Ramachandran plot: Difference between revisions

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==More recent updates==
==More recent updates==
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined ([[myoglobin]], in 1960<ref>{{cite journal |pages=422–427 |year=1960 |last1=Kendrew |first1=J.C. |last2=Dickerson |first2=R.E. |last3=Strandberg |first3=B.E. |last4=Hart |first4=R.G. |last5=Davies |first5=D.R. |last6=Phillips |first6=D.C. |last7=Shore |first7=V.C. |title=Structure of myoglobin: a three-dimensional Fourier synthesis at 2Å resolution |journal=Nature |volume=185 |doi=10.1038/185422a0 |issue=4711 |pmid=18990802}}</ref>), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray [[crystallography]] and deposited in the [[Protein Data Bank|Protein Data Bank (PDB)]]. Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris et al. 1992;<ref name="ProCheck">{{cite journal |pages=345–64 |doi=10.1002/prot.340120407 |title=Stereochemical quality of protein structure coordinates |year=1992 |last1=Morris |first1=A.L. |last2=MacArthur |first2=M.W. |last3=Hutchinson |first3=E G. |last4=Thornton |first4=J.M. |journal=Proteins: Structure, Function, and Genetics |volume=12 |issue=4 |pmid=1579569}}</ref> [[Gerard_Kleywegt|Kleywegt]] & Jones 1996;<ref>{{cite journal |pmid=8994966 |year=1996 |last1=Kleywegt |first1=G.J. |last2=Jones |first2=T.A. |title=Phi/psi-chology: Ramachandran revisited |volume=4 |issue=12 |pages=1395–400 |journal=Structure |doi=10.1016/S0969-2126(96)00147-5}}</ref> Hooft et al. 1997;<ref>{{cite journal|last1=Hooft|first1=R.W.W.|last2=Sander|first2=C.|last3=Vriend|first3=G.|title=Objectively judging the quality of a protein structure from a Ramachandran plot|journal=Comput Appl Biosci|year=1997|volume=13|issue=4|pages=425–430|doi=10.1093/bioinformatics/13.4.425|url=http://bioinformatics.oxfordjournals.org/content/13/4/425.short}}</ref> Hovmöller et al. 2002;<ref>{{cite journal |pmid=11976487 |year=2002 |last1=Hovmöller |first1=S. |last2=Zhou |first2=T. |last3=Ohlson |first3=T. |title=Conformations of amino acids in proteins |volume=58 |issue=Pt 5 |pages=768–76 |journal=Acta Crystallographica D |url=http://scripts.iucr.org/cgi-bin/paper?S0907444902003359 |doi=10.1107/S0907444902003359}}</ref> Lovell et al. 2003<ref name="penultLib">{{cite journal |pages=437–50 |doi=10.1002/prot.10286 |title=Structure validation by Cα geometry: ϕ,ψ and Cβ deviation |year=2003 |last1=Lovell |first1=S.C. |last2=Davis |first2=I.W. |last3=Arendall |first3=W.B. |last4=De Bakker |first4=P.I.W. |last5=Word |first5=J.M. |last6=Prisant |first6=M.G. |last7=Richardson |first7=J.S. |last8=Richardson |first8=D.C. |journal=Proteins: Structure, Function, and Genetics |volume=50 |issue=3 |pmid=12557186}}</ref>). The three figures at left show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.<ref name="penultLib"/> The most common regions are labeled: α for [[Alpha helix|α helix]], Lα for lefthanded helix, β for [[beta sheet|β-sheet]], and ppII for polyproline II.
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined ([[myoglobin]], in 1960<ref>{{cite journal |pages=422–427 |year=1960 |last1=Kendrew |first1=J.C. |last2=Dickerson |first2=R.E. |last3=Strandberg |first3=B.E. |last4=Hart |first4=R.G. |last5=Davies |first5=D.R. |last6=Phillips |first6=D.C. |last7=Shore |first7=V.C. |title=Structure of myoglobin: a three-dimensional Fourier synthesis at 2Å resolution |journal=Nature |volume=185 |doi=10.1038/185422a0 |issue=4711 |pmid=18990802}}</ref>), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray [[crystallography]] and deposited in the [[Protein Data Bank|Protein Data Bank (PDB)]]. Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris et al. 1992;<ref name="ProCheck">{{cite journal |pages=345–64 |doi=10.1002/prot.340120407 |title=Stereochemical quality of protein structure coordinates |year=1992 |last1=Morris |first1=A.L. |last2=MacArthur |first2=M.W. |last3=Hutchinson |first3=E G. |last4=Thornton |first4=J.M. |journal=Proteins: Structure, Function, and Genetics |volume=12 |issue=4 |pmid=1579569}}</ref> [[Gerard_Kleywegt|Kleywegt]] & Jones 1996;<ref>{{cite journal |pmid=8994966 |year=1996 |last1=Kleywegt |first1=G.J. |last2=Jones |first2=T.A. |title=Phi/psi-chology: Ramachandran revisited |volume=4 |issue=12 |pages=1395–400 |journal=Structure |doi=10.1016/S0969-2126(96)00147-5}}</ref> Hooft et al. 1997;<ref>{{cite journal|last1=Hooft|first1=R.W.W.|last2=Sander|first2=C.|last3=Vriend|first3=G.|title=Objectively judging the quality of a protein structure from a Ramachandran plot|journal=Comput Appl Biosci|year=1997|volume=13|issue=4|pages=425–430|doi=10.1093/bioinformatics/13.4.425|url=http://bioinformatics.oxfordjournals.org/content/13/4/425.short}}</ref> Hovmöller et al. 2002;<ref>{{cite journal |pmid=11976487 |year=2002 |last1=Hovmöller |first1=S. |last2=Zhou |first2=T. |last3=Ohlson |first3=T. |title=Conformations of amino acids in proteins |volume=58 |issue=Pt 5 |pages=768–76 |journal=Acta Crystallographica D |url=http://scripts.iucr.org/cgi-bin/paper?S0907444902003359 |doi=10.1107/S0907444902003359}}</ref> Lovell et al. 2003;<ref name="penultLib">{{cite journal |pages=437–50 |doi=10.1002/prot.10286 |title=Structure validation by Cα geometry: ϕ,ψ and Cβ deviation |year=2003 |last1=Lovell |first1=S.C. |last2=Davis |first2=I.W. |last3=Arendall |first3=W.B. |last4=De Bakker |first4=P.I.W. |last5=Word |first5=J.M. |last6=Prisant |first6=M.G. |last7=Richardson |first7=J.S. |last8=Richardson |first8=D.C. |journal=Proteins: Structure, Function, and Genetics |volume=50 |issue=3 |pmid=12557186}}</ref> Ting et al. 2010<ref name="ndrd">{{cite journal |pages=e1000763 |doi:10.1371/journal.pcbi.1000763 |title=Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model |year=2010 |last1=Ting |first1=D. |last2=Wang |first2=G. |last3=Mitra |first3=R. |last4=Jordan |first4=M.I. |last5=Dunbrack |first5=R.L. |journal=PLOS Computational Biology |volume=6 |issue=4 |pmid= 20442867}}</ref>
).
The three figures at left show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.<ref name="penultLib"/> The most common regions are labeled: α for [[Alpha helix|α helix]], Lα for lefthanded helix, β for [[beta sheet|β-sheet]], and ppII for polyproline II.


==Related conventions==
==Related conventions==

Revision as of 20:59, 11 January 2013

Original hard-sphere, reduced-radius, and relaxed-tau φ,ψ regions from Ramachandran, with updated labels and axes
Backbone dihedral angles φ and ψ (and ω)

A Ramachandran plot (also known as a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan,[1] is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure at left illustrates the definition of the φ and ψ backbone dihedral angles[2] (called φ and φ' by Ramachandran). The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide planar.[3] The figure at top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Calpha-C) angle in dotted lines.[4] Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.

A Ramachandran plot generated from human PCNA, a trimeric DNA clamp protein that contains both β-sheet and α-helix (PDB ID 1AXC). The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions as defined by ProCheck

Uses

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein (as at top right). A second is to show the empirical distribution of datapoints observed in a single structure (as at right, here) in usage for structure validation, or else in a database of many structures (as in the lower 3 plots at left). Either case is usually shown against outlines for the theoretically favored regions.

Amino-acid preferences

One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot. In practice this does not appear to be the case; only the methylene group at Cβ has a large influence. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH3, CH2, or CH group that starts all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot at left) for which the allowable area is considerably larger. In contrast, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows only a very limited number of possible combinations of ψ and φ (see Pro plot at left).

More recent updates

The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960[5]), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris et al. 1992;[6] Kleywegt & Jones 1996;[7] Hooft et al. 1997;[8] Hovmöller et al. 2002;[9] Lovell et al. 2003;[10] Ting et al. 2010[11] ).

The three figures at left show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.[10] The most common regions are labeled: α for α helix, Lα for lefthanded helix, β for β-sheet, and ppII for polyproline II.

Related conventions

One can also plot the dihedral angles in polysaccharides (e.g. with CARP;[12]) and other polymers in this fashion. For the first two protein side-chain dihedral angles a similar plot is the Janin Plot.

Gallery

  • Ramachandran plot for the general case; data from Lovell 2003
    Ramachandran plot for the general case; data from Lovell 2003
  • Ramachandran plot for Glycine
    Ramachandran plot for Glycine
  • Ramachandran plot for Proline
    Ramachandran plot for Proline

Software

See also PDB for a list of similar software.

References

  1. ^ Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. (1963). "Stereochemistry of polypeptide chain configurations". Journal of Molecular Biology. 7: 95–9. doi:10.1016/S0022-2836(63)80023-6. PMID 13990617.
  2. ^ Richardson, J.S. (1981). "Anatomy and Taxonomy of Protein Structures". Advances in Protein Chemistry. 34: 167–339. doi:10.1016/S0065-3233(08)60520-3. PMID 7020376.
  3. ^ Pauling, L.; Corey, H.R.; Branson (1951). "The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain". Proceedings National Academy of Sciences USA. 37 (4): 205–211. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.
  4. ^ Ramachandran, G.N.; Sasiskharan, V. (1968). "Conformation of polypeptides and proteins". Advances in Protein Chemistry. 23: 283–437.
  5. ^ Kendrew, J.C.; Dickerson, R.E.; Strandberg, B.E.; Hart, R.G.; Davies, D.R.; Phillips, D.C.; Shore, V.C. (1960). "Structure of myoglobin: a three-dimensional Fourier synthesis at 2Å resolution". Nature. 185 (4711): 422–427. doi:10.1038/185422a0. PMID 18990802.
  6. ^ Morris, A.L.; MacArthur, M.W.; Hutchinson, E G.; Thornton, J.M. (1992). "Stereochemical quality of protein structure coordinates". Proteins: Structure, Function, and Genetics. 12 (4): 345–64. doi:10.1002/prot.340120407. PMID 1579569.
  7. ^ Kleywegt, G.J.; Jones, T.A. (1996). "Phi/psi-chology: Ramachandran revisited". Structure. 4 (12): 1395–400. doi:10.1016/S0969-2126(96)00147-5. PMID 8994966.
  8. ^ Hooft, R.W.W.; Sander, C.; Vriend, G. (1997). "Objectively judging the quality of a protein structure from a Ramachandran plot". Comput Appl Biosci. 13 (4): 425–430. doi:10.1093/bioinformatics/13.4.425.
  9. ^ Hovmöller, S.; Zhou, T.; Ohlson, T. (2002). "Conformations of amino acids in proteins". Acta Crystallographica D. 58 (Pt 5): 768–76. doi:10.1107/S0907444902003359. PMID 11976487.
  10. ^ a b Lovell, S.C.; Davis, I.W.; Arendall, W.B.; De Bakker, P.I.W.; Word, J.M.; Prisant, M.G.; Richardson, J.S.; Richardson, D.C. (2003). "Structure validation by Cα geometry: ϕ,ψ and Cβ deviation". Proteins: Structure, Function, and Genetics. 50 (3): 437–50. doi:10.1002/prot.10286. PMID 12557186.
  11. ^ Ting, D.; Wang, G.; Mitra, R.; Jordan, M.I.; Dunbrack, R.L. (2010). "Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model". PLOS Computational Biology. 6 (4): e1000763. PMID 20442867. {{cite journal}}: Text "doi:10.1371/journal.pcbi.1000763" ignored (help)
  12. ^ Lütteke, T.; Frank, M.; von der Lieth, C.W. (2005). "Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB". Nucleic Acids Res. 33 (Database issue): D242-246. doi:10.1093/nar/gki013. PMID 15608187. {{cite journal}}: line feed character in |title= at position 36 (help)

Further reading

External links

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