2V93

EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN	10MM TRIS-HCL		0MM NACL	7.4	1.0 atm	310.0
2	2D HETERONUCLEAR FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF PHAGE PF1	10MM TRIS-HCL		0MM NACL	7.4	1.0 atm	310.0
3	2D TROSY- BASED INTERLEAVED 1H-T2 1H- 15N CORRELATION EXPERIMENTS	10MM TRIS-HCL		0MM NACL	7.4	1.0 atm	310.0

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600

NMR Refinement
Method	Details	Software
CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING DYNAMICS		NIH

NMR Ensemble Information
Conformer Selection Criteria	PRE AND VDW ENERGIES
Conformers Calculated Total Number	100
Conformers Submitted Total Number	50

Additional NMR Experimental Information
Details	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.

Additional NMR Experimental Information

Details

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
#	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
2	structure solution	Xplor-NIH

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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2V93

EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR