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
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
1TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN10MM TRIS-HCL0MM NACL7.41.0 atm310.0
22D HETERONUCLEAR FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF PHAGE PF110MM TRIS-HCL0MM NACL7.41.0 atm310.0
32D TROSY- BASED INTERLEAVED 1H-T2 1H- 15N CORRELATION EXPERIMENTS10MM TRIS-HCL0MM NACL7.41.0 atm310.0
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX600
NMR Refinement
MethodDetailsSoftware
CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING DYNAMICSNIH
NMR Ensemble Information
Conformer Selection CriteriaPRE AND VDW ENERGIES
Conformers Calculated Total Number100
Conformers Submitted Total Number50
Additional NMR Experimental Information
DetailsREFINEMENT 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
#ClassificationVersionSoftware NameAuthor
1refinementNIHSCHWIETERS, 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
2structure solutionXPLOR-NIH