Structure‐based thermodynamic analysis of the dissociation of protein phosphatase‐1 catalytic subunit and microcystin‐LR docked complexes

Abstract

The relationship between the structure of a free ligand in solution and the structure of its bound form in a complex is of great importance to the understanding of the energetics and mechanism of molecular recognition and complex formation. In this study, we use a structure-based thermodynamic approach to study the dissociation of the complex between the toxin microcystin-LR (MLR) and the catalytic domain of protein phosphatase-1 (PP-1c) for which the crystal structure of the complex is known. We have calculated the thermodynamic parameters (enthalpy, entropy, heat capacity, and free energy) for the dissociation of the complex from its X-ray structure and found the calculated dissociation constant (4.0 x 10(-11)) to be in excellent agreement with the reported inhibitory constant (3.9 x 10(-11)). We have also calculated the thermodynamic parameters for the dissociation of 47 PP-1c:MLR complexes generated by docking an ensemble of NMR solution structures of MLR onto the crystal structure of PP-1c. In general, we observe that the lower the root-mean-square deviation (RMSD) of the docked complex (compared to the X-ray complex) the closer its free energy of dissociation (deltaGd(o)) is to that calculated from the X-ray complex. On the other hand, we note a significant scatter between the deltaGd(o) and the RMSD of the docked complexes. We have identified a group of seven docked complexes with deltaGd(o) values very close to the one calculated from the X-ray complex but with significantly dissimilar structures. The analysis of the corresponding enthalpy and entropy of dissociation shows a compensation effect suggesting that MLR molecules with significant structural variability can bind PP-1c and that substantial conformational flexibility in the PP-1c:MLR complex may exist in solution.

Identification of a Site in Sar1 Involved in the Interaction with the Cytoplasmic Tail of Glycolipid Glycosyltransferases

“…H. J. F. M., M. V., and G. M. are career members, and CQ fellow, of the Consejo Nacional de Investigaciones Científicas y Té cnicas (CONICET) of Argentina. were reranked using the program STC (21). The complexes that ranked best (i.e.…”

“…1C). This site was further explored, and we found docked positions with free energy of binding between Ϫ8 and Ϫ10 kcal/mol using Autodock (20) and between Ϫ12 and Ϫ14 using STC (21). These binding energies suggest a high affinity constant, in the nanomolar order.…”

Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic <i>Hydrogenobacter thermophilus</i>

“…To find out the interactions between the SoxY and SoxZ proteins, as well as between thiosulfate ion and the SoxYZ complex structural thermodynamics calculator software package [27] and the Biopolymer module of Insight II were used.…”

“…In order to find the mode of binding of the proteins and the binding of thiosulfate ion with the SoxYZ protein complex structural thermodynamics calculator (STC) [27] was used. The binding free energies of the SoxYZ complex and that of the soxYZ-thiosulfate complex were determined at temperatures ranging between 50˚C and 70˚C with an interval of 5˚C as SoxYZ complex of Htherm has an optimum temperature at 60˚C.…”

Elucidation of the Molecular Recognition of Bacterial Cell Wall by Modular Pneumococcal Phage Endolysin CPL-1

“…Several runs of flexidock were performed to obtain a series of model complexes. These complexes were analyzed and clustered in families based on the following: (i) score energy from flexidock results; (ii) agreement between the experimental data and the theoretical model (the interactions were examined with the LPC program (26)); and (iii) free energy of binding (⌬G bind ) calculated with Structural Thermodynamics Calculations version 4.3 (27). The representative conformer from each group was reoptimized.…”