// ===========================================================================
// This file, chapter.js, must be provided for each chapter.htm.
// Each chapter.js file contains the settings and content for one chapter.
// Each chapter should be in a separate directory (folder).
// Each chapter directory should contain one and only one chapter.htm file.
//
// Lines beginning "//" are comments for authors. They are ignored by JTAT.
// ===========================================================================

  // ========== SECTION I: PROVIDE SLIDERS? ============

  // These control whether this Chapter has a Slab ("Cut")
  // slider, in addition to a Zoom slider, or neither.
  // You cannot have a Slab slider without also having the Zoom slider.
  // The label on the slab slider (typically "Cut" or "Slab")
  // is defined in _jsutil/config2.js
showZoomSlider = true;
showSlabSlider = true;
slabSliderLabel = "Cut"; // Optionally, may be changed to "Slab".

  // ========== SECTION II: CHAPTER TITLE, INTRODUCTION ============

  // CHAPTER TITLE IS REQUIRED
chapterTitle = '4. MHC Class I';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = '';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
// Be sure to include paragraphs within <p></p> tags. This gives them margins.
chapterIntro =
	'<p> \n\
MHC Class I consists of two chains, a large alpha chain and a smaller\n\
beta chain, called\n\
<a href="http://en.wikipedia.org/wiki/Beta-2_microglobulin"\n\
target="_blank">beta-2 microglobulin</a>.\n\
Alleles code for variations\n\
in the alpha chain. All alleles share the same\n\
invariant beta chain, whose gene is outside the MHC. The crystallographic structure\n\
is known only for the extracellular domains, which were solubilized by\n\
cleavage with papain. The transmembrane and cytoplamic domains are not\n\
shown because their structures are not known.\n\
	<\/p> \n\
';

  // ========== SECTION III: NAVIGATION (NEXT, PREVIOUS, CONTENTS, RESET) ============

  // The 3 URL's below must be relative to the current chapter.
  // The position and style of the navigation bar are set in config.js

  // Leave blank if there is only one chapter, and no contents page.
contentsButtonGoesTo = "../contents/contents.htm";

  // Leave blank if this is the first chapter.
previousChapterButtonGoesTo = "../chapter03/chapter.htm";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../chapter05/chapter.htm";

  // If the View buttons define the orientation/zoom, no Replay/Reset
  // button is needed, so provideResetButton should be false.
  // In contrast, some chapters are designed to maintain the orientation and
  // zoom set previously by the user when a new view is displayed.
  // These need a Reset button, so provideResetButton should be true.
  // When provided, a Reset button runs reset.spt in the chapter's directory.
  // It allows Reset to do something different than the "View 1" button does.
	// For more explanation, see "Add Chapters ..." in the
	// Authoring Instructions.
provideResetButton = true; // ignored when isContents.

	// The next variable applies only when provideResetButton is true.
	// If showResetInitialViewButtonAtTop is true,
	// there will be a Replay/Reset button at the top of the page
	// as well as at the bottom. If false, it will be only at the bottom.
showResetInitialViewButtonAtTop = true;


  // ========== SECTION IV: MOLECULAR VIEW BUTTONS ============

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view00.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Polypeptide chains of MHC I. \n\
<br>&nbsp; &nbsp; <font color="#c3d3ff">Alpha Chain</font>,\n\
<br>&nbsp; &nbsp; <font color="#ffa0a0">Beta Chain</font>,\n\
<br>&nbsp; &nbsp; <font color="#009600">Antigenic Peptide</font>.\n\
';

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view01.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPreButtonText] = '';

	// MOLECULAR VIEW DESCRIPTION

//<div id="jcontrol1"></div>\n\

	buttons[buttonNumber][iButtonText] =
'Domain structure of MHC I. \n\
<br>&nbsp; &nbsp;\n\
<font color="#009600"> <!--green, dkgreen-->\n\
	Antigenic Peptide,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#a04000"> <!--brown-->\n\
	Alpha chain, domain 1,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#E08000"> <!--orange-->\n\
	Alpha chain, domain 2,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#b01800"> <!--brick-->\n\
	Alpha chain, domain 3,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#887000"> <!--ckchartreuse-->\n\
	Beta<sub>2</sub> Microglobulin,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#FFC832">\n\
	Disulfide bonds,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#FF8282"> <!--pink-->\n\
	Papain cleavage locus.\n\
</font>\n\
\n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Origin of the Peptide?";
	buttons[buttonNumber][iDetailsText] =
'The <font color="#009600">peptide</font> is generated in the protein \n\
recycling center of the cell, the \n\
<a href="http://en.wikipedia.org/wiki/Proteasome" \n\
target="_blank">proteasome</a>, where ubiquitin-tagged proteins are \n\
chopped into peptides. MHC Class I does not complete assembly, or reach \n\
the surface of the cell, without a peptide. Most of the time, these \n\
peptides are derived from normal cellular constituents (<i>self</i>). \n\
It is up to  \n\
<a href="http://en.wikipedia.org/wiki/T_lymphocytes" \n\
target="_blank">T lymphocytes</a> to determine whether or not \n\
the peptides displayed by a cell are <i>self</i> or <i>foreign</i>, \n\
and to take appropriate actions in the latter case. \n\
MHC class I binds peptides without regard \n\
to whether they are <i>self</i> or <i>foreign</i>. \n\
';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
	buttons[buttonNumber][iPostButtonText] = '<div id="jcontrol1" name="jcontrol1"></div>';

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view02.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPreButtonText] =
'<a href="http://en.wikipedia.org/wiki/CD8" \n\
target="_blank">CD8</a> is a T cell co-receptor that is crucial for \n\
effective immune responses by T cells to foreign peptides presented by MHC I. \n\
CD8 binds directly to MHC I. \n\
';

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'CD8 binding site (white).\n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "CD8 Binding Site";
	buttons[buttonNumber][iDetailsText] =
'The main binding site for \n\
<a href="http://en.wikipedia.org/wiki/CD8" \n\
target="_blank">CD8</a>, \n\
residues 223-229 in the alpha chain, \n\
was determined from the contacts seen \n\
in a crystallographic structure \n\
(<a href="http://www.proteopedia.org/wiki/index.php/1bqh" \n\
target="_blank">1bqh</a>) \n\
reported in 1998 (Kern <i>et al.</i>, Immunity 9:519, \n\
<a href="http://www.ncbi.nlm.nih.gov/pubmed/9806638?dopt=Abstract" \n\
target="_blank">PMID: 9806638</a>. \n\
';

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view03.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'A spacefilling view shows the shape of the molecule.\n\
';

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view04.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Secondary structure:\n\
' + ss_key() + ".";

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view05.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Evolutionary conservation (alpha chain).\n\
The CD8-binding loop is marked with white halos.\n\
<br>&nbsp; &nbsp; <font color="#009600">Antigenic Peptide</font>.\n\
<br>' + consurf_key11();

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Technical";
	buttons[buttonNumber][iDetailsText] =
'<a href="http://proteopedia.org/wiki/index.php/Conservation%2C_Evolutionary" \n\
target="_blank">Evolutionary conservation</a> \n\
colors were generated for the alpha chain by the \n\
<a href="http://consurf.tau.ac.il" \n\
target="_blank">ConSurf Server</a> \n\
(see \n\
<a href="http://proteopedia.org/wiki/index.php/ConSurfDB_vs._ConSurf#The_ConSurf_Server" \n\
target="_blank">explanation</a>). ConSurf analyses only one chain at a time. \n\
Beta-2 microglobulin is shown in grey (no data) because it was not included \n\
in this analysis. 129 sequences from Swiss-Prot \n\
were aligned. All sequences were for MHC class I. \n\
Most were human, mouse, or gorilla sequences. \n\
You may \n\
<a href="http://firstglance.jmol.org/fg.htm?mol=' +

getPDBURL("2vaa_consurf1283965131_pipe.pdb")

+ '" target="_blank">explore \n\
the ConSurf result in FirstGlance in Jmol</a>. \n\
<br><br> \n\
<i>Insufficient data</i> \n\
(<font color="yellow">yellow</font>) \n\
means that a reliable \n\
conservation level could not \n\
be determined from the multiple sequence alignment. \n\
Despite the large number of sequences,\n\
the average pairwise distance in the multiple sequence alignment was modest,\n\
0.21, which resulted in having insufficient data for some residues (yellow).\n\
';


// End of Molecular View Buttons ===== ===== ===== ===== ===== ===== =====

	// CHAPTER CONCLUSION
	chapterConclusion =
	'<p> \n\
<i>Immunoglobulin-like domains:</i>\n\
<font color="#887000"><b>Beta<sub>2</sub> microglobulin</b></font>\n\
and the\n\
<font color="#b01800"><b>Alpha 3 domain</b></font>\n\
are protein domains with immunoglobulin-like structure\n\
(<a href="http://en.wikipedia.org/wiki/Immunoglobulin_superfamily"\n\
target="_blank">Ig superfamily domains</a>).\n\
Such domains are widely used building blocks that are found\n\
in many proteins with different functions.\n\
Each Ig domain consists of two small beta sheets connected with a disulfide\n\
bond.\n\
For more about immunoglobulin domain structure, please see the tutorial on\n\
<a href="http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody"\n\
target="_blank">Antibody</a>.\n\
</p> \n\
<span class="lightGreenText"> \n\
<center>What Do You See?</center> \n\
<ol><li> \n\
What does \"MHC\" stand for? \n\
</li><li> \n\
How many polypeptide chains make up an MHC Class I molecule, \n\
<i>not counting the antigenic peptide</i>? \n\
</li><li> \n\
How many polypeptide chains make up the MHC I peptide-binding cleft, \n\
<i>not counting the antigenic peptide</i>? \n\
</li><li> \n\
Does beta<sub>2</sub> microglobulin touch the rest of the MHC I molecule? \n\
</li><li> \n\
Which chain of MHC I is invariant? \n\
</li><li> \n\
Which MHC I domains have immunoglobulin-like structure? \n\
</li><li> \n\
Which end of the MHC I molecule is anchored to the cell membrane? \n\
</li><li> \n\
What region of MHC I is least conserved, when multiple sequences are \n\
compared in an evolutionary conservation analysis? Why? \n\
</li><li> \n\
Does CD8 bind to an evolutionarily variable or conserved region of MHC I? What two \n\
amino acids in the binding region are most highly conserved? \n\
</li></ol> \n\
</span><p> \n\
To apply other color schemes, or for further exploration, use the link \n\
below to display <font color="yellow">2vab</font> in <i>FirstGlance \n\
in Jmol</i>. \n\
	<\/p> \n\
';

  // ========== END OF chapter.js ============
