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REFINEMENT OF THE MINOR FORM OF APO MBP WAS CARRIED OUT BY CONJOINED RIGID BODY AND TORSION ANGLE SIMULATED ANNEALING SUBJECT TO A TARGET FUNCTION COMPRISING A PRE PEUDOPOTENTIAL, A QUARTIC VAN DER WAALS REPULSION TERM TO PREVENT ATOMIC OVERLAP, A MULTIDIMENSIONAL TORSION ANGLE DATABASE OF MEAN FORCE, AND APPROPRIATE TORSION ANGLE AND HYDROGEN BONDING DISTANCE RESTRAINTS WITHIN THE LINKER. THE CALCULATED GAMMA2 RATES ARE GIVEN BY A POPULATION WEIGHTED AVERAGE OF THE GAMMA2 RATES OF THE MAJOR (OPEN, 1OMP) AND MINOR STATES OF MBP. THE MINOR FORM OF APO MBP ( 5 PERCENT OCCUPANCY, CHAIN C) IS REPRESENTED BY A SECOND CONFORMER ALLOWING RIGID-BODY INTERDOMAIN MOVEMENT BY GIVING THE LINKER REGIONS (RESIDUES 106-114, 252-265 AND 314-333) FULL TORSIONAL DEGREES OF FREEDOM (WITH THE EXCEPTION OF THE HELIX, RESIDUES 315-326, WHOSE BACKBONE IS ALSO TREATED AS A RIGID BODY). THE STRUCTURE OF THE MAJOR (95 PERCENT OCCUPANCY, CHAIN O) IS FIXED DURING THE CALCULATION TO THAT OF THE CRYSTAL STRUCTURE OF APO MBP ( 1OMP). THE PARAMAGNETIC PROBES (MALEIMIDE-TEMPO, MXT) AT POSITIONS 41 (D41C) AND 211 (S211C) ARE REPRESENTED BY A SIX-CONFORMER ENSEMBLE FOR BOTH THE MAJOR OPEN AND MINOR CLOSED STATES (ALTLOC A-F, A-C AND D-F ARE FOR THE TWO DIFFERENT ENANTIOMERS OF CONJUGATED MALEIMIDE-TEMPO). ONLY THE BACKBONE COORDINATES AND THE COORDINATES OF THE PARAMAGNETIC PROBE (RESIDUES 500 AND 600) ARE DEPOSITED.
Computation: NMR Software
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Classification
Version
Software Name
Author
1
refinement
NIH
SCHWIETERS, KUSZEWSKI, CLORE OTHER REFINEMENT REMARKS. REFINEMENT OF THE MINOR FORM OF APO MBP WAS CARRIED OUT BY CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING SUBJECT TO A TARGET FUNCTION COMPRISING A PRE PEUDOPOTENTIAL, A QUARTIC VAN DER WAALS REPULSION TERM TO PREVENT ATOMIC OVERLAP, A MULTIDIMENSIONAL TORS