| DISTANCE GEOMETRY/ SIMULATED ANNEALING | ALL STRUCTURE CALCULATIONS WERE PERFORMED USING X-PLOR VERSION 3.1. FIRST 60 MONOMER STRUCTURES WERE CALCULATED FROM INTRACHAIN DISTANCE RESTRAINTS, TOGETHER WITH THE DIHEDRAL ANGLE RESTRAINTS FOR PHI AND CHI1 AND THE HYDROGEN BOND RESTRAINTS, USING THE HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (NILGES, M.; CLORE, G.M.; GRONENBORN, A.M. (1988); FEBS LETT. 229, 317-324). THE 30 BEST MONOMER STRUCTURES WERE USED AS INPUT FOR THE GENERATION OF TRIMER STARTING STRUCTURES. EACH SELECTED HELIX MONOMER WAS FIRST ORIENTED SUCH THAT ITS GEOMETRIC CENTER COINCIDED WITH THE ORIGIN AND ITS LONG AXIS LAY ALONG THE X-AXIS AND SECOND TRANSLATED BY 10 ANGSTROMS ALONG THE Y-AXIS. COORDINATES FOR THE SECOND AND THIRD SUBUNIT WERE GENERATED BY A ROTATION AROUND THE X-AXIS BY 120 OR 240 DEGREES, RESPECTIVELY. THE 30 GENERATED TRIMER STARTING STRUCTURES WERE USED AS INPUT FOR A SECOND RUN OF SIMULATED ANNEALING INCLUDING THE INTERCHAIN DISTANCE RESTRAINTS. IN THE RESULTING STRUCTURES THE INTERCHAIN DISULFIDE BONDS WERE INTRODUCED AND A FINAL RUN OF SIMULATED ANNEALING AND REFINEMENT PERFORMED. THE LAST STEPS OF REFINEMENT INCLUDED ADDITIONALLY NON-CRYSTALLOGRAPHIC SYMMETRY (NCS) CONSTRAINTS AND R^(-6)-SUM AVERAGED DISTANCE RESTRAINTS FOR AMBIGUOUS NOES (NILGES, M. (1993); PROTEINS 17, 297-309). | X-PLOR |
