a kinematic view of loop closure evangelos a. coutsias, chaok seok, matthew p. jacobson, ken a. dill...
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A Kinematic View of Loop Closure
EVANGELOS A. COUTSIAS, CHAOK SEOK, MATTHEW P. JACOBSON, KEN A. DILL
Presented by Keren Lasker
The Loop Closure problemFinding the ensemble of possible backbone
structures of a chain segment of a protein that is geometrically consistent with preceding & following parts of the chain whose structures are given.
SER ILE HIS ASP ALA ALA THR SER LEU ASN
The Tripeptide Loop-Closure ProblemC
CC
NN
Ca
CaC
CC
NN
Ca
Ca
Problem definition :
Special case
six torsion angles at three Ca atoms located
consecutively along a peptide backbone.
The atoms are fixed in space
3 variables
3 constrains
3311 ,,, CCCN
Output :
The exact position of
the loop atoms
Derivation of a 16th Degree Polynomial for the 6-angle Loop Closure
iii rr cos1 ki
ji
kj
ijkiii uupuuP 1
2
0,
)(1 :),(
),,,,( 1 iiiiiip
r1
r2
0)( 3
16
0316
j
jjkuruR
sampling with perturbation
reso lved
unresolved
resolved
unresolved
5 degree perturbation of the
NCaC angles
10 degree perturbation of the
NCaC angles
Application to Loop Modeling Use PLOP to sample all the torsions
except for a three residue gap in the middle of the loop.
TODO
Check that the bond angles are really constant in proteins?
Which angles do we try to find in the coarser proble m?
Why the consec helps , what is the big problem in non consecutive ?
Condtion 3 in the special case?