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Ramachandran plot

January 10, 2023

In biochemistry, a Ramachandran plot (also known as a Rama plot, 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 energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the 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 in the 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-Cα-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.

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). All three angles are at 180° in the conformation shown
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, but the effect of side chains is small.[5] In practice, the major effect seen is that of the presence or absence of the methylene group at Cβ.[5] 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 the side chain of all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot in gallery) 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 a limited number of possible combinations of ψ and φ (see Pro plot in gallery). The residue preceding proline ("pre-proline") also has limited combinations compared to the general case.

More recent updates

The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960[6]), 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;[7] Kleywegt & Jones 1996;[8] Hooft et al. 1997;[9] Hovmöller et al. 2002;[10] Lovell et al. 2003;[11] Anderson et al. 2005.[12] Ting et al. 2010[13]).

The four figures below 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.[11] The most common regions are labeled: α for α helix, Lα for left-handed helix, β for β-sheet, and ppII for polyproline II. Such a clustering is alternatively described in the ABEGO system, where each letter stands for α (and 310) helix, right-handed β sheets (and extended structures), left-handed helixes, left-handed sheets, and finally unplottable cis peptide bonds sometimes seen with proline; it has been used in the classification of motifs[14] and more recently for designing proteins.[15]

While the Ramachandran plot has been a textbook resource for explaining the structural behavior of peptide bond, an exhaustive exploration of how a peptide behaves in every region of the Ramachandran plot was only recently published (Mannige 2017[16]).

The Molecular Biophysics Unit at Indian Institute of Science celebrated 50 years of Ramachandran Map[17] by organizing International Conference on Biomolecular Forms and Functions from 8–11 January 2013.[18]

Related conventions

One can also plot the dihedral angles in polysaccharides (e.g. with CARP).[19]

Gallery

  •  

    Ramachandran plot for the general case; data from Lovell 2003

  •  

    Ramachandran plot for Glycine

  •  

    Ramachandran plot for Proline

  •  

    Ramachandran plot for pre-Proline

Software

  • Web-based Structural Analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB
  • MolProbity web service that produces Ramachandran plots and other validation of any PDB-format file
  • SAVES (Structure Analysis and Verification) — uses WHATCHECK, PROCHECK, and does its own internal Ramachandran Plot
  • STING
  • Pymol with the DynoPlot extension
  • VMD, distributed with dynamic Ramachandran plot plugin
  • WHAT CHECK, the stand-alone validation routines from the WHAT IF software
  • UCSF Chimera, found under the Model Panel.
  • Sirius
  • Swiss PDB Viewer
  • TALOS
  • Zeus molecular viewer — found under "Tools" menu, high quality plots with regional contours
  • Procheck
  • Neighbor-Dependent and Neighbor-Independent Ramachandran Probability Distributions[13]
  • 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). "The Anatomy and Taxonomy of Protein Structure". Anatomy and Taxonomy of Protein Structures. Advances in Protein Chemistry. Vol. 34. pp. 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 9780120342341. PMID 7020376.
  3. ^ Pauling, L.; Corey, H.R.; Branson, H. R. (1951). "The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain". Proceedings of the National Academy of Sciences of the United States of America. 37 (4): 205–211. Bibcode:1951PNAS...37..205P. 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. Vol. 23. pp. 283–437. doi:10.1016/S0065-3233(08)60402-7. ISBN 9780120342235. PMID 4882249.
  5. ^ a b Chakrabarti, Pinak; Pal, Debnath (2001). "The interrelationships of side-chain and main-chain conformations in proteins". Progress in Biophysics and Molecular Biology. 76 (1–2): 1–102. doi:10.1016/S0079-6107(01)00005-0. PMID 11389934.
  6. ^ 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. Bibcode:1960Natur.185..422K. doi:10.1038/185422a0. PMID 18990802. S2CID 4167651.
  7. ^ 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. S2CID 940786.
  8. ^ 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.
  9. ^ 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. PMID 9283757.
  10. ^ 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.
  11. ^ 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. S2CID 8358424.
  12. ^ Anderson RJ, Weng Z, Campbell RK, Jiang X (2005). "Main-chain conformational tendencies of amino acids". Proteins. 60 (4): 679–89. doi:10.1002/prot.20530. PMID 16021632. S2CID 17410997.
  13. ^ a b 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. Bibcode:2010PLSCB...6E0763T. doi:10.1371/journal.pcbi.1000763. PMC 2861699. PMID 20442867.
  14. ^ Wintjens, René T.; Rooman, Marianne J.; Wodak, Shoshana J. (January 1996). "Automatic Classification and Analysis of αα-Turn Motifs in Proteins". Journal of Molecular Biology. 255 (1): 235–253. doi:10.1006/jmbi.1996.0020. PMID 8568871.
  15. ^ Lin, Yu-Ru; Koga, Nobuyasu; Tatsumi-Koga, Rie; Liu, Gaohua; Clouser, Amanda F.; Montelione, Gaetano T.; Baker, David (6 October 2015). "Control over overall shape and size in de novo designed proteins". Proceedings of the National Academy of Sciences. 112 (40): E5478–E5485. Bibcode:2015PNAS..112E5478L. doi:10.1073/pnas.1509508112. PMC 4603489. PMID 26396255.
  16. ^ Mannige, Ranjan (16 May 2017). "An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)". PeerJ. 5: e3327. doi:10.7717/peerj.3327. PMC 5436576. PMID 28533975. Retrieved 18 May 2017.
  17. ^ "50th Anniversary of Ramachandran Plots". Professor Laurence A. Moran. Retrieved 17 January 2013.
  18. ^ . MBU, IISc, Bangalore. Archived from the original on 15 January 2013. Retrieved 28 January 2013.
  19. ^ 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. PMC 539967. PMID 15608187.

Further reading

  • Richardson, J.S. (1981). "The Anatomy and Taxonomy of Protein Structure". Anatomy and Taxonomy of Protein Structures. Advances in Protein Chemistry. Vol. 34. pp. 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 9780120342341. PMID 7020376., available on-line at Anatax[permanent dead link]
  • Branden, C.-I.; Tooze, J. (1991), Introduction to Protein Structure, Garland Publishing, NY, ISBN 0-8153-0344-0

External links

 
Wikimedia Commons has media related to Ramachandran plot.
  • DynoPlot in PyMOL wiki
  • Link to Ramachandran Plot Map of alpha-helix and beta-sheet locations
  • Link to Ramachandran plot calculated from protein structures determined by X-ray crystallography compared to the original Ramachan.
  • Proteopedia Ramachandran Plot

January 10, 2023
ramachandran, plot, biochemistry, also, known, rama, plot, ramachandran, diagram, plot, originally, developed, 1963, ramachandran, ramakrishnan, sasisekharan, visualize, energetically, allowed, regions, backbone, dihedral, angles, against, amino, acid, residue. In biochemistry a Ramachandran plot also known as a Rama plot a Ramachandran diagram or a f ps plot originally developed in 1963 by G N Ramachandran C Ramakrishnan and V Sasisekharan 1 is a way to visualize energetically allowed regions for backbone dihedral angles ps against f of amino acid residues in protein structure The figure on the left illustrates the definition of the f and ps backbone dihedral angles 2 called f and f by Ramachandran The w angle at the peptide bond is normally 180 since the partial double bond character keeps the peptide planar 3 The figure in the top right shows the allowed f ps 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 Ca 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 Original hard sphere reduced radius and relaxed tau f ps regions from Ramachandran with updated labels and axes Backbone dihedral angles f and ps and w All three angles are at 180 in the conformation shown A Ramachandran plot generated from human PCNA a trimeric DNA clamp protein that contains both b sheet and a helix PDB ID 1AXC The red brown and yellow regions represent the favored allowed and generously allowed regions as defined by ProCheck Contents 1 Uses 2 Amino acid preferences 3 More recent updates 4 Related conventions 5 Gallery 6 Software 7 References 8 Further reading 9 External linksUses EditA Ramachandran plot can be used in two somewhat different ways One is to show in theory which values or conformations of the ps and f 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 EditOne might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot but the effect of side chains is small 5 In practice the major effect seen is that of the presence or absence of the methylene group at Cb 5 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 the side chain of all other amino acids Hence it is least restricted and this is apparent in the Ramachandran plot for glycine see Gly plot in gallery for which the allowable area is considerably larger In contrast the Ramachandran plot for proline with its 5 membered ring side chain connecting Ca to backbone N shows a limited number of possible combinations of ps and f see Pro plot in gallery The residue preceding proline pre proline also has limited combinations compared to the general case More recent updates EditThe first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined myoglobin in 1960 6 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 f ps plots e g Morris et al 1992 7 Kleywegt amp Jones 1996 8 Hooft et al 1997 9 Hovmoller et al 2002 10 Lovell et al 2003 11 Anderson et al 2005 12 Tinget al 2010 13 The four figures below 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 11 The most common regions are labeled a for a helix La for left handed helix b for b sheet and ppII for polyproline II Such a clustering is alternatively described in the ABEGO system where each letter stands for a and 310 helix right handed b sheets and extended structures left handed helixes left handed sheets and finally unplottable cis peptide bonds sometimes seen with proline it has been used in the classification of motifs 14 and more recently for designing proteins 15 While the Ramachandran plot has been a textbook resource for explaining the structural behavior of peptide bond an exhaustive exploration of how a peptide behaves in every region of the Ramachandran plot was only recently published Mannige 2017 16 The Molecular Biophysics Unit at Indian Institute of Science celebrated 50 years of Ramachandran Map 17 by organizing International Conference on Biomolecular Forms and Functions from 8 11 January 2013 18 Related conventions EditOne can also plot the dihedral angles in polysaccharides e g with CARP 19 Gallery Edit Ramachandran plot for the general case data from Lovell 2003 Ramachandran plot for Glycine Ramachandran plot for Proline Ramachandran plot for pre ProlineSoftware EditWeb based Structural Analysis tool for any uploaded PDB file producing Ramachandran plots computing dihedral angles and extracting sequence from PDB Web based tool showing Ramachandran plot of any PDB entry MolProbity web service that produces Ramachandran plots and other validation of any PDB format file SAVES Structure Analysis and Verification uses WHATCHECK PROCHECK and does its own internal Ramachandran Plot STING Pymol with the DynoPlot extension VMD distributed with dynamic Ramachandran plot plugin WHAT CHECK the stand alone validation routines from the WHAT IF software UCSF Chimera found under the Model Panel Sirius Swiss PDB Viewer TALOS Zeus molecular viewer found under Tools menu high quality plots with regional contours Procheck Neighbor Dependent and Neighbor Independent Ramachandran Probability Distributions 13 See also PDB for a list of similar software References Edit 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 Richardson J S 1981 The Anatomy and Taxonomy of Protein Structure Anatomy and Taxonomy of Protein Structures Advances in Protein Chemistry Vol 34 pp 167 339 doi 10 1016 S0065 3233 08 60520 3 ISBN 9780120342341 PMID 7020376 Pauling L Corey H R Branson H R 1951 The Structure of Proteins Two Hydrogen Bonded Helical Configurations of the Polypeptide Chain Proceedings of the National Academy of Sciences of the United States of America 37 4 205 211 Bibcode 1951PNAS 37 205P doi 10 1073 pnas 37 4 205 PMC 1063337 PMID 14816373 Ramachandran G N Sasiskharan V 1968 Conformation of polypeptides and proteins Advances in Protein Chemistry Vol 23 pp 283 437 doi 10 1016 S0065 3233 08 60402 7 ISBN 9780120342235 PMID 4882249 a b Chakrabarti Pinak Pal Debnath 2001 The interrelationships of side chain and main chain conformations in proteins Progress in Biophysics and Molecular Biology 76 1 2 1 102 doi 10 1016 S0079 6107 01 00005 0 PMID 11389934 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 2A resolution Nature 185 4711 422 427 Bibcode 1960Natur 185 422K doi 10 1038 185422a0 PMID 18990802 S2CID 4167651 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 S2CID 940786 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 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 PMID 9283757 Hovmoller 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 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 Ca geometry ϕ ps and Cb deviation Proteins Structure Function and Genetics 50 3 437 50 doi 10 1002 prot 10286 PMID 12557186 S2CID 8358424 Anderson RJ Weng Z Campbell RK Jiang X 2005 Main chain conformational tendencies of amino acids Proteins 60 4 679 89 doi 10 1002 prot 20530 PMID 16021632 S2CID 17410997 a b 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 Bibcode 2010PLSCB 6E0763T doi 10 1371 journal pcbi 1000763 PMC 2861699 PMID 20442867 Wintjens Rene T Rooman Marianne J Wodak Shoshana J January 1996 Automatic Classification and Analysis of aa Turn Motifs in Proteins Journal of Molecular Biology 255 1 235 253 doi 10 1006 jmbi 1996 0020 PMID 8568871 Lin Yu Ru Koga Nobuyasu Tatsumi Koga Rie Liu Gaohua Clouser Amanda F Montelione Gaetano T Baker David 6 October 2015 Control over overall shape and size in de novo designed proteins Proceedings of the National Academy of Sciences 112 40 E5478 E5485 Bibcode 2015PNAS 112E5478L doi 10 1073 pnas 1509508112 PMC 4603489 PMID 26396255 Mannige Ranjan 16 May 2017 An exhaustive survey of regular peptide conformations using a new metric for backbone handedness h PeerJ 5 e3327 doi 10 7717 peerj 3327 PMC 5436576 PMID 28533975 Retrieved 18 May 2017 50th Anniversary of Ramachandran Plots Professor Laurence A Moran Retrieved 17 January 2013 ICBFF 2013 MBU IISc Bangalore Archived from the original on 15 January 2013 Retrieved 28 January 2013 Lutteke 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 PMC 539967 PMID 15608187 Further reading EditRichardson J S 1981 The Anatomy and Taxonomy of Protein Structure Anatomy and Taxonomy of Protein Structures Advances in Protein Chemistry Vol 34 pp 167 339 doi 10 1016 S0065 3233 08 60520 3 ISBN 9780120342341 PMID 7020376 available on line at Anatax permanent dead link Branden C I Tooze J 1991 Introduction to Protein Structure Garland Publishing NY ISBN 0 8153 0344 0External links Edit Wikimedia Commons has media related to Ramachandran plot DynoPlot in PyMOL wiki Link to Ramachandran Plot Map of alpha helix and beta sheet locations Link to Ramachandran plot calculated from protein structures determined by X ray crystallography compared to the original Ramachan Proteopedia Ramachandran Plot Retrieved from https en wikipedia org w index php title Ramachandran plot amp oldid 1109592042, wikipedia, wiki, book, books, library,

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