CALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES
Alpha-helix nucleation by a calcium-binding peptide loop.
ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: STRONG, 0.18 - 0.27 NM; MEDIUM, 0.18 - 0.40 NM; WEAK, 0.18 - 0.55 NM. PEAK INTENSITIES WERE ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM. HARMONIC RESTRAINTS FOR THE LA3+-ION WERE DEDUCED FROM THE POSITION OF THE CORRESPONDING CA2+-ION CRYSTAL STRUCTURE OF CALMODULIN (PDB CODE: 1CDM). A TOTAL OF SIX HARMONIC DISTANCE RESTRAINTS WAS INCLUDED IN ORDER TO FIX THE DISTANCE AND THE OCTAHEDRAL ARRANGEMENT OF THE SIX LIGANDS RELATIVE TO THE LA3+-ION ASSUMING THE SAME COORDINATION AS FOR THE CA2+ ION IN THE CALMODULIN CRYSTAL STRUCTURE. THE STRUCTURE CALCULATIONS USED THE AB INITIO SIMULATED ANNEALING (SA.INP) AND REFINEMENT (REFINE.INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE. THE CALCULATIONS STARTED FROM AN EXTENDED TEMPLATE WITH RANDOMIZED BACKBONE TORSION ANGLES FOLLOWED BY 50 CYCLES OF ENERGY MINIMIZATION TO REMOVE CLOSE NON-BONDED CONTACTS. THE HIGH TEMPERATURE PHASE COMPRISED 50 PS OF DYNAMICS AT 1000 K; THE FINAL 16 PS HAD AN INCREASED WEIGHT ON COVALENT GEOMETRY RESTRAINTS AND THE NOE DERIVED DISTANCE RESTRAINTS. IN THE NEXT PHASE THE SYSTEM WAS SLOWLY COOLED FROM 1000 K TO 100 K IN A TIME OF 30 PS FOLLOWED BY 200 STEPS OF ENERGY MINIMIZATION. FOR THE NOE EFFECTIVE ENERGY TERM, REPRESENTING THE INTERPROTON DISTANCES, A SOFT SQUARE-WELL POTENTIAL WAS APPLIED. THE REFINEMENT PROTOCOL CONSISTED OF A SLOW-COOLING FROM 1000 TO 100 K WITHIN 45 PS. A FORCE CONSTANT OF 200 KCAL MOL-1 RAD-1 WAS USED FOR THE DIHEDRAL ANGLE RESTRAINTS WHILE THE NOE DERIVED DISTANCE RESTRAINTS AND HARMONIC RESTRAINT WERE REPRESENTED BY A SQUARE-WELL POTENTIAL FUNCTION WITH FORCE CONSTANT OF 50 KCAL/MOL1/A2. OF THE 200 RESULTING STRUCTURES, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED USING PROCHECK AND DSSP.
SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
EF HAND CALCIUM BINDING LOOP, ALPHA-HELIX, CALCIUM-BINDING
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK