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| + | #REDIRECT [[Ramachandran_plots]] |
| - | ==Ramachandran Plots==
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| - | A Ramachandran plot has the values of psi (ψ) torsional angles on the y-axis and the values of phi (φ)torsional angles on the x-axis. More [http://en.wikipedia.org/wiki/Ramachandran_plot detailed description].
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| - | ==Torsional (dihedral) angles==
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| - | <applet load='tetr_ala.mol' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/First_view/1' caption='Tetrapeptide' />[http://en.wikipedia.org/wiki/Torsional_angle Extensive description] of torsional angles. Each peptide bond has two torsional angles - psi (ψ) and phi (φ) - which determine the geometry about the peptide bond. A tetrapeptide is used to describe and illustrate these two angles.
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.
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| - | == Determine values of other ψ and φ angles ==
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes2/4'>Draw the planes</scene> of two other peptide bonds, and then using the technique described above identify the atoms contained in and the numerical values of the ψ and φ angles of the α-carbon connected to these two planes. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama2/2'>Confirm</scene> that you obtain the correct values.
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| - | == Plots of segments of [http://en.wikipedia.org/wiki/Alpha_helix α-helix] ==
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| - | <applet load='Ahelix_2.pdb' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/Opening_helix/5' caption='Segments cut from a globular protein or segment of collagen' />
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| - | Planes are drawn on some of the peptide bonds (displayed in second Jmol applet) to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. <scene name='User:Karl_Oberholser/Ramachandran_Plots/Opening_helix/5'>(Return to initial view)</scene> If you have not viewed an &alpha:-helix end on, rotate the structure 90<sup>0</sup> so that you can view the open center of the helix. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot1/3'>Ramachandran plot</scene> of this peptide has points clustered about the values of ψ= -47 and φ= -57 which are the average values for α-helices. <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot2/3'>Adding the values</scene> of two other helical segments demonstrates that data from all three appear in one large cluster and that the helical segments can not be distinguished by the differences in their ψ and φ values.
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| - | == Plots of segments of [http://en.wikipedia.org/wiki/Beta_sheet β-sheets] ==
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Opening_sheet/7'>Planes</scene> are drawn on the two peptides making up a simple twisted β_sheet. Most β-sheets in globular proteins are twisted sheets which do not have the even parallel pleads as seen in the examples at the above wiki site. <scene name='User:Karl_Oberholser/Ramachandran_Plots/Opening_sheet2/1'>Closer view</scene> of &beta:-sheets. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot3/1'>Ramachandran plot</scene> of this twisted sheet has points clustered about the values of ψ= -135 and φ= +135 which are the average values for twisted sheets. <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot4/1'>Adding the values</scene> of three other sheet segments more clearly defines the area in which values for twisted sheets are located.
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| - | == Plot of collagen segment ==
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| - | More structural detail at [[Collagen]] and [http://www.messiah.edu/molscilab/Jmol/collagen/collagen_index.htm 3D tutorial]. <scene name='User:Karl_Oberholser/Ramachandran_Plots/Collagen_opening/1'>Peptide</scene> making up collagen has a helical structure, but <scene name='User:Karl_Oberholser/Ramachandran_Plots/Collagen_second_view/2'>the helix</scene> is less tightly wound than the α-helix. Therefore, its ψ and φ values plot at a different location on the <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_collagen/3'>Ramachandran plot</scene> than those of the α-helix.
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| - | == Plot regions ==
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| - | <applet load='Ahelix_2.pdb' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/Tripep_disallowed/3' caption='Sterically forbidden and allowed φ & ψ combinations' />Most combinations of φ and ψ are sterically forbidden, as illustrated in the tripeptide, Glu-Ser-Ala, to the right. (<scene name='User:Karl_Oberholser/Ramachandran_Plots/Tripep_disallowed/3'>initial view</scene>) With φ = 55 and ψ = -116 the Ser side chain, colored cpk, is in contact with the Ala, colored blue. For this reason, in plots of native peptides the points of data will cluster in several areas. The core regions contain the most favorable combinations of φ and ψ and have the highest number of data points, around the core region is the allowed region with fewer data points and beyond the allowed region is the generous region. The remaining area is the disallowed region. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?template=main.html&o=PROCHECK&c=999&pdbcode=1eve An example] of a plot divided into regions. The red areas of the plot found at this link are the core regions. Observe that the data point (55, -116) for Ser of the above tripeptide would fall in the disallowed region (lightest yellow region). If the Ser has φ & ψ values of -57 and -47, the <scene name='User:Karl_Oberholser/Ramachandran_Plots/Tripep_allowed/3'>Ser side chain</scene> is rotated away from the Ala and is not in contact with the Ala. The data point for the Ser in this peptide is a core region. Most, if not all, of the points in the above plots for α-helix, β-sheet and collagen fall in one of the core areas.<p>
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| - | Since Gly has only a hydrogen as a side chain, steric hindrance is not as likely to occur as φ and ψ are rotated through a series of values. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/Tripep_gly/2'>tripeptide Glu-Gly-Ala</scene> with Gly having φ and ψ values of +55 and -116, respectively, does not show the steric hindrance that the corresponding Glu-Ser-Ala (initial view) did. For that reason Gly will frequently plot on the disallowed region of a Ramachandran plot.</p>
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| - | == Plots of proteins ==
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| - | <applet load='1mbo' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/Myoglobin/2' caption='Protein structure or Its Ramachandran plot' />
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| - | [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?template=main.html&o=PROCHECK&c=999&pdbcode=1eve Ramachandran Plot showing locations of the different regions.] Use this plot as a reference when observing the plots below.<br>
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| - | '''MYOGLOBIN'''<p>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Myoglobin/2'>View of structure</scene> (Initial view): Secondary structure consist of α-helix, loops and ordered, nonrepetitive structures.<br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin/1'>Ramachandran plot</scene>: Red data points outside of the area expected for α-helix most likely involve residues at the end of the α-helix because often these have angle values that are not typical for α-helix. White points are those for loops and ordered, nonrepetitive structures. The few residues that map to the disallowed region are Gly.<br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin_model/1'>Return to model</scene> after viewing plot </p>
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| - | '''Concanavalin A'''<p>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Concanavalin_a/3'>View of structure</scene>: Twisted β-sheet with small segments of α-helix.<br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a/1'>Ramachandran plot</scene>: Most of the yellow points are located in the area for twisted β-sheets where one would expect them, and again the points in the disallowed region are Gly. <br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a_model/1'>Return to model</scene> after viewing plot. </p>
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| - | '''Acetylcholinesterase''' <p>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Acetylcholinesterase/2'>View structure</scene> <br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_acetylcholinesterase/1'>Ramachandran Plot</scene>: Close to equal amounts of α-helix, β-sheet, and ordered, nonrepetitive structures. One important exception to Gly in the disallowed region is Ser:200. Locate this residue that is located in the disallowed region. An interesting aspect concerning Ser:200 is that it is one of a triad of residues that are part of the catalytic site and are involved in the catalytic action of this enzyme. The unique φ and ψ values for Ser:200 is the major factor in positioning the side chain so that it can participate in the catalysis.<br>
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| - | <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_ache_model/1'>Return to model</scene> after viewing plot.
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