User:Angel Herraez/Sandbox Rama: Difference between revisions

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<title>Ramachandran Animation</title>

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<div style="font-size:150%;text-align:center;font-weight:bold;">
<br>
The Ramachandran Principle
</div>
<div style="font-size:130%;text-align:center;font-weight:bold;">
Phi (φ) and Psi (ψ) Angles in Proteins
</div>

<br>
<div style="width:80%;text-align:center;margin-left:10%;font-size:120%;">
The Ramachandran Principle says that
<a href="https://proteopedia.org/w/Protein_primary%2C_secondary%2C_tertiary_and_quaternary_structure" target="_blank">alpha helices, beta strands, and turns</a>
are the most likely conformations for a
<a href="https://proteopedia.org/w/Chain" target="_blank">polypeptide chain</a>
to adopt, because most other conformations are impossible
due to steric collisions between atoms.
</div>
<br>
<div style="width:90%;text-align:center;margin-left:5%;font-size:100%;">
This interactive tutorial is also available as an
<a href="https://tinyurl.com/RamachandranPrinciple" target="_blank">Animated Slideshow</a>
or
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" "="" target="_blank">YouTube Video</a>,
and there is a
<a href="https://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank">Quiz</a>.
</div>

<br>

<div style="font-size:110%;"><!-- TEXT IN TABLE -->

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<tbody><tr>
<td style="padding:10px;">
<div id="scrollingdiv" style="height:490px;overflow:auto;">

<p>
At right is a fragment of a 

<a href="https://proteopedia.org/wiki/index.php/Chain" target="_blank">polypeptide chain</a>.

In the center is a single complete alanine residue.
Check <b>Alanine</b> to identify its atoms<sup>1</sup>. The other atoms are fragments of adjacent
<a href="https://proteopedia.org/wiki/index.php/Amino_Acids" target="_blank">amino acids</a><sup>2</sup>.

<span style="background-color:#ffff80;padding:3px;">
<i>Drag with your mouse to rotate the model.</i>
</span>

</p><p>

The Alanine is covalently bonded to other amino acids through
<font color="#ff40ff"><b>peptide bonds</b></font>.
Check
<font color="#ff40ff"><b>Peptide Bonds</b></font> to locate them.

</p><p>

The double bonds between

<a href="https://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">main chain (backbone)</a>

<font color="#808080"><b><big>C</big></b></font>
and
<font color="#ff2020"><b><big>O</big></b></font>
delocalize, making the peptide bonds also have partial double bonds
(<i>half-dotted bonds</i>).
This prevents the peptide bond from rotating.

</p><p>

Each peptide bond holds six atoms
in a plane. Check <b>Planes</b> to see them.

</p><p>

The
<font color="#505050"><b>alpha carbon
(C<span style="font-family:&quot;Times New Roman&quot;, Times, serif;">α</span>)</b></font>
in the center of each amino acid 
is held in the main chain by two rotatable bonds. The

<a href="#dihedral">dihedral (torsion) angles</a>
of these bonds are called<sup>3</sup>
<font color="#00b000"><b>Phi</b></font>
and
<font color="#00b000"><b>Psi</b></font>
(in Greek letters,
<font color="#00b800"><b>φ</b></font>
and
<font color="#00b800"><b>ψ</b></font>).

<span style="background-color:#ffff80;padding:3px;">
<i>Use the radio buttons (top of right panel) to identify the rotatable main-chain bonds,
and click the -20° and +20° buttons to see them rotate.</i>
</span>

</p><p></p><center>
<hr width="50%">
Click the <b>Reset</b> button.
</center>

<p></p><p>
The balls shown are much smaller than the atoms they represent.
Check <b>van der Waals</b> to see the real sizes of the atoms<sup>4</sup>.
In fact, most
<font color="#00b800"><b>Phi</b></font>
and
<font color="#00b800"><b>Psi</b></font>
angle combinations are impossible because two atoms cannot occupy the same space.

</p><p>

Check <b>Show Clashes</b> to see where non-bonded atoms are overlapping, and thus
in physically impossible positions.
(This model simulation allows two atoms to overlap, unlike real atoms.)

</p><p>
Check <b>White</b> to make clashes easier to see.
Rotate
<font color="#00b800"><b>Phi</b></font>
and
<font color="#00b800"><b>Psi</b></font>
to find angle combinations where there are no clashes.

</p><p>
In the early 1960’s,
<a href="https://en.wikipedia.org/wiki/G._N._Ramachandran" target="_blank">G. N. Ramachandran</a>
(University of Madras, India) and coworkers
computationally determined the phi and psi angles that avoid steric collisions,
initially treating the atoms simply as rigid spheres<sup>5, 6</sup>.
They showed that the physically allowed angle combinations (that avoid clashes) correspond largely
to the secondary structures observed in proteins:
<a href="https://proteopedia.org/wiki/index.php/Secondary_structure" target="_blank">
alpha helices, beta sheets, and turns</a>.

</p><p>
Ramachandran and team also showed that the major effect of sidechains on the allowed phi and psi
angles is due to C<sub>β</sub> <sup>2</sup>.
Sidechains larger than that of alanine affect the allowed
angles by only a few percent <sup>7, 8</sup>.

</p><p>

The <i>Ramachandran Plot</i> below shows the phi and psi angles actually observed in
proteins.

</p></div></td>
<td>
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<font color="#383838">C<span style="font-family:&quot;Times New Roman&quot;, Times, serif;">α</span>
</font>

<font color="#808080">C</font>
<font color="#ffffff">H</font>
<font color="#3050ff">N</font>
<font color="#ff2020">O</font>

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</td></tr><tr><td>

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  <input type="radio" name="ppradioid" id="ppradioid_0" onclick="doRadio()" checked="">Phi φ
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165°
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165°

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<br>

<!-- SINGLE AA: ALANINE -->
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  <span class="checkmark"></span>
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<!-- COLOR PEPTIDE BONDS MAGENTA -->
<label class="container">
	<input type="checkbox" name="idpeptidebonds" id="idpeptidebonds"><font color="#ff40ff">Peptide Bonds</font>
  <span class="checkmark"></span>
</label>

<!-- PLANES -->
<span title="Six atoms are held in a plane by each peptide bond.">
<label class="container">
	<input type="checkbox" name="idplanes" id="idplanes">Planes
  <span class="checkmark"></span>
</label>
</span>

<br>

<!-- VAN DER WAALS -->
<span title="Atoms shown actual sizes.">
<label class="container">
	<input type="checkbox" name="idvdw" id="idvdw">van der Waals<sup>4</sup>
  <span class="checkmark"></span>
</label>
</span>

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<div name="divwhite" id="divwhite" style="display:none;">
<label class="container">
	<input type="checkbox" name="idwhite" id="idwhite">&nbsp;&nbsp;&nbsp;&nbsp;White
  <span class="checkmark" style="margin-left:20px;"></span>
</label>
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<!-- SHOW CLASHES -->
<label class="container">
	<input type="checkbox" name="idclashes" id="idclashes">Show Clashes
  <span class="checkmark"></span>
</label>

<div name="divtrailclashes" id="divtrailclashes" style="display:none;" title="Previous clashes remain during rotation.">
<label class="container">
	<input type="checkbox" name="idtrailclashes" id="idtrailclashes" onclick="doTrailClashes()">&nbsp;&nbsp;&nbsp;&nbsp;Trail Clashes
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<br>
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</td></tr>
</tbody></table>
</center>

<!-- RAMACHANDRAN PLOT -->
<div style="margin-left:20px;">
<img src="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/Ramachandran_plot_general_100K.jpg" align="right" border="0" width="600">
<a name="plot"></a><p><a name="plot"><br></a>
At right is a <i>Ramachandran Plot</i> <sup>9, 10</sup> with 100,000 data points taken from
high-resolution
crystal structures<sup>11</sup>. Each data point represents the
<a href="https://biomodel.uah.es/model5/prot/diedros_en.htm" target="_blank">combination of phi and psi angles</a>
occurring in a single
amino acid. Residues in an
<a href="https://proteopedia.org/wiki/index.php/Alpha_helix" target="_blank">alpha-helical</a>
conformation are marked
<b><span style="font-size:150%;font-family:&quot;Times New Roman&quot;, Times, serif;">α</span></b>,
and those in a
<a href="https://proteopedia.org/wiki/index.php/Sheets_in_Proteins" target="_blank">beta strand</a>
conformation, <big><b>β</b></big>.

The cluster of data in the upper right quadrant represents mostly
<a href="https://proteopedia.org/wiki/index.php/Turns_in_Proteins" target="_blank">turns</a>.

</p><p>

This plot excludes glycine (whose sidechain is a single hydrogen), proline
(whose sidechain is covalently linked back to the main chain), and amino acids that precede
proline. These special cases have
<a href="https://en.wikipedia.org/wiki/Ramachandran_plot#Gallery" target="_blank">different distributions</a> on Ramachandran plots.

</p>

<p><span style="background:#ffd0d0;padding:10px;line-height:2;">
Challenge your understanding with the
<a href="https://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank"><b>PRACTICE QUIZ</b></a>.
</span></p>

</div>

<b>Related Resources</b><br>
<ul><li>

<a name="dihedral">Dihedral (torsion) angles</a>
are explained with animated models rotating clockwise and counter-clockwise in the
<a href="https://tinyurl.com/RamachandranPrinciple" target="_blank">Slideshow</a> and the
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" target="_blank">YouTube Video</a>.

</li><li>

There is also a
simple visualization of phi and psi angles at
<a href="https://biomodel.uah.es/model5/prot/diedros_en.htm" target="_blank">Dihedral angles in proteins</a>
by Angel Herráez.

</li><li>

<a href="https://proteopedia.org/w/Tutorial:Ramachandran_Plot_Inspection" target="_blank">Tutorial: Ramachandran Plot Inspection</a>: an interactive Ramachandran plot with
many controls and details, by Angel Herráez. Also
<a href="https://biomodel.uah.es/model1j/prot/Ramachandran.htm" target="_blank">in Spanish</a>.

</li><li>

<a href="https://proteopedia.org/w/Ramachandran_Plot" target="_blank">Ramachandran Plot</a>: detailed explanation with example proteins and their
plots displayed in JSmol. Here you can show the Ramachandran plot for any protein structure.

</li><li>

A list of all related resources in English and Spanish:
<a href="https://proteopedia.org/w/Dihedral/Index" target="_blank">Dihedral/Index</a>.

</li><li>

<a href="https://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">Backbone representations</a> explains the relations between backbone traces
and main chain polypeptide bonds, as well as smoothed traces and ribbons.

</li></ul>

<br clear="right"><center>
<table style="background-color:#f0ffe0;border-collapse:collapse;border:1px solid green;" cellpadding="10">
<tbody><tr><td style="text-align:center;">
This tutorial is available in two locations:
<a href="https://proteopedia.org/w/Tutorial:Ramachandran_principle_and_phi_psi_angles" target="_blank">Proteopedia.Org</a>
and
<a href="https://bioinformatics.org/molvis/phipsi" target="_blank">Bioinformatics.Org</a>.

<br>
There is also a
<a href="https://tinyurl.com/RamachandranPrinciple" target="_blank"><b>Slideshow</b></a>, a
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" target="_blank"><b>YouTube Video</b></a>, and a
<a href="https://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank"><b>Practice Quiz</b></a>.


<div style="font-size:80%;text-align:right;">
<a href="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/options.htm" target="_blank">Advanced Options</a>
</div>


</td></tr></tbody></table></center><br>

<br>
<b>Notes &amp; References</b><br>
<ol>

<li>The outlines of the black dots that identify the atoms in Alanine are smaller than
the actual (van der Waals) sizes of those atoms. Check <b>van der Waals</b> to see the actual
sizes.

</li><br><li>
Each amino acid contributes 3 atoms directly to the
<a href="https://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">main chain (backbone)</a>
of covalent bonds:

<b>-<font color="#3050ff">N</font>-<font color="#383838">C<span style="font-family:&quot;Times New Roman&quot;, Times, serif;">α</span></font>-<font color="#808080">C</font></b>

The model here includes -C-C-<b>N-C-C</b>-N-C-.
The central 
<font color="#383838">C<span style="font-family:&quot;Times New Roman&quot;, Times, serif;">α</span></font> has alanine's sidechain, -CH<sub>3</sub>.
Alanine's sidechain carbon is termed C<sub>β</sub>.

</li><br><li>
Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Nemethy G, Ramachandran GN, Scheraga HA.
A proposal of standard conventions and nomenclature for the description of
polypeptide conformation. J Biol Chem. 1966 Feb 25;241(4):1004-8.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=5905118" target="_blank">PMID:5905118</a>

</li><br><li>
Actually, the <i>van der Waals</i> checkbox shows the atoms at 88% of their true
<a href="https://en.wikipedia.org/wiki/Van_der_Waals_radius" target="_blank">van der Waals radii</a>.
In the above simulation, clashes are reported when 88% of the true radii overlap.
This is in accord with the observations of
Ramachandran and Sasisekharan<sup>6</sup>, who found that allowed interatomic distances
for non-bonded atoms are ~0.4 Å less than their van der Waals radii<sup>10</sup>.
The van der Waals radius of carbon is 1.7 Å. Thus, the van der Waals distance between
the centers of two non-bonded carbon atoms is 3.4 Å. However the minimum allowed distance
is about 0.4 Å less, which is 12% less. Thus 88% of the true van der Waals radii was
used in the above simulation for detection of "clashes".

</li><br><li>
Ramachandran, G. N., Ramakrishnan, C., Sasisekharan, V.
Stereochemistry of polypeptide chain configurations.
J Mol Biol. 1963 Jul;7:95-9.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=13990617" target="_blank">PMID:13990617</a>

</li><br><li>
Ramachandran, G. N., Sasisekharan V. Conformation of polypeptides and proteins.
Adv Protein Chem. 1968;23:283-438.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=4882249" target="_blank">PMID:4882249</a>

</li><br><li>
Ramakrishnan, C., Ramachandran, G. N.
Stereochemical criteria for polypeptide and protein chain conformations. II.
Allowed conformations for a pair of peptide units. Biophys J. 1965 Nov;5(6):909-33.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=5884016" target="_blank">PMID:5884016</a>

</li><br><li>
Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in
proteins. Prog Biophys Mol Biol. 2001;76(1-2):1-102.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=11389934" target="_blank">PMID:11389934</a>

</li><br><li>
The plot shown<sup>11</sup> is 
<a href="https://en.wikipedia.org/wiki/Ramachandran_plot#/media/File:Ramachandran_plot_general_100K.jpg" target="_blank">
available in the Wikimedia Commons</a>
courtesy of Jane and David Richardson.

</li><br><li>
Ramachandran and Sasisekharan<sup>6</sup> determined inter-atomic distances of
closest approach of non-bonded atoms from crystal structures. For each pair of elements
(their Table VI), they determined an allowed distance, and a partially allowed distance.
Distances less than the partially allowed values are “very unlikely” to occur due to
steric repulsion. The allowed distances are 0.3 to 0.5 Å less than the
<a href="https://en.wikipedia.org/wiki/Van_der_Waals_radius" target="_blank">van der Waals radii</a>.
(their page 327).
The partially allowed distances are usually 0.1 Å, sometimes 0.2 Å,
less than the allowed distances. 

</li><br><li>
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG,
Richardson JS, Richardson DC.
Structure validation by C-alpha geometry: phi, psi and C-beta deviation.
Proteins. 2003 Feb 15;50(3):437-50.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=12557186" target="_blank">PMID:12557186</a>

</li></ol>

<br>
<center>
<hr width="60%">

This page is by
<a href="https://martz.molviz.org" target="_blank">Eric Martz</a>.

<br>
License:
<a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank">
Attribution-NonCommercial-ShareAlike 4.0 International</a>.

<br>
Released May 27, 2018. Enhanced June 24 and July 16, 2018.

<br>
Many thanks to
<a href="https://www.stolaf.edu/people/hansonr/" target="_blank">Bob Hanson</a>
and the
<a href="https://jmol.sourceforge.net/history/" target="_blank">JSmol Team</a>,
and to
<a href="https://proteopedia.org/w/User:Jaime_Prilusky" target="_blank">Jaime Prilusky</a>
for adaptation to Proteopedia.Org.

<hr width="60%">
</center>

<br><br><br><br>
</div>
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Angel Herraez
User:Angel Herraez/Sandbox Rama: Difference between revisions

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