| torsion angle dynamics | THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE ALIGNMENT MEDIA; A QUARTIC VAN DE WAALS REPULSION TERM, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE.
IN THIS ENTRY THE LAST COLUMN FOR
FOR THE ACTIVE SITE LOOP (RESIDUES 383-393)
REPRESENTS THE AVERAGE RMS
DIFFERENCE BETWEEN THE INDIVIDUAL 150 SIMULATED ANNEALING
STRUCTURES AND THE MEAN COORDINATE POSITIONS.
NOTE ONLY THE COORDINATES OF THE ACTIVE SITE LOOP
(RESIDUES 383-393) HAVE BEEN REFINED; THE REMAINDER
OF THE PROTEIN COORDINATES ARE HELD FIXED AT THEIR
POSITIONS IN UNPHOSPHORYLATED IIBMTL (PDB ACCESSION
CODE 1VKR). THE LAST COLUMN FOR RESIDUES OUTSIDE THE
ACTIVE SITE REPRESENTS THE AVERAGE RMS DIFFERENCE
BETWEEN THE INDIVIDUAL 100 SIMULATED ANNEALING STRUCTURES
AND THE MEAN COORDINATE POSITIONS FOR THE STRUCTURE OF
THE PREVIOUSLY DETERMINED UNPHOSPHORYLATED STATE (PDB
ACCESSION CODE 1VKR).
EXPERIMENTAL RESTRAINTS INVOLVING THE PHOSPHORYLATED
ACTIVE SITE RESIDUES 383-394:
83 NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS (8
INTRARESIDUE, 17 SEQUENTIAL, 20 MEDIUM RANGE AND 38
LONG-RANGE INTERRESIDUE)
21 TORSION ANGLES (10 PHI, 9 PSI AND TWO CHI1)
11 N-H, 11 N-C' and 11 HN-C' RDCS IN PHAGE PF1
11 N-H, 6 N-C' AND 6 HN-C' RDCS IN NEUTRAL ANISOTROPIC
GEL
10 N-H RDCS IN A POSITIVELY CHARGED ANISOTROPIC GEL
12 RESTRAINTS FOR 6 BACKBONE H-BONDS INVOLVING ONE
ACTIVE SITE RESIDUE
2 RESTRAINTS FOR A PHOSPHORYL-NH(SER391) H-BOND
DEMONSTRATED BY OBSERVATION OF A 3JNP COUPLING.
THE TOTAL NUMBER OF RDCS MEASURED FOR THE WHOLE PROTEIN
WAS: 192 IN PHAGE PF1, 139 IN NEUTRAL GEL, AND 55 IN
POSITIVE GEL. EXCLUDING A FEW OUTLIERS INVOLVING ONLY
RESIDUES 386-391 WITHIN THE ACTIVE SITE, THE REMAINING
RDCS FIT THE STRUCTURE OF THE UNPHOSPHORYLATED STATE
(COORDINATES 1VKR) EXTREMELY WELL INDICATING THAT THE
ONLY BACKBONE CONFORMATIONAL CHANGES THAT OCCUR UPON
PHOSPHORYLATION ARE LOCALIZED SPECIFICALLY TO THE
ACTIVE SITE (RESIDUES 383-393). THEREFORE ONLY THE
COORDINATES OF THE ACTIVE SITE WERE REFINED WITH THE
COORDINATES OF THE REMAINDER OF THE PROTEIN
FIXED TO THEIR POSITIONS IN 1VKR. | X-PLOR NIH |
