| RIGID BODY MINIMIZATION AND CONSTRAINED/RESTRAINED SIMULATED ANNEALING | THE STRUCTURES WERE CALCULATED BY RIGID BODY MINIMIZATION (CLORE (2000) PROC.NATL.ACAD. SCI. 97, 9021-9025; BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016) FOLLOWED BY CONSTRAINED/RESTRAINED SIMULATED ANNEALING TO REFINE THE INTERFACIAL SIDECHAIN POSITIONS AND FINE TUNE THE RELATIVE ORIENTATION OF THE TWO PROTEINS (WANG ET AL. (2000) EMBO J. IN PRESS). THE TARGET FUNCTIONS COMPRISES TERMS FOR THE NOE RESTRAINTS, THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999), AND A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136). THE STARTING COORDINATES COME FROM THE X-RAY STRUCTURES (WITH PROTONS ADDED) OF E. COLI HPR (1POH, JIA ET AL. (1993) J.BIOL.CHEM. 268, 22940-22501; RESOLUTION 1.5 A) AND IIAGLC (MOLECULE 2 OF 2F3G, FEESE ET AL. BIOCHEMISTRY 36, 16087-16096; RESOLUTION 2.0 A) IN SEVERAL DIFFERENT ORIENTATIONS WITH THE CA-CA DISTANCE BETWEEN THE ACTIVE SITE HISTIDINES RANGING FROM 28 TO 95 A, INCLUDING ORIENTATIONS WHERE THE TWO ACTIVE SITE HISTIDINES ARE NOT OPPOSED AND WHERE HPR IS DIRECTED TOWARDS THE FACE OF IIAGLC OPPOSITE TO THE IIAGLC ACTIVE SITE. ONLY THE INTERFACIAL SIDECHAINS ARE ALLOWED TO ALTER THEIR CONFORMATION; THE BACKBONE AND NON-INTERFACIAL SIDECHAINS OF ONE MOLECULE (IIAGLC) ARE HELD COMPLETELY FIXED; THE SECOND MOLECULE (HPR) CAN ROTATE AND TRANSLATE BUT THE RELATIVE COORDINATES OF ITS BACKBONE AND NON-INTERFACIAL SIDECHAINS ARE HELD FIXED.
IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS
DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING
STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS
IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE
ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A
MEASURE OF THE PRECISION WITH WHICH THE RELATIVE
OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES
NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES
OF HPR AND IIAGLC.
THREE SETS OF COORDINATES ARE GIVEN:
MODEL 1: RESTRAINED MINIMIZED MEAN
COORDINATES OF THE UNPHOSPHORYLATED HPR-IIAGLC COMPLEX
SOLVED ON THE BASIS OF 82 INTERMOLECULAR DISTANCE
RESTRAINTS (74 NOE DERIVED INTERPROTON DISTANCE
AND 8 AMBIGUOUS INTERMOLECULAR SALT BRIDGE RESTRAINTS),
12 INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(RELATED SPECIFICALLY TO NOES INVOLVING RESIDUES
315 AND 317 OF HPR), 61 NMR DERIVED SIDECHAIN TORSION
ANGLE RESTRAINTS, AND 195 1DNH DIPOLAR COUPLINGS
(118 FOR IIAGLC AND 77 FOR HPR). CROSS-VALIDATION
WAS USED FOR THE DIPOLAR COUPLINGS (CLORE AND GARRETT
(1999) J. AM. CHEM. SOC. 121, 9008-9012).
MODEL 2: RESTRAINED MINIMIZED MEAN COORDINATES FOR THE
MODEL OF THE DISSOCIATIVE PHOSPHORYL TRANSITION STATE
HPR-IIAGLC COMPLEX. EXPERIMENTAL RESTRAINTS ARE
TO THOSE USED FOR MODEL 1, EXCEPT THAT ONE
INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINT
INVOLVING HIS15 WAS REMOVED TO PERMIT A TRANSITION STATE
TO FORM. IN ADDITION, COVALENT GEOMETRY RESTRAINTS
ARE INCLUDED RELATING TO THE TRIGONAL BIPYRAMIDAL
AT THE PHOSPHORUS. NO DISTANCE RESTRAINT IS INCLUDED
FOR THE N-P BOND LENGTHS. THE CA-CA DISTANCE BETWEEN
HIS315 (HPR) and HIS90 (IIAGLC) REMAINS UNCHANGED FROM
MODEL 1, BUT THE ND1-NE2 DISTANCE BETWEEN HIS315 AND
HIS90 IS REDUCED TO 6 A, WITH ESSENTIALLY IDEALIZED
GEOMETRY OF THE PHOSPHORYL TRANSITION STATE.
THE ND1-NE2 DISTANCE CORRESPONDS TO A DISSOCIATIVE
TRANSITION STATE. THE RMS DIFFERENCE BETWEEN THE MEAN
STRUCTURES OF THE UNPHOSPHORYLATED COMPLEX (MODEL 1)
AND THE TRANSITION STATE COMPLEX IS 0.03 A FOR THE
BACKBONE ATOMS AND 0.2 A FOR THE INTERFACIAL
SIDECHAINS (EXCLUDING HIS315 AND HIS90).
MODEL 3: RESTRAINED MINIMIZED MEAN COORDINATES FOR THE
MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE
HPR-IIAGLC COMPLEX. MODEL 3 IS DERIVED FROM MODEL 2
BY CONSTRAINED/RESTRAINED MINIMIZATION IN WHICH
THE COORDINATES OF ALL BACKBONE ATOMS, WITH THE
OF RESIDUES 313-317 OF HPR AND RESIDUES 89-91 OF IIAGLC,
AND ALL NON-INTERFACIAL SIDECHAINS ARE HELD COMPLETELY
FIXED, AND IN WHICH THE N-P DISTANCES ARE RESTRAINED
TO CA. 2 A, CORRESPONDING TO AN SN2 ASSOCIATIVE
TRANSITION STATE.
HPR-IIAGLC COMPLEX
DEVIATIONS FROM IDEALIZED GEOMETRY:
BONDS 0.014 A, ANGLES 1.74 A, IMPROPER TORSIONS 1.66 A
RMS DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.057 A
RMS DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS:
0.16 DEG.
DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999)
J. AM. CHEM. SOC. 121, 9008-9012):
16.9% FOR HPR and 15.2% FOR IIAGLC
(NOTE ONLY ONE ALIGNMENT TENSOR IS USED FOR BOTH HPR
AND IIAGLC; FOR REFERENCE THE DIPOLAR COUPLING R-FACTORS
FOR THE FREE X-RAY STRUCTURES OF HPR AND IIAGLC
(USING INDIVIDUAL ALIGNMENT TENSORS FOR THE TWO PROTEINS)
ARE 16.7% and 15.0%, RESPECTIVELY). | X-PLOR |
