Engineering topics

Dikanov, Sergei A.

Publications and source records attributed to Dikanov, Sergei A..

6 records

DOE OSTI2023

A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase

The “Histidine-brace” (His-brace) copper-binding site, composed of Cu(His) 2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV–Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Influence of Polar Mutations on the Electronic and Structural Properties of Q A –· in Bacterial Reaction Centers

Not provided.

Chemistry↗

DOE OSTI2022

Influence of Polar Mutations on the Electronic and Structural Properties of Q A –· in Bacterial Reaction Centers

Reaction centers from Rb. sphaeroides with residue M265 mutated from isoleucine to threonine, serine, and asparagine (M265IT, M265IS, and M265IN, respectively) in the Q A –· state are studied by high-resolution ESEEM and ENDOR spectroscopies to investigate the structural characteristics of these mutants influencing the redox properties of the Q A site. All three mutants decrease the redox midpoint potential (E m ) of Q A by ~0.1 V, yet the mechanism for this drop in E m is unclear. In this work, we examine (i) the hydrogen bonding interactions between Q A –· and residues histidine M219 and alanine M260, (ii) the electron spin density distribution of the semiquinone, and (iii) the orientations of the ubiquinone methoxy substituents. 13 C measurements show no significant contribution of methoxy dihedral angles to the observed decrease in E m for the Q A mutants. Instead, 14 N three-pulse ESEEM data suggest electrostatic or hydrogen bond formation between the mutated M265 side chain and His-M219 N δ may be involved in the observed lowering of the Q A midpoint potential. For mutant M265IN, analysis of the proton hyperfine couplings reveals a weakened hydrogen bond network, resulting in an altered Q A –· spin density distribution. Here, the magnetic resonance study presented here is therefore most consistent with an electrostatic or structural perturbation of the His-M219 N δ hydrogen bond in these mutants as a mechanism for the ~0.1 V decrease in Q A E m .

14 SOLAR ENERGY↗

DOE OSTI2021

Local Environment of Superoxide Radical Formed on the TiO 2 Surface Produced From Ti(OiPr) 4 Exposed to H 2 O 2

A selective heterogeneous catalyst with the superoxide anion O 2 •– stable at room temperature, generated by treating Ti(OR) 4 (R=iPr, nBu) with H 2 O 2 , was previously reported and used for the oxidation of organic compounds. Furthermore, it was proposed that exceptional stability of the O 2 •– is resulted from its stabilization near Ti +4 cation on the TiO 2 surface with participation of water molecules and/or OH groups. In this article, we performed high-resolution pulsed EPR study on the O 2 •– in this catalyst with the aim to obtain quantitative information about its interactions with the surrounding molecules. Our data has shown that the O 2 •– is involved in weak hyperfine interactions with protons in the nearest environment, which do not exceed a value of 2 MHz. It corresponds to an Os…H distance of ≥ 3 Å that exclude the formation of hydrogen bonds. The analysis of possible structures of O 2 •– adsorption on TiO 2 surface taking into account our results and lack of radical mobility at room temperature previously observed in EPR spectra led us to suggest that the O 2 •– is stabilized in the form of superoxo bridge coordinated with two titanium atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure–function relationships

Abstract A set of C43(DE3) and BL21(DE3) Escherichia coli host strains that are auxotrophic for various amino acids is briefly reviewed. These strains require the addition of a defined set of one or more amino acids in the growth medium, and have been specifically designed for overproduction of membrane or water-soluble proteins selectively labelled with stable isotopes, such as 2H, 13C and 15N. The strains described here are available for use and have been deposited into public strain banks. Although they cannot fully eliminate the possibility of isotope dilution and mixing, metabolic scrambling of the different amino acid types can be minimized through a careful consideration of the bacterial metabolic pathways. The use of a suitable auxotrophic expression host strain with an appropriately isotopically labelled growth medium ensures high levels of isotope labelling efficiency as well as selectivity for providing deeper insight into protein structure–function relationships.

Biochemistry & Molecular Biology↗

DOE OSTI2020

Influence of Hyperfine Coupling Strain on Two-Dimensional ESEEM Spectra from I = 1/2 Nuclei

HYSCORE, a variant of two-dimensional ESEEM spectroscopy, is currently one of the most effective tools in high-resolution solid-state EPR spectroscopy. Our systematic studies of hydrogen bonds with semiquinones in 15 N-labeled proteins have previously provided us with an extensive collection of 15 N HYSCORE spectra produced by N–H…O nitrogen donors. Examination of these spectra has indicated in several cases lineshape distortions not described by available theoretical models. We were able to explain all observed artificial phenomena in the 15 N spectra of semiquinones considering a single mechanism—strain of the isotropic hyperfine interaction. In this review article, we introduce the HYSCORE experiment and the theoretical background for spectra of I = 1/2 nuclei in orientation-disordered samples. We then present a description of the observed lineshape distortions and an explanation of the hyperfine strain’s influence on the experimental spectra. In the final part of the article, we discuss (i) similar lineshape distortions found in previously published spectra from 15 N, 29 Si, 31 P, and 57 Fe nuclei that can be explained using the approach applied for the analysis of the 15 N spectra of semiquinones, and (ii) a recently published analysis of 31P spectra with a different type of lineshape distortion based on a more sophisticated method, where the strength of anisotropic coupling is correlated with the sign and value of the isotropic constant in different conformations of a Cu(II) complex.

30 DIRECT ENERGY CONVERSION↗