Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer.
Enzymes in biology's energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.
Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA.
Mohammadhasan
M
Dinpajooh
Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA.
Daniel R
DR
Martin
Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA.
Dmitry V
DV
Matyushov
D001419:Bacteria / Q000378:metabolism*; D020134:Catalytic Domain / Q000502:physiology*; D045304:Cytochromes c / Q000378:metabolism*; D004579:Electron Transport / Q000502:physiology*; D004789:Enzyme Activation / Q000502:physiology; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D010788:Photosynthesis / Q000502:physiology; D055672:Static Electricity
D045304:Cytochromes c