the atomic connectivity and the geometry of a
molecule, it is less useful at showing the space occupied by the electrons that surround the nuclei of
different atoms within the molecule. A different type of representation (“Mesh”) can be used to show
the volume that the molecule occupies.


Turn off “Double_Bond”
Turn on “Hydrogens” and “Mesh”
This representation shows a mesh that depicts the approximate boundary of electron density around
the different atoms in the molecule. Notice how the space occupied by electrons is not at all apparent
from a simple sticks model.

Turn on “Space_Filling”
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Here we see another, more realistic view of the relative space occupied by each atom in the molecule.
However, notice that now it becomes much more difficult to see how atoms are connected to each
other and how bonds are oriented relative to adjacent bonds.

Turn off “Mesh”
Scientists use these different representations (sticks, space filling, mesh, etc.) depending on their
particular needs when studying a molecule. Note that each representation has its own advantages and
disadvantages. For example, while the “sticks” representation provides a rather detailed look at a
macromolecule’s structure at the atomic level, it is difficult to discern the general macromolecular
shape (the structure has too much “information” in it, so to speak). This is particularly true when
viewing structures that are much larger than just a single amino acid.
Section 2: Protein Basics
In this section, we will be examining the basics of protein structure. The specific protein we will be
looking at is hemoglobin. You may be already familiar with hemoglobin; it is a protein found
prominently in red blood cells and is responsible for carrying and distributing oxygen throughout your
body.



Close your current PyMOL viewer window to exit the program.
Return to the “LS1a_PyMOL_Lab2” folder and open the “2_Protein_Basics” folder.
Click on the “Protein_Basics.pml” file. This will automatically open up the PyMOL program and load
the coordinates for hemoglobin.
Hemoglobin consists of four polypeptide chains. We will begin looking at a single amino acid of one of
the polypeptide chains and build our way up until we visualize the entire protein. In that vein, this file
begins where you left off with the amino acid valine in the now familiar “sticks” representation. In this
case, valine is simply referred to as “Amino_Acid” in the list of objects (rectangular buttons) on the
right.

Turn off “Amino_Acid” and turn on “Tripeptide.” You may need to zoom out a bit and move the
structure back to the center of the screen using the appropriate mouse buttons.
Here we can see how amino acids link together. Note how the carboxylic acid group from one amino
acid is used to link to the amine group of another to form what is called an “amide” (or a “peptide”)
bond. In this tripeptide, a lysine is bound to the N-terminal end (the side that ends with the amine) of
the valine and an alanine is bound to the C-terminal end (the side that ends with the carboxylic acid) of
the valine. Typically, we write peptide sequences from the N-terminal end to the C-terminal end, so this
example tripeptide would be written as Lys-Val-Ala.
► Question 1

Turn off “Tripeptide” and turn on “Primary.” Feel free (as always) to play around with the molecule.
You may need to readjust the frame to see the entire structure.
We are now seeing even more of one of hemoglobin’s polypeptide chains. The sequence of amino acids
in a polypeptide (or a protein) is known as either the primary sequence or the primary structure. The
primary sequence for this particular segment is:
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Nt-Ser-Ala-Gln-Val-Lys-Gly-His-Gly-Lys-Lys-Val-Ala-Asp-Ala-Leu-Thr-Asn-Ala-Val-Ala-His-Val-Ct,
or using the one-letter code: Nt-SAQVKGHGKKVADALTNAVAHV-Ct. The terms “Nt” and “Ct” stand for
“amino-terminal end” and “carboxy-terminal end,” respectively.
[A quick note about terminology: the difference between the term “polypeptide” and “protein” is the
scale. Proteins are often much larger than polypeptides, and the term polypeptide often refers to a
small portion of a protein. Both peptides and proteins are polymers of amino acids connected by
peptide bonds. The terms “polypeptide” and “protein” are sometimes used synonymously. Some key
differences are: 1) proteins are polypeptides that perform specific functions inside cells; and 2) some
proteins, such as hemoglobin, consist of several polypeptide chains.
In addition, amino acids present within a protein are commonly referred to as residues. Thus, the
phrase “N-terminal residue” refers to the amino acid that is present at the N-terminus of the protein (or
peptide). This is because the synthesis of a peptide bond between two amino acids is a “condensation
reaction” as it releases a water molecule. The bound amino acids are therefore the “residue” left after
the loss of a water molecule.]
We can simplify this structure by removing the amino acids’ side chains but keeping the “backbone”
atoms:

Turn off “Primary” and turn on “Backbone”
You may notice that the peptide backbone is starting to take on a helical shape. The term “peptide
backbone” typically applies to the Cα carbon atoms and the atoms involved in the peptide bonds, but
excludes the atoms in the side chains. The backbone view shown here excludes the side chains (the “R”
groups) that are normally attached to the Cα carbon atoms. The cartoon representation further helps to
simplify and clearly indicate the helical structure of the backbone.

Turn on “Secondary”
This cartoon represents an alpha (“α”)-helix, an example of secondary structure. Notice how the helical
cartoon lacks any detailed depictions of the atoms that form the structure. Such simplified diagrams are
often used to show the overall shapes of proteins to avoid introducing too much detail into the picture.
We will discuss specific types of secondary structures in the next segment.
To see how the amino acid side chains are oriented along the helical backbone, do the following:

Turn off “Backbone” and turn on “Helix_Sidechains”
“Helix_Sidechains” shows the orientation of the side chains relative to the helix, which are pointed
outwards rather than inwards.

Turn off “Secondary” and “Helix_Sidechains”, then turn on “Tertiary.” Zoom out to see the whole
polypeptide chain.
If we combine all of the secondary structural elements included within a polypeptide, we get a large,
compact structure called the tertiary structure of the protein. The shape of each polypeptide is unique
and depends upon the polypeptide’s unique amino acid sequence. The protein’s shape allows it to carry
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out its particular function with great efficiency; the shape of the protein is optimized for the protein’s
required function within (or outside of) the cell.

Turn on “Full_Backbone” (and keep “Tertiary” on)
Notice how well the backbone aligns with the “cartoon” representation of the tertiary structure. Again,
the cartoon is a convenient simplification of the overall structure of the protein. Let’s see what the
entire protein looks like without simplification:

Turn off “Full_Backbone” and “Tertiary,” turn on “Sticks_Rep”
While showing the entire polypeptide as sticks describes the location of each atom in the polypeptide,
it’s quite a lot of information and not as obvious what we’re looking at. Let’s examine another type of
representation.

Turn on “Surface_Rep”
This is called a surface representation. This representation depicts the actual volume and shape the
protein occupies using the van der Waal radii of each atom. It provides a great sense of what the actual
surface of the protein looks like.
► Question 2
Now let’s see what happens when multiple polypeptide chains combine to form a single functional
protein:


Turn off “Surface_Rep” and “Sticks_Rep”
Turn on “Quaternary”
Each of these differently-colored polypeptide chains is virtually identical in structure and sequence;
sometimes, a protein consists of multiple polypeptide chains that come together to form one functional
unit.
Many proteins consist of just a single polypeptide chain. However, for proteins that consist of several
different polypeptide chains, their “quarternary” structure is the level of structure at which multiple
polypeptide chains—each with their own primary, secondary, and tertiary structures—fold together
into one functional unit.
► Question 3
As we mentioned earlier, hemoglobin acts as an oxygen carrier. But where does it carry the oxygen?
Some proteins need additional structural components to perform their duties. In many cases, proteins
utilize a small molecule, called a cofactor, to assist.

Turn on “Cofactor”
In this particular case, the cofactor is a porphyrin ring, a large ring with a metal ion in the center (here,
iron is used as the central ion). Notice that each chain has its own cofactor.
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Now let’s see where the oxygen gets bound to the ring.

Turn on “Oxygen” and “Surface_Rep”
► Question 4
[Note: The oxygen molecules (O2) are shown using a surface representation for clarity, which makes
them appear much larger than the surrounding atoms in the porphyrin ring (which are shown with a
“stick” representation).]
At this point, it is worth stressing that the ability of hemoglobin to bind oxygen and its cofactors is
dependent on the structure of the protein itself. As you’ve seen, this structure is determined by the
sequence of amino acids that combine in a distinct order to form the protein. Therefore, the primary
sequence of a protein determines its structure, and its structure determines the protein’s function.
Section 3: Protein Secondary Structure

Close your current viewer, open up the folder called “3_Secondary_Structure,” and click on the file
called “Secondary_Structure.pse”. This will automatically open up the PyMOL program, and load up
the coordinates for a different protein called Top7.
In this brief section, we will be examining protein secondary structure, and how cartoons are used to
simplify visualizing protein structure. Since stick representation is a bit noisy, so let’s simplify the
protein to its backbone as we’ve done previously.

Turn off “Protein_Sticks” and turn on “Backbone”
α-helices
Eliminating the side chains alone helps simplify the structure and you can begin to see some of the basic
elements of secondary structure. Let’s examine each of these elements in greater detail.

Turn off “Backbone” and turn on “Helix_Sticks”
Now, these particular amino acids form helical secondary structures, exactly like those we saw in
hemoglobin. We can therefore simplify them in cartoon mode as helices. (By playing around with these
structures in stick representation, can you see how they are helical before turning on the cartoon
representation?) These types of structure are called α-helices, and are quite common in proteins. Here,
we’ve colored them magenta for clarity.
•
Turn off “Helix_Sticks” and turn on “Helix_Cartoon”
The cartoon representation is one of the most common ways that scientists portray α-helical regions
contained within proteins. Notice that in the cartoon representation, none of the atoms that comprise
the helix are shown. Instead, the helix cartoon outlines the shape of the peptide backbone and makes it
easier to view complex structures.
So what causes these regions to take on a helical shape? Part of the answer is that the amino acids are
able to form a series of hydrogen bonds that help to stabilize the helix. Certain amino acids favor this
secondary structure more than others.
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To take a closer look at the hydrogen bonds that are important in stabilizing helices, we will focus on
one of the two helices shown in this protein.


Turn off “Helix_Cartoon”
Turn on “Alpha_Helix”
It may help to re-center the image on your screen so that you can rotate it more easily. To do so, rightclick on the mouse and choose the “center (vis)” command.
In this image, the hydrogen atoms that are attached to the backbone nitrogen atoms are depicted in
white. Also, the image specifically shows the double bonds that form between the carbon and oxygen
atoms in the backbone.
► Question 5
Now, let’s take a look at some of the hydrogen bonds that are important in stabilizing the helix. For
simplicity, only hydrogen bonds in a short stretch of the helix are shown (the helix contains more than
just the six H-bonds that are depicted here). To see the bonds:

Successively turn on “H_bond1” through “H_bond6”
► Question 6
It is important to recognize that the network of H-bonds that stabilizes the helix stems from the
interactions between backbone amine (-NH) and backbone carbonyl (-C=O) groups. The side chains of
the amino acids are not involved in the H-bond network shown here. To help illustrate this more clearly:

Turn on “Helix_Ribbon” and “Sidechains”
Here you can see that the side chains are not forming any of the hydrogen bonds that are important in
maintaining the shape of the helix.
► Question 7
In order to get a better sense of how the side chains are distributed along a helix, it is useful to view the
helix from a different perspective. Scientists sometimes use a depiction that shows the helix as viewed
from above (rather than from the side), which can be done by rotating the helix such that one is looking
straight down its center.
 Turn off “Helix_Ribbon” and “Sidechains” and “Alpha_Helix”
 Turn off all H_bonds
 Then, turn on “Top_Down_Helix” and “Top_Down_Cartoon” (make sure to re-center and re-zoom)
Now, rotate the Top_Down helix such that you are viewing it from above looking straight down its
center. Make sure that the N-terminal end of the helix is facing you. Remember, the amine (-NH)
groups point towards the N-terminal end, while the carbonyl groups (-C=O) point towards the Cterminal end.
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Your screen should look something like this:
Once you have the N-terminal end facing you:
•
•
Turn off “Top_Down_Helix” (but keep the Top_Down_Cartoon visible), and
Turn on “With_Sidechains”
Your helix should now look something like the one shown below. Carbon atoms in the side chain are
shown in blue, oxygen in red, and Sulfur in yellow.
Scientists sometimes use a “helical wheel” diagram to represent a helix viewed from above. Such a
diagram is shown below on the right, where the side chains that are projecting from the helix are
labeled as R1, R2, etc. starting from the N-terminus.
► Question 8
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The ways in which side chains are positioned along the different faces of an alpha helix can significantly
influence the manner in which a helix is positioned relative to other proteins, or other parts of the same
protein.
► Question 9
Beta Sheets
To look at another type of secondary structure, first do the following:


Turn off “Top_Down_Cartoon” and “With_Sidechains”
Then turn on “Sheet_Sticks” (zoom out & re-center if necessary)
These strands take on a different shape than those seen in helices. Rather than curling, these strands of
peptides form long, straight sheets when aligned with each other. Thus, we simplify them in cartoon
mode as beta-strands, which combine to form beta-sheets. We’ve illustrated the sheets (and the
strands) here in blue.

Turn on “B_Sheet”
Notice how strands are represented in cartoon mode using long, flattened arrows; the arrows provide
directionality for the strands. Since amino acids, by convention, are written from N-terminal end to Cterminal end, the arrows point from the N-terminal to the C-terminal direction of the peptide strands.
Similarly to α-helices, the driving force for formation of beta-sheets is the formation of stabilizing
hydrogen bonds. In this case, H-bonds form between the backbone –NH and –C=O groups of
neighboring strands (see picture below). Again, certain amino acid sequences favor β-sheet formation
over helices or loops.
In order for a beta-sheet to form, it needs several flat peptide strands (beta strands) to align together to
form a flat sheet. Since aligned strands can run “in the same direction” or “in the opposite direction,”
we describe beta sheets as being either parallel or antiparallel. The image above is an example of an
antiparallel sheet.
► Question 10
► Question 11: Follow the instructions on your question sheet to take two images of the beta sheet:
one of the hydrophobic face and one of the hydrophilic face.
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Now let’s take a look at the protein segments that connect these secondary structure elements.

Turn off “Sheet_Sticks” and then turn on “Loop_Sticks”
These segments do not exhibit a uniform structure, as seen in the previous two examples. Rather, they
serve simply to connect the adjacent strands or helices together.

Turn on “Loops” and then turn off “Loops_Sticks”
Thus, we simplify these as loops, which are depicted as simple ribbons (in this case, yellow).

Turn on “C_Term_Sticks” and “N_Term_Sticks”
Note: You will need to scroll down the menu to see the box “N_Term_Sticks”.
In addition to loops, the N-terminal and C-terminal ends of the peptide strand are often lacking in
definite structure as well. These termini are generally depicted in a similar manner as loops, though
they don’t actually connect anything. Rather, they signify the “beginning” and “end” of the protein.



Turn off “C_Term_Sticks” and “N_Term_Sticks”
Turn on “C_Term” and N_Term”
Turn on “Helix_Cartoon” and “Sheet_Sticks”
► Question 12
And here, we now have our entire protein represented in secondary structure elements, via a cartoon
representation.
To see the protein as a single cartoon, turn off all the other elements and turn on “Protein” as follows:
 Turn off all elements by hitting the “(all)” button at the top; turn on “Protein” at the bottom.
Notice how the secondary motifs combine to generate a unique tertiary structure for the protein.
Figure 3 below is a schematic in which the secondary structural motifs are mapped out along the linear,
primary amino acid sequence. The protein begins at the amino-terminus (“N-terminus”) and concludes
at the carboxy-terminus (“C-terminus”). There are 97 amino acids total in the protein, and every 10
amino acids is ticked off along the length of the primary sequence.
Figure 3: A schematic listing the linear primary amino-acid sequence of the protein annotated with
the secondary structure of each region. The numbers on top indicate the amino acid position (there
are 97 total amino acids). The green arrows indicate β-strands and the red portions represent αhelices. The black lines between each secondary structural element are loops.
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Section 4: Bulk Water
As a final exercise, you’ll have a chance to get a better sense of what scientists believe water may look
like as a solvent.

Close your current viewer window and open the folder titled “4_Bulk_Water” and then open the file
“Water.pml”
This particular set of coordinates is not from a solved atomic structure, but rather a “simulation” of how
scientists bulk water is thought to be organized in liquid form at any given instant.
Here we see water represented in “sticks” form with the hydrogens included (without the hydrogens,
the “sticks” representation looks rather silly as just a bunch of dots where the oxygens go).
Let’s view how these molecules primarily interact with each other:

Turn on “H_Bonds”
As you may recall, the ability of water to hydrogen-bond to itself is one of the reasons it is such an
important molecule to sustain life. Hydrogen bonds are similar in nature to normal dipole-dipole
interactions, but are considerably stronger.
Atoms are understood to be nuclei surrounded by “electron clouds.” Thus, it is sometimes helpful to
view molecules from a “spheres” representation, to get a better view of how the molecules fit together.

Turn off “Sticks” and “H_Bonds,” turn on “Spheres”
Notice how closely packed together the molecules are, from this perspective.

Turn “Spheres” off and turn “Sticks” and “H_Bonds” back on
Keep in mind that in liquid form, the molecules are in constant motion, rotating freely around each
other. This “free motion” is associated with the water’s entropy.
► Question 13
14