PDB-101: Learn: Structural Biology Highlights: Designer Proteins

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class="col-xs-12 col-sm-6 sub-navbar"> <h4>Structural Biology Highlights</h4> </div> <div class="col-xs-12 col-sm-6 text-right sub-navbar"> <table> <tr> <td onclick="location.href="/learn/structural-biology-highlights/introduction"">Introduction</td> <td onclick="location.href="/learn/structural-biology-highlights/index"">Index of Articles</td> </tr> </table> </div> </div> </div> <style> #jmolTabs, #jmolTabs-0, #jmolTabs-1, #jmolTabs-2 { margin: 20px 0; } hr { border-color: #d3d7dc; } .jmolText { font-family: "Helvetica Neue",Helvetica,Arial,sans-serif; font-size: 14px; color: rgb(51, 51, 51); } #jmolApplet_canvas2d, #jmolApplet_0_canvas2d, #jmolApplet_1_canvas2d, #jmolApplet_2_canvas2d, #jmolApplet_3_canvas2d { border:1px silver solid; } .nav-tabs { background: linear-gradient(to bottom, #fff, #d3d7dc); } /* over-write bootstrap values */ .tab-content { border-left: 1px solid #ddd; border-right: 1px solid #ddd; border-bottom: 1px solid #ddd; border-bottom-right-radius: 4px; border-bottom-left-radius: 4px; padding: 15px; } .tab-content img { margin: 0 10px 10px 0; vertical-align: top; } .nav-tabs > li.active > a, .nav-tabs > li.active > a:hover, .nav-tabs > li.active > a:focus { background-color: #fff; color: #333; } .pdb101-page-content ol li { margin-bottom: 5px; } </style> <script src="/js/jsmol/JSmol.min.js"></script> <script> var minWindowDimension = Math.min($(window).width(), $(window).height()); // allow for horiz|vert configuration var jsmolSize = 500; //Math.min(minWindowDimension - 60, 500); var Info = { width: jsmolSize, height: jsmolSize, zIndexBase: 10, debug: false, use: 'HTML5', j2sPath: '/js/jsmol/j2s', disableJ2SLoadMonitor: true, // default is false disableInitialConsole: true, // default is false antialiasDisplay: true, } </script> <div data-elastic-include class="pdb101-page-content"> <h1>Designer Proteins</h1> <p><i>February 2013</i></p> <div><script> var jmolApplet_0; var script_0 = "set antialiasDisplay;frank off;background black;load FILES '/pdb/learn/structural-biology-highlights/2kl8_1.pdb' '/pdb/learn/structural-biology-highlights/fr28.overlap.pdb' '/pdb/learn/structural-biology-highlights/2lv8_1.pdb' '/pdb/learn/structural-biology-highlights/r769.overlap.pdb' '/pdb/learn/structural-biology-highlights/2ln3_1.pdb' '/pdb/learn/structural-biology-highlights/if14.overlap.pdb' '/pdb/learn/structural-biology-highlights/2lvb_1.pdb' '/pdb/learn/structural-biology-highlights/p036.overlap.pdb' '/pdb/learn/structural-biology-highlights/2lta_1.pdb' '/pdb/learn/structural-biology-highlights/rn07.overlap.pdb';model *;select all;cpk off;wireframe off;select protein;backbone 100;color [0,100,255];select 1.1 or 3.1 or 5.1 or 7.1 or 9.1;color [100,255,100];select 1.1 and (1 or 78-85);color [0,80,0];select 3.1 and (1 or 101-110);color [0,80,0];select 5.1 and (1-2 or 75-83);color [0,80,0];select 7.1 and (1 or 103-112);color [0,80,0];select 9.1 and (1-2 or 102-110);color [0,80,0];display 1.1 or 2.1;center 2.1;rotate z 180.;rotate y 67.;rotate z -9.;zoom 180.;"; $(document).ready(function() { Info.script = script_0; $("#jsmol_0").html(Jmol.getAppletHtml("jmolApplet_0", Info)); }) </script> <p><a target="_blank" target="_blank" href="http://cdn.rcsb.org/pdb101/learn/resources/structural-biology-highlights/2lv8_figure.tif"> <div><img src='http://cdn.rcsb.org/pdb101/learn/resources/structural-biology-highlights/2lv8_figure.jpg' class="img-responsive"></div> </a></p> <p>The engineering of new proteins with novel structures and functions is one of the grand challenges facing the scientific community. This goal is particularly tempting, because we can look to nature to see thousands of working examples of proteins that spontaneously fold and perform diverse functions. By looking at natural proteins, scientists have discovered many of the features that are required to create a functional protein, and now, researchers at PSI have proven that these rules may be used for design. </p> <h3>Folding Funnels</h3> <p>Proteins do not appear to fold in an ordered, stepwise manner. This would just take too long, given the long length of typical protein chains and the many conformations they can potentially adopt. Instead, everything happens at once, and a protein can reach its final form through many different pathways. This process has been termed a "folding funnel", with many different intermediate conformations all converging to one final structure. The trick of protein design is to discover the rules that lead to this type of energetic funnel, without having conformations that get stuck in improper folds.</p> <p><a target="_blank" target="_blank" href="http://cdn.rcsb.org/pdb101/learn/resources/structural-biology-highlights/design_rule.tif"><div><img src='http://cdn.rcsb.org/pdb101/learn/resources/structural-biology-highlights/design_rule.jpg' class="img-responsive"></div> </a></p> <h3>Rules for Folding</h3> <p>By studying the structures of many existing proteins, and performing many folding simulations, researchers have discovered a variety of rules for designing proteins that will fold. Many of these rules relate to the amino acid sequence, and have been known for many years, such as the preference for hydrophobic amino acids to be inside. More recently, however, researchers in David Baker's laboratory at the University of Washington have discovered a series of rules that aren't based on sequence, but instead define the optimal sizes of loops that connect different secondary structure elements and favor a particular type of folding. An example of one rule is shown here, with the loops in red: shorter loops prefer to direct an alpha helix (magenta) on one side of a parallel beta sheet (yellow), and a longer loop directs the helix to the other side.</p> <h3>Proof is in the Pudding</h3> <p>The PSI Community Outreach Program has proven the effectiveness of these rules through the synthesis and structure determination of five novel proteins. The design started with five different folding topologies from natural proteins, and then entirely new protein sequences were designed to fold into these topologies. The efficient structural pipeline at <a href="http://www.nesg.org">NESG</a> was brought to bear, and the predicted protein sequences were synthesized, characterized, and ultimately, structures were solved by NMR spectroscopy. In all cases, stably-folded proteins were obtained (PDB entries <a target="_blank" href="https://www.rcsb.org/pdb/explore/explore.do?structureId=2kl8">2kl8</a>, <a target="_blank" href="https://www.rcsb.org/pdb/explore/explore.do?structureId=2lv8">2lv8</a>, <a target="_blank" href="https://www.rcsb.org/pdb/explore/explore.do?structureId=2ln3">2ln3</a>, <a target="_blank" href="https://www.rcsb.org/pdb/explore/explore.do?structureId=2lvb">2lvb</a>and <a target="_blank" href="https://www.rcsb.org/pdb/explore/explore.do?structureId=2lta">2lta</a>). To compare the predicted structure with the structure of the actual protein, click on the image for an interactive Jmol.</p> <div class="txtc"> <p>The JSmol tab below displays an interactive JSmol <br /> </div> <div id='jmolTabs' class='jmolText'> <ul class='nav nav-tabs noprint'> <li><a data-toggle='tab' href='#tabs-1'>Image</a></li> <li class='active'><a data-toggle='tab' href='#tabs-2'>JSmol</a></li> </ul> <div class='tab-content'> <div id='tabs-1' class='tab-pane'> <div><img src='http://cdn.rcsb.org/pdb101/learn/resources/structural-biology-highlights/folds_jmol.jpg' class="img-responsive"></div> </div> <div id='tabs-2' class='tab-pane active'> <h3 id='jmolModalLabel'> Designed Proteins (PDB entries 2kl8, 2lv8, 2ln3, 2lvb and 2lta)</h3> <p>Five designed proteins are included in this Jmol, with the predicted structure in blue and the NMR structure in green. Use the buttons to switch between the different structures. The chains in the NMR structures are a bit longer, because a string of histidines was added to assist with purification of the protein.</p> <div class="jsmol" id="jsmol_0"></div> <form><br /> <br /> <input type="radio" name="radio_0_0" onclick="Jmol.script(jmolApplet_0, 'reset;display 1.1 or 2.1;center 2.1;rotate z 180.;rotate y 67.;rotate z -9.;zoom 180')" checked> Fold I   <input type="radio" name="radio_0_0" onclick="Jmol.script(jmolApplet_0, 'reset;display 3.1 or 4.1;center 4.1;rotate z -90.;rotate y 95.;rotate z -131.;zoom 180')"> Fold II   <input type="radio" name="radio_0_0" onclick="Jmol.script(jmolApplet_0, 'reset;display 5.1 or 6.1;center 6.1;rotate z 41.;rotate y 104.;rotate z -51.;zoom 180')"> Fold III   <input type="radio" name="radio_0_0" onclick="Jmol.script(jmolApplet_0, 'reset;display 7.1 or 8.1;center 8.1;rotate z -96.;rotate y 162.;rotate z 83.;zoom 180')"> Fold IV   <input type="radio" name="radio_0_0" onclick="Jmol.script(jmolApplet_0, 'reset;display 9.1 or 10.1;center 10.1;rotate z -51.;rotate y 132.;rotate z 125.;zoom 180')"> Fold V   <br /> <br /> <input type="checkbox" onclick="if(this.checked) { Jmol.script(jmolApplet_0, 'select (sidechain or alpha) and hydrophobic and not hydrogen;wireframe 50') } else { Jmol.script(jmolApplet_0, 'select hydrophobic;wireframe off')}"> show hydrophobic sidechains   <br /> <input type="checkbox" onclick="if(this.checked) { Jmol.script(jmolApplet_0, 'select (sidechain or alpha) and not hydrophobic and not hydrogen;wireframe 50') } else { Jmol.script(jmolApplet_0, 'select not hydrophobic;wireframe off')}"> show hydrophilic sidechains   <br /> </form> </div> </div> </div> <div class='sbkb-references'> <h4>References</h4> <ol> <li><p>Koga, N. et al. Principles for designing ideal protein structures. Nature 491, 222-227 (2012).</p></li> </ol> </div> </div> </div> </div> <div id="footer_main" class="hidden-print"> <div class="container"> <div class="row"> <div class="col-sm-12 col-md-7"> <p><strong>About PDB-101</strong></p> <p>Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D for a diverse and multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.</p> <p>PDB-101 is developed by the <a href="https://rcsb.org" target="_blank">RCSB PDB</a>.</p> </div> <div class="col-sm-12 col-md-5 text-center"> <p>RCSB PDB (<a href="http://nar.oxfordjournals.org/content/28/1/235.abstract" target="blank">citation</a>) is hosted by</p><img src="//cdn.rcsb.org/pdb101/common/images/Logo_Rutgers-2024.png" alt="Rutgers University logo" usemap="#rutgers-map" height="32" style="padding:0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSD-SDSC.png" alt="University of California San Diego/San Diego Supercomputer Center logos" usemap="#UCSD-SDSC-map" height="26" style="padding: 0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSF.png" alt="Univesity of California San Franciscologo" usemap="#UCSF-map" height="26" style="padding-left: 10px;"><map name="rutgers-map"> <area shape="rect" coords="0,0,115,26" href="http://www.rutgers.edu/" alt="Rutgers" target="_blank"></map><map name="UCSD-SDSC-map"> <area shape="rect" coords="0,0,150,26" href="http://ucsd.edu/" alt="UCSD" target="_blank"> <area shape="rect" coords="151,0,255,26" href="http://www.sdsc.edu/" alt="SDSC" target="_blank"></map><map name="UCSF-map"> <area shape="rect" coords="0,0,64,26" href="http://www.ucsf.edu/" alt="UCSF" target="_blank"></map><br><br> <p>RCSB PDB is a member of <span id='pdbmembers_footer'><a href='http://www.wwpdb.org/' target='_blank'><img src='//cdn.rcsb.org/pdb101/common/images/Logo_wwpdb.png' width='70'></a><span class='pipe'></span><a href='http://www.emdatabank.org/' target='_blank'><img src='https://cdn.rcsb.org/pdb101/common/images/EMDataResourcelogo.png' width='100'></a></p> </div> </div> </div> </div> <div id="footer_grant" class="hidden-print"> <div class="container"> <div class="row"> <p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank">National Institutes of Health</a> under grant R01GM157729.</p> </div> </div> </div> <div id="jira-fdbck"></div><script> //Google Analytics tracking code {/* (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-71059016-1', 'auto'); ga('send', 'pageview'); */} </script> </div> </body> </html>

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PDB-101: Learn: Structural Biology Highlights: Designer Proteins