| simulated annealing |
WE CALCULATED THE STRUCTURE OF MAP30 USING SIMULATED ANNEALING IN TORSION ANGLE SPACE STARTING FROM AN EXTENDED STRAND, FOLLOWED BY SIMULATED ANEALING IN CARTESIAN SPACE USING A MODIFIED XPLOR 3.5, CONTAINING PSEUDOPOTENTIALS FOR RESIDUAL DIPOLAR COUPLING AND A CONFORMATIONAL DATABASE. HYDROGEN BOND CONSTRAINTS, TWO FOR EACH HYDROGEN BOND (NH-O = 1.5-2.8 A AND N-O = 2.4-3.5 A), WERE DERIVED FROM NH EXCHANGE EXPERIMENTS, BACKBONE NOE PATTERNS, BACKBONE CA/CB CHEMICAL SHIFTS AND DIRECT MEASUREMENTS OF 3HJNC CONNECTIVITY ACROSS HYDROGEN BONDS, AND APPLIED IN THE LATER STAGE OF THE STRUCTURE CALCULATION. PHI AND PSI ANGLES WERE DERIVED FROM THREE-BOND 3JHNHA COUPLING CONSTANTS,
MEASURED WITH THE 3D HNHA EXPERIMENT AND A DATABASE ANALYSIS OF BACKBONE (1H, 15N, 13CA, 13CB AND C) CHEMICAL SHIFTS, USING THE PROGRAM TALOS. THE PHI DIHEDRAL ANGLE WAS RESTRAINED TO -60 DEGREES PLUS-MINUS 30 DEGREES IF JHNHA < 5.5 HZ OR TO 110 DEGREES PLUS-MINUS 50 DEGREES IF
JHNHA >8.0 HZ. CHI 1 DIHEDRAL ANGLES AND STEREOSPECIFIC ASSIGNMENTS OF BETA-
METHYLENE PROTONS WERE DERIVED FROM JHNHB AND JHAHB SCALAR COUPLING CONSTANTS
OBTAINED FROM 3D HNHB AND HACAHB-COSY EXPERIMENTS. TIGHT TURNS CLEARLY
IDENTIFIED BY NOE PATTERNS AND J-COUPLING CONSTANTS, PHI AND PSI ANGLES WERE
RESTRAINED TO THEIR STANDARD VALUES WITH PLUS-MINUS 30 DEGREES ERROR RANGE. FOR RESIDUES HAVING INTENSE INTRARESIDUE HN-HA NOES WITH POSITIVE PHI ANGLES SUGGESTED BY THE
PROGRAM TALOS, PHI WAS RESTRAINED TO 40 DEGREES PLUS-MINUS 15 DEGREES. ELECTROSTATIC SURFACES WERE
CALCULATED USING GRASP. MOLECULAR MODELS WERE GENERATED WITH QUANTA (MSI),
INSIGHT (MSI) AND MOLSCRIPT. |
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