| SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS | STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. SUBSEQUENTLY, THE PROTON- PROTON DISTANCES IN THE CALCULATED STRUCTURES WERE DETERMINED USING THE PROGRAM BACKCALC_DB 2.0 (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED SEVERAL TIMES, LEADING TO A TOTAL OF 424 INTRARESIDUAL AND 337 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X-PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR NON-BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION. | X-PLOR V3.840 |
