| 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 - THESE ARE CALCULATED FROM ALL THE
30 MODELS GIVEN IN THIS ENTRY.
NUMBERS ENCLOSED IN PARENTHESIS
REPRESENT THE MINIMIZED MEAN
STRUCTURE OBTAINED BY RESTRAINED
MINIMIZATION OF THE AVERAGE RMS.
RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)*
RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS)
ALL 1880 0.031(0.029)
INTRASUBUNIT
SHORT RANGE 784 0.019(0.020)
INTERRESIDUE
LONG RANGE 370 0.027(0.026)
INTRARESIDUE 540 0.044(0.042)
HBOND *(2)* 104 0.031(0.028)
INTERSUBUNIT
INTERPROTON 70 0.022(0.014)
HBOND 12 0.004(0.000)
TORSION ANGLES (DEGREES) 362 0.203 (0.211)
POTENTIAL ENERGY TERMS
TYPE ENERGY (KCAL/MOL)
F(NOE) *(3)* 53(48)
F(TOR) *(4)* 0.94(0.98)
F(REPEL) *(5)* 38(37)
F(SYM) *(6)* 0.15(424)
LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
-542(-474) KCAL/MOL.
DEVIATIONS FROM IDEALIZED GEOMETRY *(6)*
TYPE TOTAL NUMBER RMS DEVIATION
BONDS 2392 0.006(0.011) (ANGSTROMS)
ANGLES 4362 2.016(2.458) (DEGREES)
IMPROPERS 882 0.504(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.
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.
A TOTAL OF 30 STRUCTURES CONSISTENT WITH THE NMR DATA
WERE CALCULATED AND ARE GIVEN IN THIS ENTRY. THE PROTEIN
DATA BANK ENTRY *1IL8* CONTAIN THE COORDINATES OBTAINED BY
AVERAGING THE COORDINATES OF THESE INDIVIDUAL STRUCTURES
AND SUBJECTING THE RESULTING COORDINATES TO FURTHER
RESTRAINED MINIMIZATION.
THE FIVE N-TERMINAL RESIDUES ARE ILL-DEFINED.
THE CYS 9 - CYS 50 DISULFIDE BRIDGE IS LEFT-HANDED. | DISGEO |
