THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION
Determination of the Secondary Structure of Interleukin-8 by Nuclear Magnetic Resonance Spectroscopy
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.
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