| FOURIER DECONVOLUTION, CONFORMATIONAL GRID SEARCH A CARTESAIN
REPRESENTATION MOLECULAR MECHANIC ENERGY MINIMIZATION |
THE STRUCTURE ARE BASED ON: 1) TEN PAIRS OF INTER-SUBUNIT DISTANCES FOR THE KCSA INNER
HELICAL BUNDLE IN THE CLOSED AND THE OPEN STATES AND 2) THE USE OF THE CRYSTAL STRUCTURE
AS THE CHANNEL IN THE CLOSED STATE, AND AS THE REFERENCE STRUCTURE. THE COMPUTER PROGRAM
REDCAT SEARCHES (RESTRAINT-DRIVEN CARTESIAN TRANSFORMATION) BASED ON THE EXHAUSTIVE SAMPLING
OF RIGID-BODY MOVEMENT IN CARTESIAN SPACE FOR THE TM2 INNER BUNDLE IN THE OPEN STATE WERE
ALLOWED TO CONVERGE TO A MINIMAL PENALTY VALUE. THE ENSEMBLE OF THE 50 LOWEST PENALTY
CONFORMERS WAS SUBJECTED TO MOLECULAR MECHANIC ENERGY MINIMIZATION. FINAL REFINEMENT WAS
PERFORMED ON THE AVERAGE OPEN HELICAL BUNDLE BY ENERGY MINIMIZATION. |
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