https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Michael+PikaartProteopedia - User contributions [en]2026-09-21T20:30:31ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sandboxmjp1&diff=3808888Sandboxmjp12023-07-20T19:07:36Z<p>Michael Pikaart: </p>
<hr />
<div>==Mike's cool protein==<br />
<StructureSection load='3L1W' size='480' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandboxmjp1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== SDS PAGE gel ==<br />
[[Image:PXL 20230720 130648246.jpg|300px|left|thumb| Your Caption Text]]<br />
== Disease ==<br />
<br />
== Relevance ==<br />
Ligand <scene name='97/977756/Some_rando_ligand/1'>for this thing</scene> <br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandboxmjp1&diff=3808874Sandboxmjp12023-07-20T18:43:14Z<p>Michael Pikaart: </p>
<hr />
<div>==Mike's cool protein==<br />
<StructureSection load='3L1W' size='480' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandboxmjp1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== SDS PAGE gel ==<br />
[[Image:PXL 20230720 130648246.jpg|300px|left|thumb| Your Caption Text]]<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandboxmjp1&diff=3808871Sandboxmjp12023-07-20T18:42:12Z<p>Michael Pikaart: </p>
<hr />
<div>==Mike's cool protein==<br />
<StructureSection load='3L1W' size='480' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandboxmjp1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== SDS PAGE gel ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:PXL_20230720_130648246.jpg&diff=3808863File:PXL 20230720 130648246.jpg2023-07-20T18:34:04Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:Induced_BASIL_plasmids.jpg&diff=3808860File:Induced BASIL plasmids.jpg2023-07-20T18:30:39Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandboxmjp1&diff=3808854Sandboxmjp12023-07-20T18:24:44Z<p>Michael Pikaart: </p>
<hr />
<div>==Mike's cool protein==<br />
<StructureSection load='3L1W' size='480' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandboxmjp1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandboxmjp1&diff=3808850Sandboxmjp12023-07-20T18:23:38Z<p>Michael Pikaart: New page: ==Mike's cool protein== <StructureSection load='3L1W' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for your page '''Sandboxmjp1'''. Click a...</p>
<hr />
<div>==Mike's cool protein==<br />
<StructureSection load='3L1W' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandboxmjp1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668742Sandbox Hopecoll carbanhyd2016-08-30T16:01:06Z<p>Michael Pikaart: </p>
<hr />
<div>A quick orientation to structure and function: carbonic anhydrase<br />
<StructureSection load='1ca2' size='340' side='right' caption='Caption for this structure' scene=''><br />
<br />
There should a spinning gray structure to the right of this page. To make it a little pretty, let's add some <scene name='74/740511/Carbonic_anhyd_secondary/1'>COLOR</scene> by clicking the green link. You should be able to rotate and zoom on this structure. Then open<br />
http://www.rcsb.org/pdb/101/motm.do?momID=49, which will direct you to a page on<br />
the RCSB website in the form of a Molecule of the Month article from a few years ago.<br />
There are three web pages associated with this article, which you navigate by clicking the<br />
Next and Previous buttone. Read these three pages, and answer<br />
the questions in this google doc: <br />
<br />
It's due Friday, Sept 2<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668741Sandbox Hopecoll carbanhyd2016-08-30T15:57:25Z<p>Michael Pikaart: </p>
<hr />
<div>A quick orientation to structure and function: carbonic anhydrase<br />
<StructureSection load='1ca2' size='340' side='right' caption='Caption for this structure' scene=''><br />
<br />
There should a spinning gray structure to the right of this page. To make it a little pretty, let's add some <scene name='74/740511/Carbonic_anhyd_secondary/1'>COLOR</scene> by clicking the green link. You should be able to rotate and zoom on this structure. Then open<br />
http://www.rcsb.org/pdb/101/motm.do?momID=49, which will direct you to a page on<br />
the RCSB website in the form of a Molecule of the Month article from a few years ago.<br />
There are three web pages associated with this article, which you navigate by clicking the<br />
Next and Previous button<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668740Sandbox Hopecoll carbanhyd2016-08-30T15:52:10Z<p>Michael Pikaart: </p>
<hr />
<div>A quick orientation to structure and function: carbonic anhydrase<br />
<StructureSection load='1ca2' size='340' side='right' caption='Caption for this structure' scene=''><br />
<br />
There should a spinning gray structure to the right of this page. To make it a little pretty, let's add some <scene name='74/740511/Carbonic_anhyd_secondary/1'>COLOR</scene> by clicking the green link.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668739Sandbox Hopecoll carbanhyd2016-08-30T15:48:44Z<p>Michael Pikaart: </p>
<hr />
<div>A quick orientation to structure and function: carbonic anhydrase<br />
<StructureSection load='1ca2' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668738Sandbox Hopecoll carbanhyd2016-08-30T14:44:43Z<p>Michael Pikaart: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')== 0<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668736Sandbox Hopecoll carbanhyd2016-08-30T14:32:02Z<p>Michael Pikaart: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')== 0<br />
<StructureSection load='1ca2' size='340' side='right' caption='Carbonic Anhydrase' scene=''><br />
<br />
<scene name='74/740511/Carbonic_anhyd_secondary/1'>TextToBeDisplayed</scene><br />
<br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668734Sandbox Hopecoll carbanhyd2016-08-30T14:22:42Z<p>Michael Pikaart: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')== 0<br />
<StructureSection load='1ca2' size='340' side='right' caption='Carbonic Anhydrase' scene=''><br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668733Sandbox Hopecoll carbanhyd2016-08-30T14:20:56Z<p>Michael Pikaart: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')== 0<br />
<StructureSection load='1ca2' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Sandbox_Hopecoll_carbanhyd&diff=2668732Sandbox Hopecoll carbanhyd2016-08-30T14:20:00Z<p>Michael Pikaart: New page: ==Your Heading Here (maybe something like 'Structure')== 0 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for y...</p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')== 0<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Sandbox Hopecoll carbanhyd'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1119168Michael Pikaart/Biochem StructureIntro2010-09-12T00:05:07Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene>: Here the beta sheet strands of elastase are highlighted. You can see the emergence of the higher-order domains formed within the protein's structure.<br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>A beta turn linking two anti-parallel beta strands</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116386Michael Pikaart/Biochem StructureIntro2010-08-30T13:10:56Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene>: Here the beta sheet strands of elastase are highlighted. You can see the emergence of the higher-order domains formed within the protein's structure.<br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>A beta turn linking two anti-parallel beta strands</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116385Michael Pikaart/Biochem StructureIntro2010-08-30T13:05:23Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene>: Here the beta sheet strands of elastase are highlighted. You can see the emergence of the higher-order domains formed within the protein's structure.<br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>A Beta turn linking two anti-parallel beta strands</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116384Michael Pikaart/Biochem StructureIntro2010-08-30T13:03:06Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene>: Here the beta sheet strands of elastase are highlighted. You can see the emergence of the higher-order domains formed within the protein's structure.<br />
<br />
<br />
<scene name='Michael_Pikaart/Biochem_StructureIntro/Carbonic_anydrase_1ca2_beta/1'>TextToBeDisplayed</scene>: This is a close-up look at classical beta turn in the enzyme carbonic anhydrase. Inter-strand hydrogen bonds are shown in green. See if you can identify the two amino acid residues at the tip of the beta turn.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1116383Michael Pikaart/Biochem StructureIntro2010-08-30T12:27:23Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/2'>Beta sheet sections from elastase</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114435Michael Pikaart/Biochem StructureIntro2010-08-23T17:41:20Z<p>Michael Pikaart: Pikaart Sandbox 1 moved to Michael Pikaart/Biochem StructureIntro</p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/1'>Beta sheet sections from elastase</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114434Michael Pikaart/Biochem StructureIntro2010-08-23T17:38:40Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/1'>Beta sheet sections from elastase</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114433Michael Pikaart/Biochem StructureIntro2010-08-23T17:31:30Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='1est' size='400' frame='true' align='right' caption='Insert caption here' /><br />
<br />
<br />
<scene name='Pikaart_Sandbox_1/Beta_sheets_from_elastase/1'>Beta sheet sections from elastase</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114432Michael Pikaart/Biochem StructureIntro2010-08-23T17:25:29Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
== Beta sheet ==<br />
<br />
A second type of structure commonly found in proteins is the beta sheet. Unlike the helix, there is not a rotational component to this structure. Because of this, a single length of beta sheet structure cannot complete intra-strand hydrogen bonding. Rather, the hydrogen bonding that stabilizes beta sheet structures occurs between neighboring strands. These strands can either be parallel or antiparallel. In either orientation, there must be a stretch of linker polypeptide in a continuous polypeptide - this may be as short as two amino acids in a so-called beta turn, or a longer stretch of polypeptide with its own secondary structure. A protein which has significant beta sheet secondary structure is the protease elastase: <applet load='est1' size='400' frame='true' align='right' caption='Insert caption here' /></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114431Michael Pikaart/Biochem StructureIntro2010-08-23T17:17:10Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene><br />
<br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene><br />
<br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene><br />
<br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.<br />
<br />
<br />
== Beta sheet ==</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114430Michael Pikaart/Biochem StructureIntro2010-08-23T17:15:57Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> <br />
Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene> <br />
This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene> <br />
Here is a look at one of the GCN4 polypeptides in contact with DNA. Two side chains in proximity to the DNA are shown as balls, the DNA in stick form.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114429Michael Pikaart/Biochem StructureIntro2010-08-23T17:13:24Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene> This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?<br />
<br />
<scene name='Pikaart_Sandbox_1/Gcn4_dbd/1'>The DNA binding domain</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:DBD.pdb&diff=1114428File:DBD.pdb2010-08-23T17:07:10Z<p>Michael Pikaart: Dna binding domain from GCN4</p>
<hr />
<div>== Summary ==<br />
Dna binding domain from GCN4<br />
== Licensing ==<br />
{{self|cc-by-sa-3.0}}</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114427Michael Pikaart/Biochem StructureIntro2010-08-23T16:55:04Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>The dimerization interface</scene> This scene shows you the region of the dimerized proteins where they contact each other. The hydrophobic amino acid side chains leucine and valine are shown in green. Note how the amphipathic character of each helix. However, there is one amino acid side chain at the dimer interface which is not hydrophobic - can you tell which it is?</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114426Michael Pikaart/Biochem StructureIntro2010-08-23T16:50:37Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then '''click the green links below''' to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style," then pick "Scheme," and then "CPK Spacefill."<br />
<br />
<scene name='Pikaart_Sandbox_1/Zipper/1'>TextToBeDisplayed</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114425Michael Pikaart/Biochem StructureIntro2010-08-23T16:39:05Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then click the green links below to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene> Zoom in and out a bit and make sure you can distinguish the backbone atoms from the side chains. See if you can tell by inspection what amino acids are present in this bit of helix. The green dashed lines show the i to i+4th residue hydrogen bonds. If you rotate the helix so you can see right down the helical axis, you would be lead to believe that there is quite a bit of space down the middle. To convince yourself that the helix is actually very tightly packed, left-click on the structure, chose "Style,"</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114424Michael Pikaart/Biochem StructureIntro2010-08-23T16:34:33Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then click the green links below to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/3'>Two helical turns</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114422Michael Pikaart/Biochem StructureIntro2010-08-23T16:22:13Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then click the green links below to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
<br />
<scene name='Pikaart_Sandbox_1/Helix_closeup/2'>TextToBeDisplayed</scene></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114421Michael Pikaart/Biochem StructureIntro2010-08-23T15:57:24Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /><br />
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then click the green links below to walk through a number of close-ups of the molecule.<br />
Let's take a closer look at a bit of the alpha helix.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114420Michael Pikaart/Biochem StructureIntro2010-08-23T15:51:51Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114419Michael Pikaart/Biochem StructureIntro2010-08-23T15:50:39Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<applet load='1ysa' size='400' frame='true' align='right' caption='Insert caption here' /></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114418Michael Pikaart/Biochem StructureIntro2010-08-23T15:42:45Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects like these:<br />
<br />
[[Image:GardenSnail.jpg|200px]]<br />
[[Image:041106024 twiners xlg.jpg|200px]]<br />
[[Image:Screw.jpg|200px]]<br />
[[Image:1.1156091400.the-famous-spiral-staircase.jpg|200px]]<br />
<br />
Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD])</div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:1.1156091400.the-famous-spiral-staircase.jpg&diff=1114415File:1.1156091400.the-famous-spiral-staircase.jpg2010-08-23T15:28:57Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:Screw.jpg&diff=1114414File:Screw.jpg2010-08-23T15:28:26Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:041106024_twiners_xlg.jpg&diff=1114413File:041106024 twiners xlg.jpg2010-08-23T15:27:38Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:GardenSnail.jpg&diff=1114412File:GardenSnail.jpg2010-08-23T15:27:16Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114411Michael Pikaart/Biochem StructureIntro2010-08-23T15:24:51Z<p>Michael Pikaart: </p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] <big>Chem311 Course Page 1 Introduction to protein structure</big><br />
<br />
<br />
== Introduction ==<br />
A protein's function depends on the proper folding of the linear polymeric chain of amino acids making up its polypeptide sequence. Folding of a polypeptide occurs by way of rotation of the single bonds in either side of each amino acid residue's alpha carbon, characterized by the &Phi; and &Psi; angles. In folded proteins, stretches of amino acids typically have a re-iterated and restricted set of &Phi; and &Psi; angles, giving rise to a length of stable secondary structure. If this structure has a rotational displacement, the result is a helical secondary structure; if the structure occurs in a zig-zag arrangement, a sheet secondary structure results. Here we will explore these two types of secondary structures, as found in actual proteins. <br />
<br />
== Alpha helix ==<br />
Helix or screw structures are found in lots of contexts, both in nature and in man-made objects.</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Michael_Pikaart/Biochem_StructureIntro&diff=1114410Michael Pikaart/Biochem StructureIntro2010-08-23T14:54:00Z<p>Michael Pikaart: New page: 100px Chem311 Course Page 1 - Introduction to protein structure</p>
<hr />
<div>[[Image:Gata_dna.jpg|100px]] Chem311 Course Page 1 - Introduction to protein structure</div>Michael Pikaarthttps://proteopedia.org/index.php?title=File:Gata_dna.jpg&diff=1114409File:Gata dna.jpg2010-08-23T14:50:09Z<p>Michael Pikaart: </p>
<hr />
<div></div>Michael Pikaarthttps://proteopedia.org/index.php?title=Talk:Valosin_Containing_Protein_D120&diff=1114408Talk:Valosin Containing Protein D1202010-08-23T14:32:58Z<p>Michael Pikaart: Talk:Sandbox moved to Talk:Pikaart Sandbox: made a new sandbox page for classroom use</p>
<hr />
<div>#REDIRECT [[Talk:Pikaart Sandbox]]</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Talk:Pikaart_Sandbox&diff=1114407Talk:Pikaart Sandbox2010-08-23T14:32:58Z<p>Michael Pikaart: Talk:Sandbox moved to Talk:Pikaart Sandbox: made a new sandbox page for classroom use</p>
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<div>#REDIRECT [[Talk:Sandbox-test]]</div>Michael Pikaarthttps://proteopedia.org/index.php?title=Valosin_Containing_Protein_D120&diff=1114406Valosin Containing Protein D1202010-08-23T14:32:58Z<p>Michael Pikaart: Sandbox moved to Pikaart Sandbox: made a new sandbox page for classroom use</p>
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<div>#REDIRECT [[Pikaart Sandbox]]</div>Michael Pikaart