Ramchand plot By KK Sahu Sir

Introduction

History

Experiment of Ramachandran

Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Peptide bond is rigid & planar

Torsion angle (Φ and Ψ)

Ramachandran plot
For helices
For β strands

Significance of Ramachandran plot

Conclusion

Reference

1. RAMACHANDRAN MAP
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
SYNOPSIS

3. HISTORY
Corey&Pauling(1953)determinedtheidealvaluefortheentire
backbonebondlengthandbondangles.
G.N.Ramachandranet.al.(1963)determinedthevaluesforthe
pairsofdihedralanglesabouttheCαatoms,whicharelimitedby
stericconstraints.
Ramachandranbiggestcontributionwashiscorrectproposalfor
thetriplehelicalstructureof“collagen”.
Ramachandranusedcomputermodelsofsmallpolypeptidesto
systematicallyvaryφandψwiththeobjectiveoffindingstable
conformations.

4. EXPERIMENT OF RAMACHANDRAN
Thepossibilitiesofproteinconformationwerebasedon
certainassumptions.
Peptidebondisrigidanddonotallowrotation.
Themoleculemayberotatedabouttheothersingle
bondinthebackbonethatistheN-CαbondandCα-C’
bond.
Allatomsarerepresentedashardsphere,therebeing
nochanceofinter-penetration.
Therearenootherattractiveorrepulsiveforces.
(Gupta, 2005)

5. Ramachandransolvedoneofthefirstproteinfiberstructure,
thetriple-coilofcollagen,
Thepeptidebondisplanarandtrans,thentheconformation
oftheproteinbackbonecanbedescribedbytheφandψdihedral
angles.
Heanalyzedallthestericclashesintheproteinbackboneas
afunctionφandψ.

6. Heshowedthattheallowedvaluesofφandψ(gray)brokein
tobroadlythreeregions,whichareknownasα,α
L,andβ.
Fig-1: -The Ramachandran map
(www.activorcorporation.net/ramachandran)

7. STRUCTURE OF PROTEINS
Primarystructure:-
Thelinearsequenceofaminoacidsformingthebackboneof
proteins(polypeptides).
Peptidebondisformedbytheaminoacidlinkedbycarboxylgroup
ofoneaminoacidwiththeα-aminogroupofanotheraminoacid.
Fig-2: -Primary structure of protein
(www.activorcorporation.net)

8. Secondary structure: -
The spatial arrangement of protein by twisting or folding of
the polypeptide chain.
Linus Pauling and Robert Coreypredict the existence of
these secondary structure in 1951.
The most common secondary structure are α-helix & β-
sheet.

9. 1.α-helix :-
Theα-helixisthemostcommonspiralstructureofprotein.
Aα-helixcanberighthanded(clockwise)orlefthanded(anticlockwise).
Theaminoacidresiduesinaα-helixhaveconformationwithφ=-60andψ=
–45to–50.
Fig-3: -Secondary structure (α-
helix)of protein
(www.nature.com/.../images/importance_f3.gif)

10. 2.β-Pleated sheet: -
In β-Conformation, the backbone of the polypeptide chain isextended
in to a zigzagstructure.
There two types of β-Pleated sheet i.e. parallel and antiparallel.
Fig-4: -Secondary structure (β-Pleated sheet)of protein
(www.nature.com/.../images/importance_f3.gif)

11. Tertiary structure: -
The three dimensional arrangement of protein is referred to
as tertiary structure.
This type of arrangement ensures stability of the molecule.
Fig-5: -The structure of Myoglobin
(Nelson & Cox, 2005)

12. Quaternary structure: -
Someoftheproteinsarecomposedoftwoormore
polypeptidechainsreferredassubunits&formthespatial
arrangement.
Fig-6: -The structure of Hemoglobin.
(http://trc.ucdavis.edu/biosci10v/bis10v/week2/2webimages/0143.gif)

13. PEPTIDE BOND IS RIGID AND PLANAR
Theinteractionofaminogroupofoneaminoacidwithcarboxylgroupofanother
aminoacidresultsintheformationofanamidelinkageknownaspeptidebond.
TheamideC-NbondinapeptideissomewhatshorterthantheC-Nbondina
simpleamineandthatatomsassociatedwiththebondarecoplanar.
Thisindicatedaresonanceorpartialsharingofpairsofelectronsbetweenthe
carbonyloxygenatomandtheamidenitrogen.
Theoxygenhaspartialnegativechargeandnitrogenapartialpositivecharge
settingupasmallelectricdipole.
Fig-7: -Peptide bond has double bond character due to resonance.
(Nelson & Cox, 2005)

14. PEPTIDE BOND IS RIGID AND PLANAR
Fig-8: -Trans and Cis forms of peptide bond.
(www.nature.com/.../images/importance.gif)
Twoconfigurationsarepossibleforaplanarpeptidebond.
Thispreferencefortransoverciscanbeexplainedbythefact
thatstericclashesbetweengroupattachedtotheCαatoms
hindersformationofcisform,butdonotoccurintrans
configuration.
RotationinapeptidechainispermittedaboutCα-NandCα-C
bonds.

15. The bond angles resulting from rotation at Cα are labeled φ (phi) for Cα-N
bond and ψ (psi) for Cα-C bond.
Both φ and ψ are defined as 180°, φ and ψ can have any value between -
180°and +180°,
But many values are prohibited by steric interferencebetween atoms in
the polypeptide backbone and amino acid side chains.
Allowed values for φ and ψ can be shown graphically by simple plotting φ
versus ψ, an arrangement known as Ramachandran plot.
PEPTIDE BOND IS RIGID AND PLANAR
Fig-9: -Peptide bond is rigid & planar
(Nelson & Cox, 2005)

16. TORSION ANGLE (Φ and Ψ)
Described the polypeptide backbone conformation
Atorsionangle(ordihedralangle)isananglearoundabondwhich
definestheshapeofaproteinbackbone.
Aproteins3-Dstructurecanbeuniquelydefinedbysequenceoftorsion
anglesalongitschain,calledφ(phi)andψ(psi).
TheangleofrotationoftheCα–Nbondiscalledφangleandthatofthe
Cα–Cbondiscalledψangle.
Thesearetheonlydegreesoffreedom,theconformationofthewhole
mainchainofthepolypeptideiscompletelydeterminedwhentheφandψ
anglesforeachaminoacidaredefined.

17. TORSION ANGLE (Φ and Ψ)
Described the polypeptide backbone conformation
ΦandΨcanhaveanyvaluebetween-180°
and+180°,butmanyvaluesofφandψare
prohibitedbystericinterferencebetweenatoms
inthepolypeptidebackboneandtheaminoacid
sidechains.
Theconformationinwhichφandψareboth
0°isprohibitedforthisreason(steric
interference).
Thisconformationisusedmerelyasa
referencepointfordescribingtheanglesof
rotation.
Fig-10: -The Torsional degrees of freedom in a peptide unit.
(Voet & Voet, 2005)

18. RAMACHANDRAN PLOT
ARamachandranplotdevelopedbyGopalasamudram Narayana
Ramachandran,isawaytovisualizedihedralangleφandψofaminoacid
residuesinproteinstructure.
G.N.Ramachandranusedcomputermodelsofsmallpolypeptidesto
systematicallyvaryφandψwiththeobjectiveoffindingstableconformations.
Atomsweretreatedashardsphereswithdimensionscorrespondingtotheir
Vanderwaalsradii.
Conformationsdeemedpossiblearethosethatinvolvelittleornosteric
interference,basedoncalculationsusingknownVanderwaalsradiiandbond
angles.

19. TheGlyresidue,whichislesssrtericallyhindered,exhibitsamuch
broaderrangeofallowedconformationsbecauseGlyhasanH-atom,
withasmallVanderwaalradiiinsteadofamethylgroupattheβ
position.
RAMACHANDRAN PLOT
Fully allowed
At limits of
allowability
Fig 11:-Ramachandran Plot for Polyglycine
(Voet & Voet, 2005)

20. RAMACHANDRAN PLOT
TheallowedrangesforbranchedaminoacidresiduessuchasVal,Ile,
andThraresomewhatsmallerthanforAla.
RamachandranplotforProlineshowsonlyaverylimitedno.ofpossible
combinationsofφandψbecausepresenceofafivememberedringwhich
preventtherotationabouttheCα-Nbond,whichfixesφatabout-35°to-85°.
Pro
Fig-12: -Ramachandran plot for
L-Ala residues.
(Nelson & Cox, 2005)

21. RAMACHANDRAN PLOT FOR HELICS
Bothrightandlefthandedhelicesliesintheregionsofallowed
conformationsintheRamachandrandiagram.
However,righthandedhelicesareenergeticallymorefavorable
becausethereislessstericclashbetweenthesidechainsandthe
backbone.
Essentiallyallαhelicesfoundinproteinsarerighthanded.
Fig-13: -Ramachandran Diagram for Helices.
(Stryer, 2006)

22. RAMACHANDRAN PLOT FOR β STRANDS
The β-sheet is almost fully extended rather than being tightly coiled
as in the α helices.
The red area shows the sterically allowed conformations of the
extended, β strand like structures.
Fig-14: -Ramachandran Diagram for
β-stands.
(Stryer, 2006)

23. SIGNIFICANCE OF RAMACHANDRAN PLOT
Ramachandranplotwasthefirstverificationtoolforproteinstructures.
Itdisplaysthedihedralanglesφ(phi)andψ(psi)ofallresidues.
Itisaverypowerfultooltoidentifyerrorsinproteinstructures.
Ithasbecomeastandardtoolindeterminingtheproteinstructureandin
definingsecondarystructuresintermsofα-helicesandβsheetcontents.
Itallowsthedisplayofdistributionofresiduesintheproteinintermsof
theirφandψangles.
Theregionintheplothelpsinidentifyingresiduesthatareinallowedand
disallowedregionsoftheRamachandranplot.

24. CONCLUSION
Theatomicdescriptionofbiologicalmoleculesincomputationalsimulations
havepromotedsignificantadvancesinthecomprehensionofthebiologicalprocess
aswellasproposednewinsightsinthedesignofmoleculestosatisfyspecific
properties.
Ramachandrandescribedproteinsthroughgraphonthebasisoftheirstructure,
size,shape,massandweight.
Differentproteinswhichmoderatebetweenthesecharactersarefoundscattered
inthegraph.
TheRamachandranplotwasconceivedasatheoreticalmeansofpredictingthe
allowedconformationalspaceofasingleaminoacidinapeptide.
TheRamachandranplothasprovenitselfasanunequalledtoolinunderstanding
theconformationalspaceavailableforproteinsandinanalysisofnewly
determinedproteinstructures.

25. REFERENCE
S.no. Name of the Book Author Year & Edition
1 Principles of BiochemistryNelson & Cox2005, 4
th
edition
2 Fundamentals of
Biochemistry
Dr. J.L. Jain2005, 6
th
edition
3 Biochemistry Voet & Voet2005, 4
th
edition
4 Biochemistry Lubert Stryer2006, 5
th
edition
5 Biochemistry U. Satyanarayana2007, 3
rd
revised
edition
6 Molecular biology & genetic
engineering
P. K. Gupta2005, 3
rd
reprint
edition
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