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Biophysical Journal 86:2773-2785 (2004)
© 2004 The Biophysical Society

Modeling Electron Transfer Thermodynamics in Protein Complexes: Interaction between Two Cytochromes c3

Vitor H. Teixeira, António M. Baptista and Cláudio M. Soares

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal

Correspondence: Address reprint requests to Dr. Cláudio M. Soares, Tel.: 351-21-446-9610; Fax: 351-21-441-1277; E-mail: claudio{at}itqb.unl.pt.

Redox protein complexes between type I and type II tetraheme cytochromes c3 from Desulfovibrio vulgaris Hildenborough are here analyzed using theoretical methodologies. Various complexes were generated using rigid-body docking techniques, and the two lowest energy complexes (1 and 2) were relaxed using molecular dynamics simulations with explicit solvent and subjected to further characterization. Complex 1 corresponds to an interaction between hemes I from both cytochromes c3. Complex 2 corresponds to an interaction between the heme IV from type I and the heme I from type II cytochrome c3. Binding free energy calculations using molecular mechanics, Poisson-Boltzmann, and surface accessibility methods show that complex 2 is more stable than complex 1. Thermodynamic calculations on complex 2 show that complex formation induces changes in the reduction potential of both cytochromes c3, but the changes are larger in the type I cytochrome c3 (the largest one occurring on heme IV, of ~80 mV). These changes are sufficient to invert the global titration curves of both cytochromes, generating directionally in electron transfer from type I to type II cytochrome c3, a phenomenon of obvious thermodynamic origin and consequences, but also with kinetic implications. The existence of processes like this occurring at complex formation may constitute a natural design of efficient redox chains.




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