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User:Karl Oberholser/Ramachandran Plots

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Ramachandran Plots

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 detailed description.

Torsional (dihedral) angles

Tetrapeptide
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.


of two peptide bonds. with green halos the four atoms making up the ψ. Determine and display the numerical value of ψ by double clicking on the nitrogen of the peptide bond, single clicking on the next two marked 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 'Mark' and restart the clicking on the atoms.) atoms involved in φ with green halos. Measure and display the numerical value of φ using the technique described above. the direction of rotation and the values of ψ and φ.

Determine values of the other ψ and φ angles

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. that you obtain the correct values.

Plots of segments of α-helix

Segments cut from a globular protein or segment of collagen

Planes are drawn on some of the peptide bonds to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. The of this peptide has points clustered about the values of ψ= -47 and φ= -57 which are the average values for α-helices. 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 their Ramachandran plots.


Plots of segments of β-sheets

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. The of this twisted sheet has points clustered about the values of ψ= -135 and φ= +135 which are the average values for twisted sheets. of three other sheet segments more clearly defines the area in which values for twisted sheets are located.

Plot of collagen segment

More structural detail at Collagen and 3D tutorial. making up collagen has a helical structure, but it is less tightly wound than the α-helix. Therefore, its ψ and φ values plot at a different location on the than those of the α-helix.


Plot regions

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. () 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. 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 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.

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 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.



Plots of proteins

Protein structure or Its Ramachandran plot

Ramachandran Plot showing locations of the different regions. Use this plot as a reference when observing the plots below.

MYOGLOBIN

(Initial view): Secondary structure consist of α-helix, loops and ordered, nonrepetitive structures.
: 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.
after viewing plot

Concanavalin A

: Twisted β-sheet with small segments of α-helix.
: 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.
after viewing plot.

Acetylcholinesterase


: 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.
after viewing plot.

Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Karl Oberholser

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