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We use real-time density functional theory on a real-space grid to calculate electronic excitations of bacteriochlorophyll chromophores of the light-harvesting complex 2 (LH2). Comparison with Gaussian basis set calculations allows us to assess the numerical trust range for computing electron dynamics in coupled chromophores with both types of techniques. Tuned range-separated hybrid calculations for one bacteriochlorophyll as well as two coupled ones are used as a reference against which we compare results from the adiabatic time-dependent local density approximation (TDLDA). The tuned range-separated hybrid calculations lead to a qualitatively correct description of the electronic excitations and couplings. They allow us to identify spurious charge-transfer excitations that are obtained with the TDLDA. When we take into account the environment that the LH2 protein complex forms for the bacteriochlorophylls, we find that it substantially shifts the energy of the spurious charge-transfer excitations, restoring a qualitatively correct electronic coupling of the dominant excitations also for TDLDA. [ABSTRACT FROM AUTHOR]

The kinetics of the charge-transfer systems are formulated in a microstate form to understand the simulations of the electron transfer between the tetraheme subunit and the special pair of the photosynthetic reaction of the proteins. The analysis reveals that the electron-transfer rate constants can be easily obtained by using the combination of the various electrostatic calculations with the existing empirical rate law.

Molecular dynamics simulation study is used to investigate the differential effects of three closely-related sterols, cholesterol, ergosterol and lanosterol on the dipalmitoyl phosphatidylcholine membrane. The findings prove that ergosterol is the most efficient of all three, as it helps in promoting the liquid-ordered phase, as well as the lipid domain formation in the membrane.

A procedure is introduced to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. The proton pump bacteriorhodopsin is used as an example to show on a structural level how the membrane potential affects the energetics of the protonation of proteins.

Calculation of pK(sub a) values of the cluster ligand histidines using a combined density functional theory/continuum electrostatics approach is reported. It is concluded that the structural differences are the primary reason for the different pH-titration behavior of the proteins and the shift caused by neutralizing the negative charges in ferredoxin Rieske proteins is larger than the shift caused by removing the hydrogen bonds toward the cluster in bc-type Rieske proteins.

The framework of the decoupled sites representation (DSR), previously developed in the context of pH titration, is extended to include cooperative ligand binding as well as multiple conformations and multiple ligands. It cam be used to elucidate the connection between the experimentally observed binding curves and parameters of underlying microscopic models.Z

The all-ferrous Rieske cluster, [[2Fe-2S].sup.0], has been produced in solution and characterized by protein-film voltammetry and UV-visible, EPR, and Mossbauer spectroscopies, The [[2Fe-2S].sup.0] cluster, in the overexpressed soluble domain of the Rieske protein from the bovine cytochrome b[c.sub.1] complex, is formed at -0.73 V at pH 7. Therefore, at pH 7, the [[2Fe-2S].sup.1+/0] couple is 1.0 V below the [[2Fe-2S].sup.2+/1+] couple. The two cluster-bound ferrous irons are both high spin (S = 2), and they are coupled antiferromagnetically (-J [is greater than or equal to] 30 [cm.sup.-1], H = -2JS1xS2) to give a diamagnetic (S = 0) ground state. The ability of the Rieske cluster to exist in three oxidation states (2+, 1+, and 0) without an accompanying coupled reaction, such as a conformational change or protonation, is highly unusual. However, uncoupled reduction to the [[2Fe-2S].sup.0] state occurs at pH > 9.8 only, and at high pH the intact cluster persists in solution for < 1 min. At pH < 9.8, the all-ferrous cluster is stabilized significantly by protonation. A combination of experimental data and calculations based on density functional theory suggests strongly that the proton binds to one of the cluster [[micro].sub.2]-sulfides, consistent with observations that reduced [3Fe-4S] clusters are protonated also. The implications for our understanding of coupled reactions at iron-sulfur clusters and of the factors that determine the relative stabilities of their different oxidation states are discussed.

The kinetic experiments, calculations of electrostatic properties and a new theoretical treatment of pH effects are combined together to study the effects of pH on protein association. The anomalous pK(sub a) values of certain amino acid residues in both cytochrone c and plastocyanin are seen to be significant for their biological functions.

Research has been conducted on the individual titratable sites interactions in a molecule. A method of decomposition of any complex titration behavior into simple standard components has been developed and the results are discussed.

Indole, as a part of tryptophan, can serve as an anchor for platinum(II) and palladium(II) binding to peptides and proteins. Studies have stated that labeling by transition-metal complexes make possible selective cleavage of amide bonds and new possibilities of protein structure, and open new directions for research into the bioinorganic and biological chemistry of tryptophan.

Electron transfer between quinones in the bacterial photosynthetic reaction center (bRC), a pigment-protein complex in the membrane of purple bacteria, has been studied, being coupled to a conformational rearrangement using Rhodobacter sphaeroides and comparing results to those with Rhodopseudomonas viridis. A strongly coupled pair of titratable groups binds about one proton in the dark-adapted X-ray structure and about two protons in the light-exposed structure. Possible mechanisms for the gated electron transfer are discussed.