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Visualization.html
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<html>
</head>
<meta charset="utf-8">
<title>
Computational Str.Bio. Visualizing Biomolecules
</title>
<link rel="stylesheet" href="comp.css">
</head>
<body>
<h1>
<pre>
############################
# VISUALIZING BIOMOLECULES #
############################
</pre>
</h1>
<div class="topnav">
<a href="./Index.html">Home</a>
<a href="./Main.html">Previous Page</a>
</div>
<p>~ Proteins are mainly imaged using three means: Cryo-Electron Microscopy (CryoEM), Homology Modeling, and X-Ray Crystallography</p>
<p>~ In order to store this imaging data for future use, protein (as well as other macromolecules) are stored as Protein DataBank files, or PDBs</p>
<p>~ PDB files are text-files which provide basic meta-data identifying the compound, the academic publication the image is from, and the biological source of the compound</p>
<p>~ All PDB files are given a unique acession code, known as a PDBID</p>
<p>~ The example below is a PDB file of Human Haemoglobin <a href="https://www.wwpdb.org/pdb?id=pdb_00001a3n">(1A3N)</a> the protein responsible for giving erythrocytes (red blood cells, or RBCs) their ability to transport oxygen throughout the body </p>
<p>
<pre>
<blockquote style="color: #33ff33;">
HEADER OXYGEN TRANSPORT 22-JAN-98 1A3N
TITLE DEOXY HUMAN HEMOGLOBIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HEMOGLOBIN (ALPHA CHAIN);
COMPND 3 CHAIN: A, C;
COMPND 4 MOL_ID: 2;
COMPND 5 MOLECULE: HEMOGLOBIN (BETA CHAIN);
COMPND 6 CHAIN: B, D
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 TISSUE: BLOOD;
SOURCE 6 CELL: RED CELL;
SOURCE 7 MOL_ID: 2;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_COMMON: HUMAN;
SOURCE 10 ORGANISM_TAXID: 9606;
SOURCE 11 TISSUE: BLOOD;
SOURCE 12 CELL: RED CELL
KEYWDS OXYGEN TRANSPORT, HEME, RESPIRATORY PROTEIN, ERYTHROCYTE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.TAME,B.VALLONE
REVDAT 2 24-FEB-09 1A3N 1 VERSN
REVDAT 1 29-APR-98 1A3N 0
JRNL AUTH J.R.TAME,B.VALLONE
JRNL TITL THE STRUCTURES OF DEOXY HUMAN HAEMOGLOBIN AND THE
JRNL TITL 2 MUTANT HB TYRALPHA42HIS AT 120 K.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 805 2000
JRNL REFN ISSN 0907-4449
</blockquote>
</pre>
</p>
<p>~ Included within a PDB is also data concerning how the compound in question was analyzed and imaged to begin with, and often includes possible errors in the analysis, such as missing atoms, or atoms that are anomolously close to each other</p>
<p>
<pre>
<blockquote style="color:#33ff33;">
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : MAY-97
REMARK 200 TEMPERATURE (KELVIN) : 120
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NI FILTER
REMARK 200 OPTICS : MIRROR
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NZ LYS B 66 O HOH B 243 0.96
REMARK 500 O HOH D 248 O HOH D 256 2.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
</blockquote>
</pre>
</p>
<p>~ Included in every PDB is a table of every atom with its corresponding amino acid (the building block of a protein), and its coordinate position. Also included is a table of the protein's amino acid sequence. This allows the protein to entirely be reconstructed from its PDB file, down to the atom</p>
<p>
<pre>
<blockquote style="color:#33ff33;">
SEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA
SEQRES 2 A 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA
SEQRES 3 A 141 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR
HELIX 1 1 PRO A 4 SER A 35 1 32
HELIX 2 2 PRO A 37 TYR A 42 5 6
ATOM 1 N VAL A 1 10.720 19.523 6.163 1.00 21.36 N
ATOM 2 CA VAL A 1 10.228 20.761 6.807 1.00 24.26 C
ATOM 3 C VAL A 1 8.705 20.714 6.878 1.00 18.62 C
ATOM 4 O VAL A 1 8.164 20.005 6.015 1.00 19.87 O
ATOM 5 CB VAL A 1 10.602 22.000 5.966 1.00 27.19 C
ATOM 6 CG1 VAL A 1 10.307 23.296 6.700 1.00 31.86 C
ATOM 7 CG2 VAL A 1 12.065 21.951 5.544 1.00 31.74 C
ATOM 8 N LEU A 2 8.091 21.453 7.775 1.00 16.19 N
</blockquote>
</pre>
</p>
<p>~ The problem with storing PDBs, is that the the file is entirely numbers and terms!</p>
<p>~ While computers can handle this information easily , it is diffcult for people to make sense of </p>
<p>~ To resolve this, we have to use tools to visualize this data. The most famous tool is <a href="https://pymol.org/2/">PyMOL</a>, a Python and C++ dependent macromolecule visualization platform </p>
<p>~ PyMOL takes a PDB, and uses the Open Graphics Library <a href="https://www.opengl.org/">(OpenGL)</a>, to reconstruct a highly accurate image of the macromolecule in question</p>
<p>~ PyMOL accepts plugins, allowing for niche visualizations or on-demand computational analysis on the PDB structure</p>
<center>
<figure>
<img src="./pymol.png" alt= "Screenshot of PyMOL, default, with no plugins" style="float:center;width:600px;height:400px;">
<figcaption style="color:#ffb000;font-size:18px">Screenshot of PyMOL, with Hemoglobin (PDB 1A3N)</figcaption>
</figure>
</center>
<p> ~ The ultimate goal is of PyMOL is to create accurate representations of macromolecules, like the aforementioned Haemoglobin (PDB 1A3N), which has been visualized below, with the oxygen binding sites in green</p>
<center>
<img src="./1a3nHemo.gif" alt="Hemoglobing rotating GIF"
style="float:center;width:900px;height:340px;">
</center>
<span style="background-color: #ffb000;color: black;font-size:20px">(END)</span>
</body>
</html>