• Corpus ID: 250311373

Mathematical Model for Chemical Reactions in Electrolyte Applied to Cytochrome $c$ Oxidase: an Electro-osmotic Approach

  title={Mathematical Model for Chemical Reactions in Electrolyte Applied to Cytochrome \$c\$ Oxidase: an Electro-osmotic Approach},
  author={Shixin X{\'u} and Robert S. Eisenberg and Zilong Song and Huaxiong Huang},
A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and dissipative functionals. The energy variation method is generalized to deal with open systems with inputs of charge, mass, and energy. The open systems can transform input energy of one type into output energy of another type. The generalized method is used to… 

Setting Boundaries for Statistical Mechanics

It is shown that statistical mechanics without bounds (in space) is impossible as well as imperfect, if the molecules interact as charged particles, as nearly all atoms do.



Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.

Exploring the proton pump mechanism of cytochrome c oxidase in real time

Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts

Kinetic gating of the proton pump in cytochrome c oxidase

The fundamental mechanism identified here for the efficient conversion of chemical energy into an electrochemical potential should prove relevant also for other molecular machines and novel fuel-cell designs.

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.

A variational method EnVarA (energy variational analysis) is used that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions of ions next to a charged wall.

Insights into the mechanism of proton transport in cytochrome c oxidase.

It is shown why the reduction of heme a is essential for proton pumping and the "valve" role of the Glu242 residue (bovine CcO notation) and the gate role of d-propionate ofheme a(3) (PRDa3) in the explicit PT are explicitly demonstrated for the first time.

Initiation of the proton pump of cytochrome c oxidase

It is shown that some mutant enzymes incapable of proton pumping nevertheless initiate catalysis by proton transfer to a proton-loading site through a conserved tyrosine in the so-called D-channel that determines the efficiency of this reaction.

Elementary steps of proton translocation in the catalytic cycle of cytochrome oxidase.

Water-gated mechanism of proton translocation by cytochrome c oxidase.

The catalytic cycle of cytochrome c oxidase is not the sum of its two halves.

It is shown by time-resolved membrane potential and pH measurements with cytochrome oxidase liposomes that, with both phases in succession, two protons are translocated during each phase, one during each individual electron transfer step.