PubMed · 13619425
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G MACHATA. 1958. [Alcohol dehydrogenase method].. https://pubmed.ncbi.nlm.nih.gov/13619425/
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The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries.
The catalytic chemistry of the thermophilic Bacillus stearothermophilus alcohol dehydrogenase (HtADH) closely resembles that of mesophilic horse liver alcohol dehydrogenase (HLADH). Molecular dynamics (MD) simulations of the htADH x NAD+ x EtO- complex at 298, 323, and 348 K show that the structure of the ligated Zn2+...EtO- complex varies slightly with change in temperature. The MD-created Boltzmann distribution of htADH x NAD+ x EtO- structures establishes the formation of multiple states which increase in number with a decrease in temperature. The motions of the cofactor domain are highly correlated with the motions of NAD+ at the optimal growth temperature (348 K), with NAD+ being pushed toward the substrate by Val260. With a decrease in temperature, the motion together of the cofactor and substrate is reversed, and at 298 K, the nicotinamide ring of the cofactor moves away from the substrate. Both the distance between and the angle of approach of C4 of NAD+ and HD of EtO- become distorted from those of the reactive conformation. The percentages of ground state present as the reactive conformation at different temperatures are approximately correlated with the kcat for the htADH enzymatic reaction. The rate constant for the htADH x NAD+ x EtOH --> htADH x NAD+ x EtO- proton dissociation, which is mediated by Thr40-OH, becomes slower at lower temperatures. The time-dependent distance between EtO- and Thr40-OH reveals that the Thr40 hydroxyl group sways between the substrate and NAD+ ribose 2'-hydroxyl group at the optimal enzyme growth temperature, and this movement is effectively frozen out as the temperature decreases. The temperature dependence of active site conformations is due to the change in both long-range and short-range motions of the E x S complex.
The excellent catalytic activity of a novel carbon nanomaterial, soluble carbon nanofiber (CNF) with good dispersion and wettability, to the oxidation of dihydronicotinamide adenine dinucleotide (NADH) was described for biosensing application. The edge plane sites and oxygen-rich groups presented on the CNF surface could be partially responsible for its electrocatalytic behavior, which induced a substantial decrease by 573 mV in the overpotential of NADH oxidation reaction (compared to a bare electrode). The CNF-coated electrode thus allowed highly sensitive amperometric detection of NADH with a low limit of detection (0.11 muM), low applied potential (+0.06 V), and minimization of surface fouling. Such ability of CNF to promote the electron transfer between NADH and the electrode suggested a new, promising biocompatible platform for development of dehydrogenase-based amperometric biosensors. With alcohol dehydrogenase (ADH) as a model, the ADH/CNF-modified electrode could be constructed by a simple casting process. The proposed biosensor showed rapid and highly sensitive amperometric response to ethanol with acceptable preparation reproducibility and excellent stability.