| STRUCTURE DETERMINATION. THE METHOD USED TO DETERMINE AND
REFINE THE STRUCTURE IS THE HYBRID DISTANCE
GEOMETRY-SIMULATED ANNEALING METHOD (M. NILGES,
G.M. CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317, (1988))
USING THE PROGRAMS *DISGEO* (T.F. HAVEL, QCPE NO. 507,
INDIANA UNIVERSITY) AND *XPLOR* (A.T. BRUNGER, YALE
UNIVERSITY, NEW HAVEN, CT 06511).
STRUCTURAL STATISTICS -
RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)*
RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS)
ALL 1880 0.029
INTRASUBUNIT
SHORT RANGE 784 0.020
INTERRESIDUE
LONG RANGE 370 0.026
INTRARESIDUE 540 0.042
HBOND *(2)* 104 0.028
INTERSUBUNIT
INTERPROTON 70 0.014
HBOND 12 0.000
POTENTIAL ENERGY TERMS
TYPE ENERGY (KCAL/MOL)
F(NOE) *(3)* 48.
F(TOR) *(4)* 0.98
F(REPEL) *(5)* 37.
F(SYM) *(6)* 424.
LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
-474 KCAL/MOL. IT IS NOT INCLUDED INTO THE TARGET
FUNCTION FOR SIMULATED ANNEALING.
DEVIATIONS FROM IDEALIZED GEOMETRY *(7)*
TYPE TOTAL NUMBER RMS DEVIATION
BONDS 2392 0.011 (ANGSTROMS)
ANGLES 4362 2.458 (DEGREES)
IMPROPERS 882 0.485 (DEGREES)
NOTES.
*(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS
IS CALCULATED WITH RESPECT TO THE UPPER AND
LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF
THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN
0.3 ANGSTROMS.
*(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO
RESTRAINTS - R(NH-O) 1.7 TO 2.3 ANGSTROMS AND
R(N-O) 2.4 TO 3.3 ANGSTROMS.
*(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL
50 KCAL/MOL/ANGSTROM**2.
*(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE
CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A
SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO
RESTRICT THE RANGES OF TORSION ANGLES.
*(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM
F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF
4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE
VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD
VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY
FUNCTION.
*(6)* F(SYM) IS AN EFFECTIVE HARMONIC POTENTIAL USED TO
MAINTAIN SYMMETRY BETWEEN THE TWO SUBUNITS WITH
A FORCE CONSTANT SET TO 300.0 KCAL/MOL/ANGSTROMS**2
*(7)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY
AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE
PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION
OF PROLINES) IN THE TRANS CONFORMATION. IN THE
DYNAMICAL SIMULATED ANNEALING CALCULATIONS.
A TOTAL OF 30 STRUCTURES CONSISTENT WITH THE NMR DATA
WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES
OBTAINED BY AVERAGING THE COORDINATES OF THE 29 INDIVIDUAL
STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO
FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THE
30 STRUCTURES ARE GIVEN IN THE PROTEIN DATA BANK ENTRY
*2IL8*.
THE 3D STRUCTURE OF THE INTERLEUKIN-8 DIMER IN SOLUTION
DERIVED FROM NMR EXPERIMENTS IS BASED ON 1880 EXPERIMENTAL
DISTANCE RESTRAINTS (OF WHICH 82 ARE INTERSUBUNIT) AND 362
TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING
CONSTANT MEASUREMENTS. A COMPLETE LIST OF EXPERIMENTAL
RESTRAINTS HAS BEEN DEPOSITED WITH THE BROOKHAVEN PROTEIN
DATA BANK AND IS LOCATED IN ENTRY R1IL8MR.
THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE
AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL STRUCTURES
AND THE MEAN COORDINATE POSITIONS.
THE FIVE N-TERMINAL RESIDUES ARE ILL-DEFINED.
THE CYS 9 - CYS 50 DISULFIDE BRIDGE IS LEFT-HANDED. | DISGEO |