| Abstract
| - Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalentinteractions within protein supersecondary structures. In this study, the fast Fourier transform rigid-bodydocking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding proteincalbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1−43) and EF2 (residues 44−75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitroexperiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutatedcalbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 Å with respectto the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independentin silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, thatis, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linearcorrelations between thermodynamic data and ZDOCK scores were built, providing a tested tool for veryfast in silico predictions of the free energy of association of protein−protein complexes solved at the atomiclevel and known to not undergo significant conformational changes upon binding.
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