Ramachandran plot
A Ramachandran plot (also known as a Ramachandran Map or a Ramachandran diagram) is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure. It shows the possible conformations of φ and ψ angles for a polypeptide.
Contents
Phi/Psi and Residue Type
Residues in Ramachandran plots are usually sorted into four separate types:
- Glycine (the small side chain makes the protein backbone very flexible)
- Proline (their large side chain restricts backbone movement)
- Pre-Proline (proline even messed up any residue before it)
- General (not Proline, not Glycine, not before a Proline)
Lovell, et al. Definition
"As the number of protein structures that have been solved has increased, our knowledge concerning the empirical distribution of phi/psi angles in proteins has improved. In 2003, Lovell and coworkers published updated definitions of the 'Preferred' and 'Allowed but Disfavoured' regions of the Ramachandran plot.[1] Nearly 100,000 residues from 500 structures with resolution better than or equal to 1.8 Angstroms were used to define the empirical distribution."—Peter N. Robinson[2]
Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).
- Source: Lovell, et al.[1]
Kleywegt and Jones Definition
"A classic definition of the core areas of the Ramachandran plot is described by Kleywegt and Jones.[3][4] This definition divides the phi/psi space into two regions: Core and noncore. The core regions are given by the 10° x 10° regions that together account for 98% of all non-glycine residues in a large sample of protein structures."—Peter N. Robinson[2]
This week's unusual Ramachandran plots
Every week, Kleywegt and Jones (after updating their local copy of the PDB) check the Ramachandran plots of all protein chains. All chains that have 20 or more residues, and of which at least 10% are outliers are listed in this file: http://xray.bmc.uu.se/gerard/rama/ramathisweek.txt (Note that this list may include NMR and theoretical models.)
Beta turns
Reverse turns are a common feature of protein structures that allow a significant change in the direction of the polypeptide chain. So-called beta turns are a well-studied subset of reverse turns.
The standard criteria for defining a beta turn are that a beta turn comprises four amino acid residues, whereby the distance between the first and the last alpha carbon is less than 7 Angstroms and the central two residues are not helical. Eight conventional turn types (I,I',II,II',VIa, VIb, VIII, and other) are defined according to the phi and psi angles of the second and third residues:
| Beta turn types | ||||
|---|---|---|---|---|
| Type | phi(i+1) | psi(i+1) | phi(i+2) | psi(i+2) |
| I | -60° | -30° | -90° | 0° |
| I' | 60° | 30° | 90° | 0° |
| II | -60° | 120° | 80° | 0° |
| II' | 60° | -120° | -80° | 0° |
| VIa | -60° | 120° | -90° | 0° |
| VIb | -120° | 120° | -60° | 0° |
| VIII | -60° | -30° | -120° | 120° |
"A tetrapeptide can be classified into one of the above types if all four angles fall within 30° of the 'ideal' angles given in the table.[5] Beta turns not fulfilling the requirements for one of the above turns are classified as 'other'. Many unclassifiable turns represent distortions of the the conventional turn types, lying just outside the standard limits. Therefore, the same authors showed that it is possible to increase the number of classifiable turns by allowing one of the four angles to deviate by as much as 45°.[6]"—Peter N. Robinson[2]
References
- ↑ 1.0 1.1 Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC (2003). Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins, 50(3):437-50.
- ↑ 2.0 2.1 2.2 Ramachandran: A Java Program For Drawing Ramachandran Plots (accessed: 2006-11-04)
- ↑ Kleywegt GJ, Jones TA (1996). Phi/psi-chology: Ramachandran revisited. Structure, 4(12):1395-400.
- ↑ Ramachandran revisited (accessed: 2006-11-04)
- ↑ 5.0 5.1 Wilmot CM, Thornton JM (1988). Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol, 203:221-32.
- ↑ Wilmot CM, Thornton JM (1990). Beta-turns and their distortions: a proposed new nomenclature. Protein Eng, 3:479-93.
See also
- MolProbity
- RAMPAGE
- Rotamer tables — rotamer parameters used in the rotamer program (in ccp4)
