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CAD–ICAD complex structure derived from saturation transfer experiment and simulated annealing without using pairwise NOE information
Author(s) -
Matsuda Tomoki,
Nakajima Nobuyuki,
Yamazaki Toshio,
Nakamura Haruki
Publication year - 2004
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.656
Subject(s) - icad , simulated annealing , cad , chemistry , annealing (glass) , biological system , saturation (graph theory) , biophysics , crystallography , materials science , computer science , physics , algorithm , mathematics , thermodynamics , biology , biochemistry , combinatorics , gene
Saturation transfer experiments were performed for the 2 H‐ and 15 N‐labeled mouse CAD domain of the caspase‐activated deoxyribonuclease and the CAD domain of its inhibitor to reveal the protein–protein complexed conformation. Based on the physical model for the spin diffusion, a novel method was developed to reconstruct the complexed structure using the simulated annealing calculation. The complementarity in the molecular surface shape and the electrostatic potential distribution provide a good measure for the assessment of the putative complexed conformation, despite much less experimental information than the conventional distance geometry calculation. Copyright © 2004 John Wiley & Sons, Ltd.