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Protein Partnering & Function: Protein Surface Charge
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<strong>Protein Partnering & Function:</strong> Protein Surface
Charge
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<p class="mainidea">
How does charge affect the properties of proteins?
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The complex peaks and valleys of a protein are made even more distinct
by the pattern of charges present at the surface. Every different
protein has its own shape and charge pattern, giving it a unique
molecular ID. In this way, molecules can recognize each other by both
shape and charge.
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<b>Your job: </b>Compare charges at the surface of the protein
with the atoms underneath to understand what causes the charge.<br><br><img src="surfaceChargeBio.png" align="right"><br><b>What
to do: </b>To see underlying amino acids, click in the yellow
circles in the model, or use the buttons below. Use the "Sidechain
surface" buttons to view the surface color more clearly (solid) or
to view the atoms underneath (translucent).
</p>
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<b>View:</b>
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<b>Sidechain surface: </b>
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<input value="Solid" name="button2" script="script:nativescript:plugin:1:color isosurface opaque" id="button2" type="submit">
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<input value="Translucent" name="button5" script="script:nativescript:plugin:1:color isosurface translucent" id="button5" type="submit">
</td>
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<input value="Reset all" name="button1" script="script:textbox:3:selectcomponent 0 false; script:textbox:3:selectcomponent 1 false; script:textbox:3:selectcomponent 2 false; script:nativescript:plugin:1:set echo area1Echo hidden; set echo area2Echo hidden; set echo zoomEcho hidden; moveto 1.0 { 770 282 573 98.07} 85 0.0 0.0 {1.3679996 -1.7515001 -5.9615006} 20.098276 {0.0 0.0 0.0} 8.439582 11.647305 50.0; delay 0.2; set echo circle1 displayed; set echo circle2 displayed; color isosurface opaque" id="button1" type="submit">
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<p class="question">
Which word best describes the character of the amino acid under the
protein surface <a href="nativescript:plugin:1:script area3.spt">here</a>?
(Click to see it in the model.) Choose the BEST answer:
</p>
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Which word best describes the character of the amino acid under the
protein surface <a href="nativescript:plugin:1:script area4.spt">here</a>?
(Click to see it in the model.) Select the BEST answer:
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polar
nonpolar
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Areas of neutral charge are hydrophobic. Why do you think we don't we
see much in the way of neutral areas on the surface of this protein? <a href="script:page:0:message <t><font face=verdana> This protein is found in in the watery environment of the cytoplasm.</font></t>">Hint</a>
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Simple answer: Charged parts of the protein are on the outside, because they are more attracted to water than neutral parts. Hydrophobic parts of the protein are on the inside. Advanced answer: Since water is more attracted to the polar and charged side chains, hydrophobic side chains move to the interior of a protein as it folds.
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<p class="question">
Imagine that the region shown <a href="nativescript:plugin:1:script area5.spt">here</a>
could bind stongly to another protein. Describe the shape and charge of
the part of the other protein that binds here.
</p>
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The other molecule would have a cavity or deep pocket that would be complementary in shape to this "knob". In addition the pocket would be polar, with areas of positive and negative charge that would align with the opposing charges on the knob.
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