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Biophys J, August 2001, p. 737-750, Vol. 81, No. 2

Free Energy Decomposition of Protein-Protein Interactions

Sergey Yu. Noskov* and Carmay Lim*dagger

 *Institute of Biomedical Sciences, Academia Sinica, 11529 Taipei, and  dagger Department of Chemistry, National Tsing-Hua University, 300 Hsinchu, Taiwan

A free energy decomposition scheme has been developed and tested on antibody-antigen and protease-inhibitor binding for which accurate experimental structures were available for both free and bound proteins. Using the x-ray coordinates of the free and bound proteins, the absolute binding free energy was computed assuming additivity of three well-defined, physical processes: desolvation of the x-ray structures, isomerization of the x-ray conformation to a nearby local minimum in the gas-phase, and subsequent noncovalent complex formation in the gas phase. This free energy scheme, together with the Generalized Born model for computing the electrostatic solvation free energy, yielded binding free energies in remarkable agreement with experimental data. Two assumptions commonly used in theoretical treatments; viz., the rigid-binding approximation (which assumes no conformational change upon complexation) and the neglect of vdW interactions, were found to yield large errors in the binding free energy. Protein-protein vdW and electrostatic interactions between complementary surfaces over a relatively large area (1400-1700 Å2) were found to drive antibody-antigen and protease-inhibitor binding.

Biophys J, August 2001, p. 737-750, Vol. 81, No. 2
© 2001 by the Biophysical Society   0006-3495/01/08/737/14  $2.00


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