Protein Folding Cell and Mol Biology Labs
(see end of this file for selected text pages on CDK2/cyclin, Calmodulin, protein folding
diseases, prions and chaperones
Protein Structure Sites: Protein Folding (Chapt. 3 of World of the Cell) and
Enzymes (Chapt. 6):
How a protein folds in 3D space is important for protein function. If a protein does not
fold properly, it can lead to disease such as Alzheimer's disease, cystic fibrosis, Mad Cow
disease, certain form of emphysema, even many cancers: take a look at
www.faseb.org/opar/protfold/protein.htm. Look through this paper (briefly, but an exam
question may come from these and other web sites noted below).
Look at this web site: the UCHSC web site and read about protein folding (CLICK
HERE). Look in the upper left corner, under MODULES, and click on the second listing
PROTEIN. Briefly look at the protein slides.
Read the specific pages in our text, go over the lecture slides: put all our info on weak
bonding, levels of protein structure, and our understanding of rickety protein structure
into HOW AN ENZYME WORKS. When a substrate binds, the enzyme is distorted;
what does this mean? Look at this Flash animation showing the first steps of the enzyme
mechanism of carbarboxypeptidase A: CLICK HERE. (to download free Flash player,
click here). The animation shows that amino acids move as new weak bonds form
between the protein and the substrate. It is found on my cell bio web page.
We will also view the active site of "carb A" and see the motion of the R groups as they
bind to the substrate with the program called KINEMAGE or MAGE programs (see
below). As noted, the binding of substrate to carboxypeptidase A (the enzyme whose
mechanism we study in class) distorts the enzyme. See the amino acids that move as the
substrate binds (this is the INDUCED FIT MODEL) and you will use your mouse to
rotate the image.
You may be able to skip the following:A newer version of MAGE is always available; if
you want to download the latest version (you may have to if computer problems arise), go
to download the newer MAGE or KineMAGE program (ver. 6.42 is currently the
newest): http://kinemage.biochem.duke.edu/software/index.php. Look under:
OS/Platform, Windows and save the program file under local disk C:, in folder called
“MAGE protein structure.” The files used by the MAGE program – files ending in “kin”
are already on the computer lab computers (C:/MAGE protein structure/WIN) but you
can also find them on the home page for MAGE/KINEMAGE: click here. Many sample
kinemages are also available on: http://kinemage.biochem.duke.edu. You can of
course transfer those *.kin files to your own computer and then view them as
above. However, if you want Mage to act as a built-in part of your browser, then
merely follow the instructions in your Web browser to define Mage as a helper
application, with ".kin" as its signal file extension.
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Exercises Using Mage
(if you really want to get into this subject, you should buy Introduction to Protein
Structure by Carl Branden and J Tooze; second edition; but for this lab course, you
do not need it).
A "kinemage" (kinetic image) is an authored illustration presented as an
interactive computer display. Operations on the displayed kinemage respond
immediately: the entire image can be rotated in real time, parts of the display can
be turned on or off, points can be identified by picking them, and the change
between different forms can be animated. The image can be recentered, zoomed,
put in stereo, or the front and back clipped away; distances between atoms,
angles, and dihedrals can be measured. The kinemage can be edited on-screen:
colors changed, multiple viewpoints saved, button names edited, lines pruned
away or new ones drawn, etc.
MAGE program is found on the C: drive: double click on “My computer” in the
upper left hand part of the desktop, double click on Local Disk C:, and find the
folder “MAGE protein structure” and look under WIN subfolder. In this
subfolder, click on the most up to date version of MAGE: MAGE 5_4. EXE (not
the older 4 version)—see more detail below on this program. As noted, a newer version
is typically available on the web and you may have to use the newer version if the older
5_4 version has problems.
Once the MAGE program is started, then select "Open New File" from the "File"
menu. The kin files are in the same WIN subfolder (C:/MAGE protein
structure/WIN). Once the kinemage file: “Demo5_4a.kin,” read some or all of the
scrollable text, click on the graphics window to select and bring it forward, and
rotate the image by dragging the mouse. Click on the caption window at the
bottom and read it, click on the text window on the left side to merely look at it.
"Open File" under the "File" pulldown menu lets one open a new kinemage file,
and "Quit" lets one exit from MAGE. (If you can't get the program running,
please read the "Trouble-shooting" section below!)
We will use this “Demo5_4a.kin” file. The text with instructions is reproduced
below (print off)—the instructions below have been edited-use this version. You
can also view the text on one computer screen and then view the images on the
other. YOU WILL ANSWER QUESTIONS AT THE END OF THE EXERCISE
(and record answers to statements in the text below in your lab notebook).
Contents of file DEMO5_3A.KIN:
READER'S TUTORIAL (scroll this window to read text):
*{Kin 1}* CPase A active site motions (basic operations, pointIDs, animation)
*{Kin 2}* Carbonic anhydrase, Calphas & active site (zoom, center, stereo, views, find,
kaleidoscope)
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*{Kin 3}* Streptavidin/biotin complex (ball&sticks, viewIDs)
*{Kin 5}* Leucine zipper structure (slab, ztrans, options, write Postscript)
*{Kin 6}* Alpha helix (measures, drawline, construction, prune, dragline, and labels)
(skip skip: *{Kin 4}* Geodesic dome and Demo5_3b.kin)
KINEMAGE 1}* - Motion in the active site of Carboxypeptidase A
Make sure you read the caption in addition to the text reproduced below!!
To see kinemage 1, click on the graphics window. This kinemage is an animation of
the change between the conformations of carboxypeptidase A with and without bound
substrate (Gly-Tyr- two amino acids connected together). Many features of the kinemage
display are self-explanatory, and can be worked out by exploring the possibilities
yourself.
The windows can be moved around by dragging their top bars, or resized by dragging
in the lower right corner. The text and caption windows are scrollable; the graphics
image is rescaled when its window is resized. If you fill the screen with it, you can bring
the text back by choosing 'show text' under the 'Help' pulldown menu. Later, you can
select another kinemage by pulling down the 'Kinemage' menu and either releasing on
'Next' or choosing a different number (refer to the list at the beginning of the text
window).
Use the mouse to ROTATE the image: dragging across the top of the graphics
window will rotate around Z (in the plane of the screen) and dragging anywhere else will
rotate around the Y or the X axis or a combination. To reset the image to the start-up
view, pull down the 'Views' menu and release on View1.
To ANIMATE the carboxypeptidase image, click repeatedly on the 'animate' button at
the bottom of the button panel in the graphics window (alternatively, animate by pressing
the 'a' character on the keyboard). Some computers may not show the animate button.
The big changes here are the appearance of the Gly-Tyr (red) and the motion of
Tyr 248 (cyan), but many other parts of the structure move slightly. Review the FLASH
animation on my web site:
http://carbon.cudenver.edu/~bstith/Lam%20animation.swf
Turn to a different orientation and try the animation again.
Now TURN ON and OFF the various display groups and sets, by clicking in the
appropriate button box. Turn off the 'Tyr 248' button; this one is a "master" button so the
Tyr 248 disappear for both conformations. Turn off the substrate 'GlyTyr' as well, and
animate again, to see motions of the other sidechains (sidechains are the R groups of the
amino acids).
Then animate with just the main chain on (and Zn turned on), to see subtle shifts
in the backbone.
Click on VIEWS in the top menu bar, and select another view (e.g., active sites).
Now try out some INFORMATIONal features to measure the distance between two
atoms. Turn on the Markers (click box in the upper right), pick an atom and click on itone of the two markers will move there. A 'pointID' for that atom is printed at the bottom
left of the graphics window; this would usually contain residue name and number and
atom name. Pick a second atom - the markers follow along, the pointID for the second
atom is shown, and the distance between the two atoms is given in Angstroms. (PointID
and distance functions work fine without the markers on, once you are familiar with
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them.) You can measure the distance between two atoms, or between the same atom in
two different conformations (before and after substrate binding).
Let’s try measuring the movement of Tyr248 as the substrate binds (making new weak
bonds between substrate and the enzyme, pulling and distorting the enzyme into a better
form). Click on the box next to “Markers” in the upper right side of the screen. Then
click on the very tip of the Try248 (cyan or blue) – you will see text in the lower left of
the graphics screen. Then click on Animate to get the substrate (red) bound to the active
site, and this moves the tyrosine dramatically. Now click again on the tip of the Tyr248
and you see a distance number in the lower left corner. Record the distance in your lab
notebook (it is given in Angstroms or 10-10 meter; a carbon to carbon bond is about 1.5
Angstrom).
Another method of measuring: Click on the box titled "labels," you should now see key
amino acids on the structure of carboxypeptidase. Use the zoom, also on the left, to focus
in on the Tyrosine 248 (Tyr 248). To help you orient the protein, click on "Display" then
click on the "Flatland XY Scroll" - this will allow for you to slide the protein around
while zooming in. Now, once you have no problem seeing the Tyr 248 click on
"ANIMATE" which is on the left again. You will see the cyclic group of Tyrosine move
a great distance (in molecular terms)- you will be determining the distance between the
conformational shifts.
Another method of measurement: To do this method you need to click "Tools" and then
click "Find," now make sure the "search will match entire word or number" is NOT
clicked. In the first text box input "tyr 248 oh" and click "Find" - you should now see a
grayish ball on the tip of the Tyrosine. Now click on "Tools" then click "Measure" and
then "Display" and "Kaleidoscope." Use your mouse to click on the gray ball then click
on "ANIMATE" and you should see it move over, but there will be a residual image of
the first conformation. Now click on the tip that Tyr has been moved to, this will create a
line that measures the distance. NOTE: if your rotate the protein while in "Kaleidoscope"
mode it will smear the image. You can hit Ctrl, Alt and Print Screen to copy the screen
and paste it in word so you can print it out.
For each menu a 'Help' entry, such as 'Edit Help', gives brief explanations of the
menu items. 'MAGE key shortcuts', under 'Help', tells you about keyboard shortcuts
(like 's' for stereo, ‘a’ for animate).
The 'Tools' menu contains some commonly-used features such as 'Find' and
'measures', but also features of more specialized use. To return from a message box, just
click in it. 'XYZ point' turns on a display of the currently picked x,y,z values at the top of
the screen, and 'gnomon' turns on a green marker at the current center of rotation, with
lines parallel to the x,y,z axes of the molecular coordinates.
-----------------------------------------------*{KINEMAGE 2}* - carbonic anhydrase Calphas, active site, & mutants
Read the caption also!!
The second kinemage (pull down the kinemage menu and release on 'next') shows the
C alpha BACKBONE of human carbonic anhydrase II, highlighting the active-site Zinc
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and its ligands (blue) and a loop (white) whose sidechain roles were studied using
saturation mutagenesis, by Joseph Krebs and Carol Fierke at Duke University. Rotate
this figure to appreciate the big, curving beta sheet, the active site cavity, and the position
of the loop.
IMPORTANT: “Calpha” is the term for the backbone of the amino acid chain; the
R groups stick off of this backbone. See textbook page 44, top left (not figure 3-3 but
above it). Use the web if you do not remember the backbone and R group structure of
proteins.
On the "Tools" pulldown menu is a function called "FIND", which searches for
character strings in the pointID's. Suppose, for instance, you remember that Proline 30
and Proline 202 in carbonic anhydrase are cis prolines and you want to see where they are
in the structure. In the "Find" dialog box, ask it to look for the two strings "pro" and
"202" ("find" is not sensitive to upper vs lower case). It will put a marker on the point, or
center it if you turn on pickcenter. "Find" acts just like a mouse-click, so you can also
use it to do things like add a label or draw a line, if those functions are enabled. It will
not find a point that is not currently displayed. If you now "find" Pro 30 (as a "search
from beginning"), the information line will tell you how far apart the two prolines are.
Turn the markers back off afterward.
Try out the ZOOM function, starting from View1. The sliders at the right side of the
graphics window work just like ordinary scroll bars: you can move them slowly by
clicking on the arrows, or make larger jumps by clicking in the open scrollbar, or you can
drag the slider. Try clicking once or twice in the lower part of the zoom scrollbar to
enlarge the image by large steps, then on the upper arrow to reduce it slowly. Then zoom
in further; the maximum zoom factor is 10.
With the zoom factor at about 3.0, choose "STEREO on" under the "Display"
pulldown menu, or more conveniently type the 's' key on the keyboard. MAGE stereo
divides the graphics window in half vertically, with left and right images differing by a 6
degree rotation. Such side-by-side stereo can be used with a suitable viewer, or else just
by relaxing your eyes to focus toward infinity, letting the two images drift together until
they overlap, and then focusing on the fused image to see 3-D. Each half-window is
clipped at the centerline as well as the edges, so that the stereo can be used with large, or
even zoomed, images. However, you may often want either a smaller zoom factor than in
mono, or a different window shape. You can toggle between wall-eye and cross-eye
stereo by typing 'c'; such a setting will last until you toggle it off or the program is quit
and restarted. CHEMISTS ARE OFTEN REALLY GOOD AT CROSSING THEIR
EYES SUFFICIENTLY TO VIEW IN STEREO.
Things like zoom factor can also be preset by the author: choose View4 and turn on
"mutant sc". Turn off the gold Calphas for a clear view of the loop, and turn them back
on to judge what is buried. Experiment with changing the thickness of the "zslab" to
control how much depth is shown. If the "zclip" button is turned off, the slab will only
control the amount of depth-cuing. Multiple mutants were isolated for each site in this
loop, and the role of each amino acid was deduced from the pattern of effects observed
for its mutants. Five such categories are COLOR-KEYED and labelled. Magenta
residues are found important for folding of the molecule; they are mainly aromatics on
the beta sheet. Green residues affect the rate of CO2 hydration and yellow residues affect
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the pKa; both sets are close to the active site (except for Glu 205). The red residue is
important for thermostability; it is a cis proline at the end of the loop (the same Pro 202
we "found" earlier). Changes in the gray amino acids did not have significant effects.
In View4 with the mutants on, invoke the "KALEIDOSCOPE" function by
pressing the 'k' key. Then rotate slowly, optimizing the aesthetic effects. The 'f' key (for
"flatland") will let you scroll in the plane of the screen. Toggle 'k' and 'f' again to return
to normal rotation.
*{KINEMAGE 3}* - Streptavidin/biotin complex
Read the caption! These proteins are used a lot in biology because they bind to each
other so strongly. To attach two molecules together, biologists will attach one structure
to avidin, and another structure to “strep,” and use “strep-avidin” to bring the two
structures together.
Kin. 3 uses a BALL-AND-STICK representation to highlight the tight binding of
biotin to a site tucked in one end of the beta-barrel of a streptavidin subunit. Stereo really
enhances View1. Color-coded balls show the non-C atoms of the biotin and the protein
atoms to which they H-bond. [The balls are specified by a "balllist" in the kinemage file;
Mage draws a colored circle, with a small highlight, at each of the balllist points and
shortens the adjacent vectors appropriately.] Note that the views here have brief labels
called 'VIEWID's, specified by the author when saving the view. View2 and View3 are
overviews from the side and the end of the beta barrel; turn off the sidechains to see the
position of the biotin, and turn off the biotin to see the crevice waiting to bind it.
Skip the following: *{KINEMAGE 4}* - Geodesic dome construction
Continue here: *{KINEMAGE 5}* - Leucine Zipper
Leucine zippers bind to DNA, and this binding turns on or
turns off genes.
Proteins with leucine zippers include transcription factors
(proteins that
turn on or off genes by binding DNA). AP-1 (see
illustration) is a
transcription factor with a leucine zipper (zipper made up of
two proteins
called Jun and Fos) with 2 helices and looks like a zipper
with
leucine residues (green color) lining on the inside of the
zipper. AP-1 is a transcription factor that binds to DNA and
then
turns off or on certain genes. Leucine zippers are found in
other transcription
factors and their function is to bind DNA like a closepin on a
rope. Hormones
turn on transcription factors that then control genes.
Kin. 5 shows the GCN4 leucine zipper dimer,
viewed from the end. The two chains have
identical sequences and are oriented
parallel, with the N-termini toward you.
Just the Calphas and the interface
sidechains are shown. Toggle off the 'zclip'
button to see the full depth. Supercoiling allows the two helices to stay the same distance
apart along their entire length; in contrast, most paired helices in globular proteins are
straighter and diverge toward the ends. Here, the inter-helical contacts are made by sets
of residues that look like wide rungs on a ladder (choose View2 to see a side view of the
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"ladder"). Every other rung contains a pair of orange leucines; alternate rungs contain
pairs of gold valines (except for Met 2, and the hotpink Asn 16 near the middle).
Choose View6 and turn off all but the Leu sidechains, to try out some of the 'Display'
options and the WRITE POSTSCRIPT feature. This view looks directly down one helix,
with the other one coiling around it. On the 'Display' menu, turn on 'Black&White' to get
a black-on white image, and then turn off 'OneWidth' to get line-width depth-cuing. [The
third linewidth option, 'ThinLine', gives lines only one pixel wide; it speeds up rotation
on some PC's, and is good for superpositions of multiple structures.] Now choose 'Write
PostScript' on the 'File' menu: Mage will write a PostScript file of the contents of the
graphics window, with smooth lines.
For a detailed tour of the Leu zipper helix-helix contacts, choose View3 and move the
slider to the top of the ZTRANS scrollbar; you should see just a little backbone and the
sidechains of Met 2 at the beginning of each helix. [Turn off Black&White and
MultiWidth.] Now hold down the mouse near the bottom of the ztrans scrollbar (just
above the arrow) to move the structure through the visible slab. A little more than one
"rung", or layer, will be in view at a time. Notice how similar the geometry is for each
rung of Leucine sidechains (orange). Valine rungs (gold or hotpink) are also similar to
one another, but different in detail from Leucine rungs. Hold at the top of the scrollbar to
go back the other way.
To see a grouping of contact residues that looks more like a zipper, choose View4,
turn off "heptad sc" and turn on "zipper sc". Although the major contacts are made sideto-side within one rung or layer, there are also two vertical zippers of sidechains (green in
front, and pink in back) for which a stripe of leucines from one helix interdigitate with a
stripe of valines from the other helix. Look just at the green ones ("front zip") and then
just at the pink ones ("rear zip"). View5 looks at the two zipper layers from the side.
*{KINEMAGE 6}* - Alpha-helix: measures and the "draw new" tools
Let’s study an alpha helix taken from a protein. Reread your text pages 48 and 49 to
review the helix structure (or review by the web; look up helix structure). Remember
what the R group of an amino acid is (look it up in text or on web).
Kinemage 6 shows an asparagine (Asn- an amino acid) as the "N-cap" (the first residue,
half in and half out) of an alpha-helix (from thermolysin). That Asn sidechain mimics the
conformation and interactions of another residue's-worth of main chain at the beginning
of the helix. Click on the Od1 of Asn 280 (red atom, on gold sidechain), then click on the
main chain N just below it (blue atom) - the information line should say "n gln 283", with
a distance of about 2.7 A. Move around, try all views (especially the closeup), and/or use
stereo to see the geometry.
Skip all the next detailed series of steps for this image.
Open up another kin file: C5BETA.kin. Look at the first image: what protein is this?
Look at view 2 of the first image. For this and other images, just look through them
briefly.
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Open C3ALPHA.kin; go to the third image of human growth hormone and study its
structure. Animate it two ways. Look up human growth hormone in your text or the web.
Open C2Motifs.kin; go to the third image and look at a beta pleated sheet. Note the H
bonds keep it together.
Let’s look at membrane proteins. Open C12membr.kin and look at an aquaporin (or
porin)—image numbers 2 and 3. The Nobel prize was given away last year for studies on
this membrane protein that allows water to rapidly move through it from one side of the
membrane to the other. Porins are very important in cell biology- for example, they play
an important function in kidney function.
Finally, we will spend a bit more time on the following. Look at the animation of the
effect of cyclin or Ca binding to proteins (calmodulin and CDK2) in C6FLDFLX.kin file.
Calmodulin and cdk2 are images 8 and 9. What do these two proteins do? Read the
pages from the Introduction to Protein Structure book on Cyclin, CDK2 and calmodulinsee end of this file. Enlarge the pages to look closely at the figures and take notes in your
lab notebook (hint: cyclin builds up to a concentration that allows it to bind cdk2 and this
helps activate cdk2; active cdk2 moves the cell from G1 to S phase leading to cell
division).
Know how cdk2 is turned on by cyclin binding- also find ATP binding to the kinase
(kinases take phosphate from ATP and attach the phosphate to another protein to turn it
on or off).
Just spend a brief period of time looking at hexokinase (image 7) –as the substrate binds,
the enzyme bends its two domains over the substrate- see the motion as new weak bonds
form and distort the protein. Compare this to that of hexokinase binding substrate in Fig.
6-6b in your text (6th ed; earlier editions should have it).
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Questions to answer during your use of MAGE and the demo kin file:
(place these questions and your answers in your lab notebook- as this is a Word
file, you can type into it!)
1. Draw the active site of carboxypeptidase A and what happens to Tyr 248 when the
substrate binds.
2. Using the carboxypeptidase A animation, measure the distance Tyr 248 moves;
measure the distance at the tip of Tyr 248 points before and after the substrate binds.
Describe how you did this in your lab notebook. Remember that the average protein is
about 5 nm in diameter (5 nanometers/nm or 5 x 10-9 meters is equivalent to 50
Angstroms; 10 Angstroms is 1 nanometer).
3. Describe how to find the distance between the two prolines (amino acids number 30
and 202 in the chain) in carbonic anhydrase and provide the distance.
4. Sketch a simplification of the second kineimage; view it and read the caption below to
make the sketch. Point to the active site, zinc and the amino acids that bind to zinc and
lock it into the enzyme (three histidines).
5. In the next kineimage, view the streptavidin and biotin image by going to View and
advancing to the second image. Rotate the image after getting rid of each part under
Streptavidin except the Calphas (reduce complexity by unclicking the various boxes).
Which of the two is like a barrel?
Which is a small molecule?
How is the barrel made (what is the name of its structure?)
Which level of protein structure does this barrel represent?
6. Look up streptavidin and biotin on the web and tell me what they are used for in
biology. (hint: Companies use them as the bind each other with great strength).
7. What are leucine zippers used for (image 4)? What is their function? What type of
protein has them?
8. How do the Leucine rungs (orange) differ from the Valine rungs (gold or hotpink)?
Follow directions and look at view 3 and 4, go through from top to bottom, and then draw
the differences you note (small drawings not whole structure).
9. What do the blue lines represent in the next kinemage #5? Hint: They hold the alpha
helix together…
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10. What is superoxide dismutase made up of (mostly)? Are the strands parallel or
antiparallel (note arrows point which way?). Draw the barrel showing the twist present.
11. Draw human growth hormone (use the ribbon method) and describe its structure in
words. Where does the “final” helix go? Note that this hormone binds to a receptor to do
what (check web or text)?
12. In C2Motifs.kin; the fourth image shows the hairpin loop motif that occurs in many
proteins. Draw the hairpins (trace over computer screen?) and compare your drawing to
that in the text (Fig. 3-9b; see lecture slides on web).
13. Draw porin structure and note what makes it up. Which way do the arrows point?
How many strands make up the structure? What would you call this structure or shape?
What do porins do? Note what kind of amino acid side chains (or R groups) stick out on
the outside and on in the inside of the structure- explain why they are where they are.
Measure the apparent width of the channel.
14. Cdk2 causes the cell to enter S phase (from G1)- needed for cell division. CDK2 is a
kinase -an enzyme that takes a phosphate from ATP, then puts the phosphate on other
proteins to turn the other protein off or on. Cyclin is a protein that binds to CDK2, forms
new weak bonds to CDK2 to distort and help activate CDK2.
CDK2 has two domains:
a. a small domain, at the ____ terminus (proteins have a beginning, the N
terminus and the end, the C terminus). This small domain also has ____________
(abbreviation of 7 amino acids) that is found in all kinases.
b. A larger domain that is mostly alpha helix and has the ___ ________ with
Threonine 160 (Thr 160).
ATP binds where on CDK2? ____________
Cyclin has two similar domains. One of these 2 domains has the cyclin box that binds to
the PSTAIRE helix (red) and T loop (yellow) of CDK2.
When the cyclin box finds to CDK2, CDK2 changes in two major ways:
1. To make the active site of CDK2 complete, ______ moves INTO the active
site (it is needed by the enzyme for catalysis).
2. ____ ____________ moves out of the active site so that substrate can come
in (the section of protein blocks the active site). At the molecular level, this movement is
huge; 20 Angstrom (10-10 meter). Furthermore, an alpha helix in this section becomes a
B pleated sheet strand.
15. Calmodulin:
This protein binds four Calcium ions (two at each end), then binds to another protein to
turn the other protein on. Calmodulin (without calcium) has a ________________ shape,
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and an ________ ___________ at each end- this domain binds Calcium. Can you use
your right hand to make this shape that binds calcium ?
Use your hand and show where calcium would bind (see discussion/illustration below).
When calcium binds, calmodulin turns into a globular protein that wraps around another
protein to activate the other protein.
From Introduction to Protein Structure
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Proteins bind Ca ions through an “EF hand” motif; use your
right hand to model the E helix (red)- the right forefinger, the
flexed middle finger is the green loop that binds calcium
(pink), and the F helix is blue and is the thumb. Can you
find the EF hands in calmodulin?
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For the PowerPoint lecture; text from World of the Cell (6th ed);
Disease, Chaperones and Protein Folding
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