| simulated annealing |
THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302) AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR RESTRAINTS (NOE-DERIVED INTERPROTON DISTANCE, TORSION ANGLE, 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON-BONDED CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION ANGLE (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) AND BASE-BASE POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 (2001)) DATABASE POTENTIALS OF MEAN FORCE.
IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF
THE 125 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
ABOUT THE MEAN COORDINATE POSITIONS: RESIDUES 1-9 and
86-89 OF THE PROTEIN ARE DISORDERED IN THE COMPLEX.
ALTHOUGH THE SINGLE-STRANDED DNA IS B-LIKE, THE
COORDINATES OF THOSE PORTIONS OF THE SS-DNA NOT IN
CONTACT WITH THE PROTEIN COULD NOT BE ACCURATELY DETERMINED
(BASES 101-104 and 110). THEREFORE ONLY THE COORDINATES OF
RESIDUES 10-85 AND NUCLEOTIDES 105-109 ARE PRESENTED.
SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON
1986 EXPERIMENTAL NMR RESTRAINTS
DISTANCES 1289
TORSION ANGLES 266
13CA/CB SHIFTS 144
1DNH DIPOLARS IN PEG/HEXANOL 63
1DNC' DIPOLARS IN PEG/HEXANOL 44
2DHNC' DIPOLARS IN PEG/HEXANOL 40
1DNH DIPOLARS IN PHAGE PF1 56
1DNC' DIPOLARS IN PHAGE PF1 42
2DHNC' DIPOLARS IN PHAGE PF1 42
BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS
INTRARESIDUE 315
SEQUENTIAL 282
MEDIUM RANGE 197
LONG RANGE 300
BACKBONE H-BONDS 54 RESTRAINTS FOR 27 H-BONDS
INTRA-DNA DISTANCES 68
INTERMOLECULAR DISTANCES 73 |
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