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F Neese

Publications and source records attributed to F Neese.

9 recordsLinked to original sources
PubMed2005

Calculating absorption shifts for retinal proteins: computational challenges.

Rhodopsins can modulate the optical properties of their chromophores over a wide range of wavelengths. The mechanism for this spectral tuning is based on the response of the retinal chromophore to external stress and the interaction with the charged, polar, and polarizable amino acids of the protein environment and is connected to its large change in dipole moment upon excitation, its large electronic polarizability, and its structural flexibility. In this work, we investigate the accuracy of computational approaches for modeling changes in absorption energies with respect to changes in geometry and applied external electric fields. We illustrate the high sensitivity of absorption energies on the ground-state structure of retinal, which varies significantly with the computational method used for geometry optimization. The response to external fields, in particular to point charges which model the protein environment in combined quantum mechanical/molecular mechanical (QM/MM) applications, is a crucial feature, which is not properly represented by previously used methods, such as time-dependent density functional theory (TDDFT), complete active space self-consistent field (CASSCF), and Hartree-Fock (HF) or semiempirical configuration interaction singles (CIS). This is discussed in detail for bacteriorhodopsin (bR), a protein which blue-shifts retinal gas-phase excitation energy by about 0.5 eV. As a result of this study, we propose a procedure which combines structure optimization or molecular dynamics simulation using DFT methods with a semiempirical or ab initio multireference configuration interaction treatment of the excitation energies. Using a conventional QM/MM point charge representation of the protein environment, we obtain an absorption energy for bR of 2.34 eV. This result is already close to the experimental value of 2.18 eV, even without considering the effects of protein polarization, differential dispersion, and conformational sampling.

Absorption↗
PubMed2005

EPR experiments to elucidate the structure of the ready and unready states of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.

Isolation and purification of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F under aerobic conditions leads to a mixture of two states, Ni-A (unready) and Ni-B (ready). The two states are distinguished by different activation times and different EPR spectra. HYSCORE and ENDOR data and DFT calculations show that both states have an exchangeable proton, albeit with a different (1)H hyperfine coupling. This proton is assigned to the bridging ligand between Ni and Fe. For Ni-B, a hydroxo ligand is found. For Ni-A, either a hydroxo in a different orientation or a hydroperoxo-bridging ligand is present.

Desulfovibrio vulgaris↗
PubMed2002

Pentahaem cytochrome c nitrite reductase: reaction with hydroxylamine, a potential reaction intermediate and substrate.

The pentahaem enzyme cytochrome c nitrite reductase catalyses the reduction of nitrite to ammonia, a key reaction in the biological nitrogen cycle. The enzyme can also transform nitrogen monoxide and hydroxylamine, two potential bound reaction intermediates, into ammonia. Structural and mechanistic aspects of the multihaem enzyme are discussed in comparison with hydroxylamine oxidoreductase, a trimeric protein with eight haem molecules per subunit.

Cytochromes a1↗
PubMed2001

Molecular and electronic structure of [Mn(V)N(cyclam-acetato)]PF6. A combined experimental and DFT study.

From the reaction of Li(cyclam-acetate), MnCl(2).4H(2)O, and KPF(6) in methanol brown microcrystals of [Mn(III)Cl(cyclam-acetato)]PF(6) (1) were obtained in the presence of air (cyclam-acetic acid = 1,4,8,11-tetraazacyclotetradecane-1-acetic acid). The reaction of 1 in aqueous NH(3) solution with NaOCl produced blue crystals of [Mn(V)N(cyclam-acetato)]PF(6) (2). Complexes 1 and 2 were characterized by single-crystal X-ray crystallography, IR and Raman, electronic absorption, and (1)H, (13)C, and (15)N NMR spectroscopies. Their magnetochemistry as well as their electrochemistry have been investigated. The complexes [MnN(cyclam-acetato)](+/2+) were studied by theoretical calculations at the DFT and semiempirical levels in order to obtain more insight into the ground and excited states of the Mn(V)(triple bond)N unit. Structural and spectroscopic parameters were successfully calculated and compared to experiment. A pictorial description of the bonding has been developed.

Journal Article↗
PubMed2000

Structural investigations of the CuA centre of nitrous oxide reductase from Pseudomonas stutzeri by site-directed mutagenesis and X-ray absorption spectroscopy.

Nitrous oxide reductase is the terminal component of a respiratory chain that utilizes N2O in lieu of oxygen. It is a homodimer carrying in each subunit the electron transfer site, CuA, and the substrate-reducing catalytic centre, CuZ. Spectroscopic data have provided robust evidence for CuA as a binuclear, mixed-valence metal site. To provide further structural information on the CuA centre of N2O reductase, site directed mutagenesis and Cu K-edge X-ray absorption spectroscopic investigation have been undertaken. Candidate amino acids as ligands for the CuA centre of the enzyme from Pseudomonas stutzeri ATCC14405 were substituted by evolutionary conserved residues or amino acids similar to the wild-type residues. The mutations identified the amino acids His583, Cys618, Cys622 and Met629 as ligands of Cu1, and Cys618, Cys622 and His626 as the minimal set of ligands for Cu2 of the CuA centre. Other amino acid substitutions indicated His494 as a likely ligand of CuZ, and an indirect role for Asp580, compatible with a docking function for the electron donor. Cu binding and spectroscopic properties of recombinant N2O reductase proteins point at intersubunit or interdomain interaction of CuA and CuZ. Cu K-edge X-ray absorption spectra have been recorded to investigate the local environment of the Cu centres in N2O reductase. Cu K-edge Extended X-ray Absorption Fine Structure (EXAFS) for binuclear Cu chemical systems show clear evidence for Cu backscattering at approximately 2.5 A. The Cu K-edge EXAFS of the CuA centre of N2O reductase is very similar to that of the CuA centre of cytochrome c oxidase and the optimum simulation of the experimental data involves backscattering from a histidine group with Cu-N of 1.92 A, two sulfur atoms at 2.24 A and a Cu atom at 2. 43 A, and allows for the presence of a further light atom (oxygen or nitrogen) at 2.05 A. The interpretation of the CuA EXAFS is in line with ligands assigned by site-directed mutagenesis. By a difference spectrum approach, using the Cu K-edge EXAFS of the holoenzyme and that of the CuA-only form, histidine was identified as a major contributor to the backscattering. A structural model for the CuA centre of N2O reductase has been generated on the basis of the atomic coordinates for the homologous domain of cytochrome c oxidase and incorporating our current results and previous spectroscopic data.

Amino Acid Sequence↗
PubMed1995

Trapping of nitric oxide formed during photolysis of sodium nitroprusside in aqueous and lipid phases: an electron spin resonance study.

Photolytic decomposition of sodium nitroprusside (SNP), a widely used nitrovasodilator, produced nitric oxide (.NO), which was continuously monitored by electron spin resonance (ESR) spectroscopy. The .NO present in the aqueous or the lipid phase was trapped by either a hydrophilic or a hydrophobic nitronyl nitroxide, respectively, to form the corresponding imino nitroxide. The conversion of nitronyl nitroxide to imino nitroxide was monitored by ESR spectrometry. The quantum yield for the generation of .NO from SNP, measured from the rate of decay of nitronyl nitroxide, was 0.201 +/- 0.007 and 0.324 +/- 0.01 (mean +/- SD, n = 3) at 420 nm and 320 nm, respectively. The action spectrum for .NO generation was found to overlap the optical absorption spectrum of SNP closely. A mechanism for the reaction between SNP and nitronyl nitroxide in the presence of light is proposed and computer-aided simulation of this mechanism using published rate constants agreed well with experimental data. The methodology described here may be used to assay .NO production continuously during photoactivation of .NO donors in aqueous and lipid environments. Biological implications of this methodology are discussed.

Electron Spin Resonance Spectroscopy↗
PubMed1995

Reactions of nitric oxide with nitronyl nitroxides and oxygen: prediction of nitrite and nitrate formation by kinetic simulation.

Nitric oxide reacts with nitronyl nitroxides (NNO) to form imino nitroxides (INO) and this transformation can be monitored using electron spin resonance spectroscopy. Recently, Akaike et al., reported that NNO such as 2-phenyl-4,4,5,5-tetramethylimidazoline-3-oxide-1-oxyl (PTIO) and its derivatives (e.g., carboxy-PTIO) react with nitric oxide (.NO) in a 1:1 stoichiometry forming 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl (PTI) or the respective product (e.g., carboxy-PTI) together with nitrite and nitrate (Akaike et al., Biochemistry 32, 827-332, 1993). In this paper, we reevaluate their results and show that the stoichiometry of the reaction between PTIO and .NO is 0.63 +/- 0.06:1.0. The reason for this discrepancy is due to an erroneous assumption by Akaike et al., that the stoichiometry for the reaction between .NO and O2 is 2:1 in aqueous solution. If the data reported by Akaike et al., were recalculated using a 4:1 stoichiometry established for the aqueous oxidation of .NO, the reaction between .NO and PTIO would give a stoichiometry of 0.5:1.0 in closer agreement with our data. We propose mechanism for the reaction between PTIO and .NO in aqueous solution. This mechanism predicts that the stoichiometry between carboxy-PTIO and .NO is dependent on the rate of generation of .NO and is 1:1 only at low rates of .NO generation (i.e., 10(-13) M/s). However the stoichiometry approaches 0.5:1.0 at higher rates of .NO production or when it is added as a bolus. The ratio between nitrite and nitrate also varies as a function of the rate of generation of .NO. The model agrees with previous experimental observations that the aqueous oxidation of .NO in air saturated solutions will exclusively form nitrite and predicts that .NO will only generate substantial amounts of nitrate if it is released at a rate less than 10(-17) M/s. This may have important consequences in cellular systems where the concentration of .NO is typically measured from nitrite production.

Benzoates↗