Difference between revisions of "Ramachandran plot"

Revision as of 03:37, 23 August 2007

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.

Phi/Psi and Residue Type

Residues in Ramachandran plots are usually sorted into four separate types:

• General (not Proline, not Glycine, not before a Proline)
• 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)

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]

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 Ångströms 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 (φ) and psi (ψ) torsion angles of the second and third residues.

Tetrapeptide conformations and solvent effects

Note: The following section is for the tetrapeptide, HCO-L-Ala-L-Pro-Gly-Gly-OMe.

  φ1     φ1         φ2    φ2         φ3    φ3         φ4     φ4
N----Ca----C'----N----Ca----C'----N----Ca----C'----N----Ca----C'----O----CH3
     Ala1             Pro2             Gly3             Gly4

The Table 2 uses CNDO/2 molecular orbital total energies in kcal/mole, molecular dipole moments in Debyes, and expose molecular surface areas in Ų.

where,

1. Prefered in vacuo conformation of HCO-APGG-OMe with a type II β-turn between Ala₁ C=O and Gly₄ NH and a 14-membered H-bonded ring between Gly₄ C=O and Ala₁ NH.
2. A type I β-turn conformation stabilized by a 14-membered H-bond ring as in 1 above with the torsion angles given in Table 2.
3. A type II β-turn conformation with φ₁ = -100° and ψ₁ = -20° for Ala₁ residue where the 14-membered H-bond is absent. Gly₄ residue was fixed at an energetically favourable conformation with φ₄ = 50° and ψ₄ = ±180°.
4. A type II β-turn conformation with φ₁ = 50° and ψ₁ = 140° for Ala₁ residue where the 14-membered H-bond is absent. The Gly₄ residue was fixed at the same energetically favourable conformation as in 3 above.
5. A type I β-turn conformation with φ₁ = -100° and ψ₁ = -20° for Ala₁ residue where the 14-membered H-bond is absent. The Gly₄ residue was fixed at the same energetically favourable conformation as in 3 above.

"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°.^[7]"—Peter N. Robinson^[2]

Calculation of E_solute

E_solute represents the intrinsic intramolecular interactions and is calculated using partitioned potential energy functions.^[6] E_solute consists of four terms:

1. van der Waals interaction energy;
2. electrostatic interaction energy;
3. torsional energy across N—C^α, C^α—C', and C^α—C^β bonds. Proline side chains are assumed to remain in a fixed geometry; and
4. hydrogen-bonding energy.

Dihedral angles of biological molecules

The backbone dihedral angles of proteins are called φ (involving the backbone atoms C'-N-Cα-C'), ψ (involving the backbone atoms N-Cα-C'-N) and ω (involving the backbone atoms Cα-C'-N-Cα). Thus, φ controls the C'-C' distance, ψ controls the N-N distance and ω controls the Cα-Cα distance.

The planarity of the peptide bond usually restricts ω to be 180° (the typical trans case) or 0° (the rare cis case). The distance between the Cα atoms in the trans and cis isomers is approximately 3.8 and 2.8 Å, respectively. The cis isomer is mainly observed in X-Pro peptide bonds (where X is any amino acid).

The sidechain dihedral angles of proteins are denoted as χ1-χ5, depending on the distance up the sidechain. The χ1 dihedral angle is defined by atoms N-Cα-Cβ-Cγ, the χ2 dihedral angle is defined by atoms Cα-Cβ-Cγ-Cδ, and so on.

The sidechain dihedral angles tend to cluster near 180°, 60°, and -60°, which are called the trans, gauche+, and gauche- conformations. The choice of sidechain dihedral angles is affected by the neighbouring backbone and sidechain dihedrals; for example, the gauche+ conformation is rarely followed by the gauche+ conformation (and vice versa) because of the increased likelihood of atomic collisions.

Dihedral angles have also been defined by the IUPAC for other molecules, such as the nucleic acids (DNA and RNA) and for polysaccharides.

References

1. ↑ ^{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. ↑ ^{2.0 2.1 2.2} Ramachandran: A Java Program For Drawing Ramachandran Plots (accessed: 2006-11-04)
3. ↑ Kleywegt GJ, Jones TA (1996). Phi/psi-chology: Ramachandran revisited. Structure, 4(12):1395-400.
4. ↑ Ramachandran revisited (accessed: 2006-11-04)
5. ↑ ^{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.
6. ↑ ^{6.0 6.1} Renugopalakrishnan V, Khaled MA, Rapaka RS, Urry DW (1981). The tetrapeptide, HCO-L-Ala-L-Pro-Gly-Gly-OMe: conformations and solvent effects. Biomolecular Structure, Conformation, Function, and Evolution - Volume 2. Pergamon Press - Oxford.
7. ↑ 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)

External links

• Richardson Lab and Kinemage homepage
• Calculating Ramachandran (phi/psi) Angles — by Peter Cock
• Drawing Ramachandran (phi/psi) plots for Proteins with R — by Peter Cock
• AAindex — Amino acid indices and similarity matrices
• wikipedia:Ramachandran plot