Monte Carlo Simulations of Glu-242 in Cytochrome c Oxidase.

Monte Carlo (MC) simulations of conformational changes and protonation of Glu-242, a key residue that shuttles protons in cytochrome c oxidase (CcO), are reported. Previous studies suggest that this residue may play a role of the valve of the enzyme proton pump. Here we examine how sensitive the results of simulations are to the computational method used.

Histidine in continuum electrostatics protonation state calculations.

A modification to the standard continuum electrostatics approach to calculate protein pK(a)s, which allows for the decoupling of histidine tautomers within a two-state model, is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two-state formalism, because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine's charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation.

Proteins as strongly correlated protonic systems.

Determination of the protonation state of enzymes is a challenging problem in computational biophysics largely due to the vast number of possible protonic configurations. The protonation state dynamics of respiratory complex I was investigated via Monte Carlo and asynchronous dynamics simulations and a novel eigenvector analysis. Many low lying states were identified and examined.

Redox-coupled protonation of respiratory complex I: the hydrophilic domain.

Respiratory complex I, NADH:ubiquinone oxidoreductase, is a large and complex integral membrane enzyme found in respiring bacteria and mitochondria. It is responsible in part for generating the proton gradient necessary for ATP production. Complex I serves as both a proton pump and an entry point for electrons into the respiratory chain.

Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves.

Recently, Euro et al. [Biochem. 47, 3185 (2008) ] have reported titration data for seven of nine FeS redox centers of complex I from Escherichiacoli.

Electrostatics of the FeS clusters in respiratory complex I.

Respiratory complex I couples the transfer of electrons from NADH to ubiquinone and the translocation of protons across the mitochondrial membrane. A detailed understanding of the midpoint reduction potentials (E(m)) of each redox center and the factors which influence those potentials are critical in the elucidation of the mechanism of electron transfer in this enzyme. We present accurate electrostatic interaction energies for the iron-sulfur (FeS) clusters of complex I to facilitate the development of models and the interpretation of experiments in connection to electron transfer (ET) in this enzyme.

Atomic tungsten for ultrafast hard X-ray generation.

High-resolution X-ray absorption measurements (with an accuracy of +/-0.3 eV) of ZnSO(4) (aq) were performed with ultrafast selected energy X-ray absorption spectroscopy (USEXAS) using a laser-driven tungsten target X-ray source. The results were used to determine the absolute spectral positions of characteristic emission lines.

Structural characterization of alpha-helices of implicitly solvated poly-alanine.

The structural characteristics of alpha-helices in poly-alanine-based peptides have been investigated via molecular dynamics simulation with the goal of understanding the basic features of peptide simulations within the context of a model system, classical molecular dynamics with generalized Born (GB) solvation, and to shed insight into the formation and stabilization of alpha-helices in short peptides. The effects of peptide length, terminal charges, proline substitution, and temperature on the alpha-helical secondary structure have been studied. The simulations have shown that distinct secondary structure begins to develop in peptides with lengths approaching 10 residues while ambiguous structures occur in shorter peptides.