Ramachandran plot-2.doc

8/9/2019 Ramachandran plot-2.doc

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Ramachandrans Plot

In a polypeptide, the main chain N-C alphaand C alpha-Cbonds relatively

are free to rotate. These rotationsare represented by the torsion angles, phi

and psi, respectively.G.N.Ramachandran used computer models of small polypeptides to

systematically varyphi() and psi() with the objective of finding stable

conformations. For each conformation, the structure was eamined for

close contacts between atoms. !toms were treated as hard spheres with

dimensions correspondin" to their van der Waalsradii. Therefore, phi ()

and psi () an"les, which cause spheres to collide, correspond to sterically

disallowed conformations of the polypeptide bac#bone.


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Prediction of terically Permissible tructure !rom the "se of

Ramachandran Plot#

Rotations about the $%N bond are labeled with the phi (), and rotations

about the $%carbonyl carbon are labeled psi (

). The peptide bond itselftends to be planer, with two allowed states& a. the trans, of the peptide

bond 'oinin" the C$%and N& groupsis nearly always '()

and b.cis,

0

(rarely). *he principle that two atoms cannot occupy the same

space+ limits the values of conformational angles.The allowed ranges of

and + for $'(), fall into defined regions in a "raph called

,Ramachandran plot.

ll possible conformations of a polypeptide chain+ therefore can be

described in terms of their + conformational angles+ a description

that automatically ta/es account of the fi0ed geometric features of the

polypeptide bac/bone. Thus any polypeptide conformation can be

represented as a point on a plot of versus , where and have values

that ran"e from %*to +*. y convention, the formation correspondin"

to - *, - * is one in which both peptide planes that are connected to acommon $ atom lie in the same plane. Positive-variations in

correspond to cloc/wise rotations of the preceeding peptide about the

C

-N bond when viewed from C

toward N'. Positive variations in

correspond to cloc/wise rotations of the succeeding peptide about the C

-C1bond when viewed from C

toward C1.


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!& !n"le !toms

is defined as positive for cloc#wise rotation of $%, when loo#in" alon" the $%N/

bond. In this conformation, * .

!& !n"le !toms

is defined as positive for cloc#wise rotation of N/+

, when loo#in" alon" the $

%$

bond. Glysine residue re"ion

Ramachandran plot, showin" which atomic collisions (usin" a hard%sphere

approimation) produce the restrictions of the main%chain an"les and . The

cross%hatchedre"ions are allowed for all residues, and each boundary of a prohibited

re"ion is labeled with the atoms that collide in that conformation. !dditional shaded

re"ions are for "lycine residues only. 0ach boundary of a prohibited re"ion islabeled with the atoms that collide in that conformation.

& !n"le 1ositive

Rotation

& !n"le 1ositive

Rotation


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0periments with models that approimate the polypeptide atoms are hard

spheres, with appropriate van der 2aals radii, 3uic#ly reveal that many

+

angular combinations are impossible because of steric interactions or

collisions between atoms along the bac/bone or between bac/bone

atoms and the side-chain R groups.For eample, it is clear that at any

circumstance the - *, - * conformation is near to impossible. The

reason is that this conformation results in non-covalently bonded inter-

atomic contacts that are considerably less than the sum of the van der

Waals radii of the atoms involved. In fact, of all the possible ,

combinations, only a relatively restricted number of conformations are

sterically allowed.

*he Ramachandran plot shows e0plicitly how the accessible regions of

+ space are limited by steric interactions among the polypeptide

bac/bone and side-chain groups+ assuming that the atomic groups

behave as rigid spheres having appropriate van der Waals radii. Inreality, the atoms in molecules do not behave as ri"id spheres, so real

proteins span a sli"htly "reater ran"e of values than su""ested by this plot. R

What do you mean by teric interactions2

!toms ta#e up space and cannot occupy the same space at the sametime. $ovalent bonds connect them and these bonds cannot be bro#en.

4o the movements that are more concerned involve rotations only.

!nd it has been seen previously that there are only two an"les that

rotate in a "iven residue, , .


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30planation#Red areain the fi"ure delimits ener"etically preferred regionsof and ,

while, the yellow area in the fi"ure delimit sterically-disallowed regions.

The conformations of most amino acids fall into either right-handed

alpha-heli0 or -sheet regions. 4lycine has access to additional

conformations. In particular it can form left-handed heli0# 5. 5ost

residues fall in or near the allowed regions, althou"h a few are forced by the

foldin" into ener"etically less-favourablestates. *he goal is to identify the

intramolecular interactions that ma/e certain combinations of torsion

angles unfavorable. 4uch interactions arise whenever two atoms orfunctional "roups penetrate each other6s van der 2aals radii.

The allowed re"ions "enerate standard conformations. ! stretch of

consecutive residues in the conformation (typically 7%8* in native states of

"lobular proteins) "enerates an %heli. Repeatin" the conformation

"enerates an etended %strand. Two or more %strands can interact laterally

to form %sheets. /elices and sheets are 9standard: or 9prefabricated:

structural pieces that form components of the conformations of most

proteins. They are stabili;ed by relatively wea# interactions, hydro"en

bonds, between mainchain atoms.

Conclusion& win" to the basic "eometric properties of the polypeptide

chain, the sterically allowed conformations are "reatly restricted by the

occurrence of unfavourable steric interactions between various atomic

"roups. !s a result, fibrous proteins with re"ularly repeatin" structures can

be defined by sin"le values for the coordinates and . 1roteins that have

The plot is similar to a topo"raphical map,

where ener"y, instead of altitude, is shownwith the contours. 4urroundin" phi-*,

psi-* there is a hi"h ener"y


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less re"ularly repeatin" structures would re3uire more than a sin"le set

coordinates but nevertheless they would be epected to obey the same set of

limits established by the Ramachandran plot.

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Ramachandran plot-2.doc