ABSORPTION OF METHYLBACTERIOPHEOPHORBIDE a SINGLE CRYSTALS: SPECTRAL SHIFTS DUE TO π-π INTERACTIONS

Abstract— Polarized absorption spectra were obtained for a single crystal of methylbacteriophorbide a (MeBPhide a). The Q_y band is red-shifted ∽ 1660 cm^-1 (∽ 110 nm) relative to MeBPhide a in a CH₂Cl₂/benzene solution. This is equivalent to the largest red shifts observed for in vivo bacteriochlorophyll a. The Soret band exhibits a smaller red shift and a significant reduction in intensity, and the Q_x band is not observed. The crystal spectra are qualitatively similar to spectra reported for several other aggregated (bacterio)chlorophyll and bacteriopheophytin systems. Since crystalline MeBPhide a contains no Mg, water or hydrogen bonding (Barkigia etal. , 1981), these results demonstrate that the spectral changes associated with the aggregation of photosynthetic chromophores can arise solely from IT-IT interactions between macrocycles.     

Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids

The hydroxylation of fatty acids is an appealing reaction in synthetic chemistry, although the lack of selective catalysts hampers its industrial implementation. In this study, we have engineered a highly regioselective fungal peroxygenase for the ω-1 hydroxylation of fatty acids with quenched stepwise over-oxidation. One single mutation near the Phe catalytic tripod narrowed the heme cavity, promoting a dramatic shift toward subterminal hydroxylation with a drop in the over-oxidation activity. While crystallographic soaking experiments and molecular dynamic simulations shed light on this unique oxidation pattern, the selective biocatalyst was produced by Pichia pastoris at 0.4 g L⁻¹ in a fed-batch bioreactor and used in the preparative synthesis of 1.4 g of (ω-1)-hydroxytetradecanoic acid with 95 % regioselectivity and 83 % ee for the S enantiomer.     

Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration

The connection between free-energy surfaces and chevron plots has been investigated in a laser temperature jump kinetic study of a small ultrafast folding protein, the 35-residue subdomain from the villin headpiece. Unlike all other proteins that have been studied so far, no measurable dependence of the unfolding/refolding relaxation rate on denaturant concentration was observed over a wide range of guanidinium chloride concentration. Analysis with a simple Ising-like theoretical model shows that this denaturant-invariant relaxation rate can be explained by a large movement of the major free energy barrier, together with a denaturant- and reaction coordinate-dependent diffusion coefficient.     

The uniqueness of hierarchically extended backward solutions of the Wright–Fisher model

The diffusion approximation of the Wright-Fisher model of population genetics leads to partial differentiable equations, the Kolmogorov forward and backward equations, with a leading term that degenerates at the boundary. This degeneracy has the consequence that standard PDE tools do not apply, and solutions lack regularity properties. In this paper, we develop a regularizing blow-up scheme for the iteratively extended global solutions of the backward Kolmogorov equation presented in a previous paper, which are constructed from a known class of solutions, and establish their uniqueness for the stationary case. As the model describes the random genetic drift of several alleles at the same locus from a backward perspective, the occurring singularities result from the loss of an allele. While in an analytical approach, this provides substantial difficulties, from a biological or geometric perspective, this is a natural process that can be analyzed in detail. The presented scheme regularizes the solution via a carefully constructed iterative transformation of the domain.     

Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data

Differential scanning calorimetry was used to measure the temperature dependence of the absolute heat capacity of the 35-residue subdomain of the villin headpiece, a protein that folds in 5 mus and is therefore assumed to have a small free-energy barrier separating folded and unfolded states. To obtain an estimate of the barrier height from the calorimetric data, two models, a variable-barrier model and an Ising-like model, were used to fit the heat capacity in excess of the folded state over the temperature range 15-125 degrees C. The variable-barrier model is based on an empirical mathematical form for the density of states, with four adjustable parameters and the enthalpy (H) as a reaction coordinate. The Ising-like model is based on the inter-residue contact map of the X-ray structure with exact enumeration of approximately 10(5) possible conformations, with two adjustable parameters in the partition function, and either the fraction of native contacts (Q) or the number of ordered residues (P) as reaction coordinates. The variable-barrier model provides an excellent fit to the data and yields a barrier height at the folding temperature ranging from 0.4 to 1.1 kcal mol(-1), while the Ising-like model provides a less good fit and yields barrier heights of 2.3 +/- 0.1 kcal mol(-1) and 2.1 +/- 0.1 kcal mol(-1) for the Q and P reaction coordinates, respectively. In both models, the barrier to folding increases with increasing temperature. Assuming a sufficiently large activation energy for diffusion on the free-energy surfaces, both models are consistent with the observation of a temperature-independent folding rate in previously published laser temperature-jump experiments. Analysis of this kinetic data, using an approximate form for the pre-exponential factor of Kramers theory and the 70 ns relaxation time for the fast phase that precedes the unfolding/refolding relaxation to determine the diffusion coefficient, results in a barrier height of 1.6 +/- 0.3 kcal mol-1 for an unspecified reaction coordinate. Although no independent test of the validity of the H, Q, or P reaction coordinates is given, the barrier-height estimates obtained with the three reaction coordinates are in quite good agreement with the value derived from a Kramers analysis of the kinetics that makes no assumptions about the reaction coordinate. However, the higher estimates obtained using Q or P appear more consistent with the finding of barrier-crossing kinetics of a villin mutant that folds in 700 ns, corresponding to a 1.3 kcal mol-1 reduction in the folding barrier relative to wild-type. All of the results suggest that the free-energy barrier to folding is sufficiently low that it should be possible to engineer this protein or find solution conditions that would eliminate the barrier to create the "downhill" folding scenario of Wolynes and Onuchic.     

Peroxygenase‐Catalyzed Oxyfunctionalization Reactions Promoted by the Complete Oxidation of Methanol

Peroxygenases catalyze a broad range of (stereo)selective oxyfunctionalization reactions. However, to access their full catalytic potential, peroxygenases need a balanced provision of hydrogen peroxide to achieve high catalytic activity while minimizing oxidative inactivation. Herein, we report an enzymatic cascade process that employs methanol as a sacrificial electron donor for the reductive activation of molecular oxygen. Full oxidation of methanol is achieved, generating three equivalents of hydrogen peroxide that can be used completely for the stereoselective hydroxylation of ethylbenzene as a model reaction. Overall we propose and demonstrate an atom‐efficient and easily applicable alternative to established hydrogen peroxide generation methods, which enables the efficient use of peroxygenases for oxyfunctionalization reactions.