Yunna Kim

on the atlas · 30

• Parkinson's Disease: Neuron1 savers
• Staging of brain pathology related to sporadic Parkinson's disease - PubMed1 savers
• Low clinical diagnostic accuracy of early vs advanced Parkinson disease: Clinicopathologic study - PMC1 savers
• Low clinical diagnostic accuracy of early vs advanced Parkinson disease | Neurology1 savers
• Accuracy of the Early Diagnosis of Parkinson’s Disease - PMC1 savers
• The coming age of data-driven medicine: translational bioinformatics' next frontier - PMC1 savers
• Specificity of glucose oxidase - ScienceDirect1 savers
• Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase | PNAS1 savers
• Determination of glucose oxidase oxidation-reduction potentials and the oxygen reactivity of fully reduced and semiquinoid forms. - Journal of Biological Chemistry1 savers
• Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination - PMC1 savers
• Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC1 savers
• Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)1 savers
• Acetic Acid Bacteria: Physiology and Carbon Sources Oxidation - PMC1 savers
• Frontiers | Oxidative Fermentation of Acetic Acid Bacteria and Its Products1 savers
• Analysis of growth of Gluconobacter oxydans in glucose containing media | Archives of Microbiology1 savers
• Glucose oxidase — An overview - ScienceDirect1 savers
• Explainable machine learning models based on multimodal time-series data for the early detection of Parkinson’s disease - ScienceDirect1 savers
• Prognostic Modeling of Parkinson's Disease Progression Using Early Longitudinal Patterns of Change - Ren - 2021 - Movement Disorders - Wiley Online Library1 savers
• Enhancing early Parkinson’s disease detection through multimodal deep learning and explainable AI: insights from the PPMI database | Scientific Reports1 savers
• Discovery of Parkinson's disease states and disease progression modelling: a longitudinal data study using machine learning - The Lancet Digital Health1 savers
• Prognostic Modeling of Parkinson’s Disease Progression Using Early Longitudinal Patterns of Change - PMC1 savers
• Automatic classification and prediction models for early Parkinson’s disease diagnosis from SPECT imaging - ScienceDirect1 savers
• Prediction of Parkinson’s Disease Using Machine Learning Methods - PMC1 savers
• protocol1 savers
• Data Dashboard | Parkinson's Progression Markers Initiative1 savers
• Data-Driven Based Approach to Aid Parkinson’s Disease Diagnosis - PMC1 savers
• Clinical Diagnostic Accuracy of Parkinson's Disease: Where Do We Stand? - PubMed1 savers
• Prodromal non-motor symptoms of Parkinson’s disease - PMC1 savers
• Mining imaging and clinical data with machine learning approaches for the diagnosis and early detection of Parkinson’s disease | npj Parkinson's Disease1 savers
• Prediction of Parkinson’s Disease Using Machine Learning Methods - PMC1 savers

highlights · 475

• gical diagnosis as the gold sta

  Clinical Diagnostic Accuracy of Parkinson's Disease: Where Do We Stand? - PubMed

• kinson's disease (PD) progre

  The Parkinson's progression markers initiative (PPMI) – establishing a PD biomarker cohort - Marek - 2018 - Annals of Clinical and Translational Neurology - Wiley Online Library

• The enzyme appears to catalyze the oxidation of the beta form only, and the mutarotation of the alpha form is rate limiting.

  Specificity of glucose oxidase - ScienceDirect

• The active site is optimized at low pH, but not at high pH

  Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase | PNAS

• pH dependence of the rates is caused by protonation of a highly conserved histidine in the active site.

  Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase | PNAS

• Limiting rate constants of kcat/KM(O2) = (5.7 ± 1.8) × 102 M−1⋅s−1 and kcat/KM(O2) = (1.5 ± 0.3) × 106 M−1⋅s−1 are observed at high and low pH, respectively. Reactions exhibit oxygen-18 kinetic isotope effects but no solvent kinetic isotope effects, consistent with mechanisms of rate-limiting electron transfer from flavin to O2.

  Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase | PNAS

• We studied the oxygen reactivity of the 2-electron reduced form of the enzyme over a wide wavelength range and failed to detect either oxygenated flavin derivatives or semiquinoid forms as intermediates. The rate of reoxidation of fully reduced glucose oxidase at pH 9.3 was dependent on ionic strength.

  Determination of glucose oxidase oxidation-reduction potentials and the oxygen reactivity of fully reduced and semiquinoid forms. - Journal of Biological Chemistry

• The potentials indicated that glucose oxidase radicals are stabilized by kinetic factors and not by thermodynamic energy barriers. The pK for the glucose oxidase radical was 7.28 from dead time stopped flow measurements and the extinction coefficient of the neutral semiquinone was 4140 M-1 cm-1 at 570 nm.

  Determination of glucose oxidase oxidation-reduction potentials and the oxygen reactivity of fully reduced and semiquinoid forms. - Journal of Biological Chemistry

• The midpoint potentials at 25 degrees were: pH 5.3 EFl1ox + e- H+ equilibrium EFlH. Em1 = -0.063 +/- 0.011 V EFlH. + e- + H+ equilibrium EFlredH2 Em2 = -0.065 +/- 0.007 V pH 9.3 EFlox + e- EFi- Em1 = -0.200 +/- 0.010 V EFi- + e- + H+ equilibrium EFlredH- Em2 = -0.240 +/- 0.005 V All potentials were measured versus the standard hydrogen electrode (SHE).

  Determination of glucose oxidase oxidation-reduction potentials and the oxygen reactivity of fully reduced and semiquinoid forms. - Journal of Biological Chemistry

• We study the glucose oxidase-catalyzed oxidation of glucose, the catalase-accelerated breakdown of hydrogen peroxide, their combination in cell-free culture, and glucose-driven cellular respiration.

  Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination - PMC

• GOx is glycosylated, with carbohydrates, mostly mannose-like sugars, comprising between 10 and 16% of its final molecular weight [27,36,50].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• More particularly, a study using H/D isotope substitution found that reduced glycosylation appeared to lower the enthalpy of activation and, therefore, increase the activity of the enzyme [52].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The removal of 95% of the GOx carbohydrate content had a noticeable effect on the kinetics of glucose oxidation, its stability at low pH and the number of available isoelectric forms but did not affect its thermal stability or the optimal pH and temperature of the catalytic reaction [50,51].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The second electron transfer step, from the flavin semiquinone radical to the superoxide anion, happens quickly, with a second-order rate constant of 109 M−1· s−1 [49].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The second electron transfer step, from the flavin semiquinone radical to the superoxide anion, happens quickly, with a second-order rate constant of 109 M−1· s−1 [49].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Generally, O2 oxidizes organic substrates by transferring electrons one at a time, forming free-radical intermediates, and most analyses of of the oxidative half-reaction assumed a step-wise electron transfer [34,48]. The rate-limiting step appears to be the transfer of the first electron from flavin to O2 to produce the flavin semiquinone radical and the superoxide anion [41].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• In the active site, one of the O2 atoms is 2.7 Å away from the N1 flavin ring while the second is 3.0 Å away from the His-516 ring.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The oxygen bound in a small pocket formed by shifting His-516 up towards the active-site opening and displacing the active-site water molecule so that it lay outside hydrogen-bonding range of FAD (its closest approach was 3.7 Å from the N5 atom of FAD).

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The kinetic and thermodynamic parameters for the oxygen-binding step suggest that O2 easily and rapidly diffuses into the enzyme

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Considerations of resonance suggest that hydride transfer should create a negative charge around the FAD N1 atom, which have been confirmed by NMR studies of GOx at pH 5.6 in the absence of oxygen [45]. Following the reduction half-reaction, the enzyme is left in a reduced form with a bound glucono-𝛿-lactone. The product is then displaced by water or possibly O2 and the oxidation half-reaction follows.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Hydride transfer occurs in a concerted step in which a proton is removed from the glucose O1 hydroxyl group by a basic group on the enzyme while a hydride is transferred from the glucose C1 to the flavin N5 [43].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Glucose binding is thought to displace the water molecule observed in the active site of the GOx crystal structures, which abstracts a proton from His-516 as it leaves (this abstraction appears to be necessary, according to modeling studies, because His-516 cannot adopt a proper catalytic position when doubly-protonated) [10].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Several lines of evidence ascribed this p𝐾a value to His-516 [40,41]. The most likely mechanism involves a base-catalyzed hydride transfer from the glucose C1 to the flavin N5.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• the most likely mechanism of the GOx reduction half-reaction (EA ↔ FP), the GOx–O2 complex (FB) and the GOx–H2O2 complex (EQ).

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• A indicates glucose, P indicates glucono-𝛿-lactone, B represents O2, Q represents H2O2, E represents the oxidized form of GOx bound to FAD, and F stands for the reduced form of GOx bound to FADH2.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• GOx operates using a Ping-Pong Bi Bi mechanism in which 𝛽-d-glucose oxidation and O2 reduction occur in two different steps [35,39,40,41] (Figure 4). This allows the oxidation and reduction half reactions to be analyzed independently using steady state kinetics. pH profiling showed that the p𝐾a of the amino-acid side-chains in the active site of the enzyme–substrate complex is between 6.9–7.8 [35,42].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• we will concentrate on the “natural” reaction using 𝛽-d-glucose as the substrate and O2 as the electron acceptor.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Their modeling suggested that the residues most important for the enzyme–substrate complex included the catalytic His-516 and His-559 along with Tyr-68, Thr-110, Phe-414, Trp-426, Arg-512 and Asn-514. His-516 and His-559 formed hydrogen-bonds directly with the O1 hydroxyl group, which is expected to lose a proton in the catalytic step, while Asn-514, Arg-512, Tyr-68 and O4 of the FAD all form hydrogen-bonds to the remaining glucose hydroxyl groups, thereby, anchoring the substrate in position.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• All but one of the GOx crystal structures also have a water molecule at the center of the active site, forming hydrogen-bonds to both His-516 and His-559 and lying 3.0 Å away from the N1 ring of FAD (Figure 3a). The location of this water molecule has been taken to represent the likely position of the O1 hydroxyl group of 𝛽-d-glucose [10]. Kinetic, structural and thermodynamic data have allowed likely roles to be assigned to these residues

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The residues potentially important for catalytic activity are colored magenta; those which are thought to be involved in binding 𝛽-d-glucose are colored cyan. The water molecule near the center is thought to indicate the approximate location of the 𝛽-d-glucose O1 hydroxyl in the substrate-bound conformation.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• In the complete dimer, the active site lies at the bottom of a deep, cone-shaped cavity whose apex is centered on the N5 atom of the middle flavin ring, the one that accepts the hydride during reduction. Only three amino-acid side-chains are near this center, His-516, His-559, and Glu-412 (Figure 3). His-559 is fixed by a strong hydrogen-bond to Glu-412 and Glu-412 is largely fixed by the side-chains of the surrounding residues (Ala-349, Phe-351, Phe-414, Trp-426 and Leu-428). The side-chain of His-516 is less constrained and is more conformationally flexible [12].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• In addition to forming part of the FAD-binding site, residues 75–98 also from part of the wall of the active site cavity of the second monomer in the dimer: the complete dimer is needed to properly assemble a complete active site cavity, which may account at least in part for the dimeric form of the holoenzyme [27,33].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• after the dissociation of FAD, the enzyme is not in a monomeric state but appears to form aggregates [30] and that the dimer does not dissociate during thermal denaturation [31]. GOx does appear to dissociate into monomers at pH 5 and below in the presence of sodium n-dodecyl sulfate [32].

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The FAD groups are located near the dimer interface but are more than 22 Å apart, making it unlikely that they communicate with one another through allostery (Figure 2b).

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• In this context, it can be seen that the residues responsible for forming the FAD-binding pocket come from all parts of the polypeptide chain. The majority of the binding site is formed by residues from the N-terminal part of the sequence. Residues from the central region provide additional support, while most of the residues from the C-terminal region form the edges of the flavin binding pocket and also contribute two of the three active site residues.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The monomer is comprised of a single folding domain with a rather complicated topology. When viewed in a manner that emphasizes the secondary structure elements while minimizing the contribution of the unstructured loops (as in Figure 2a,b), two subdomains can be seen, each one centered around a five-stranded 𝛽-sheet. These two subdomains can be associated with FAD-binding on the one hand and substrate binding on the other.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Although the active form in solution is a dimer, the asymmetric unit of each structure contains only monomer with the second monomer occupying a symmetry-related site.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The members of this family are all FAD-dependent oxidoreductases that share a common fold [7,8]. They consist of two functional domains, an N-terminal FAD-binding domain, which contains a strictly conserved 𝛽⁢𝛼⁢𝛽 mononucleotide-binding motif and a more variable substrate binding-domain. As the name suggests, the members of this family oxidize a variety of substrates containing hydroxyl functional groups, including mono and di-saccharides, alcohols, cholesterol and choline. GOx is perhaps the most thoroughly characterized of these, and its mechanism will be described more thoroughly below.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Although its rate constant is still several orders of magnitude below the diffusion limit, GOx has a much higher 𝑘cat/𝐾M (on the order of 106M−1·s−1) compared with most other oxidoreductases, prompting at least one researcher to call it “the Ferrari of the oxidases”

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• The high specificity, high turnover and high stability of GOx

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• specific to 𝛽-d-glucose

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• the oxidases use a two-step mechanism in which a bound flavin adenine dinucleotide (FAD) co-factor is used to oxidize glucose to form glucono-𝛿-lactone and an enzyme-FADH2 intermediate followed by electron transfer to O2 to form H2O2 (Figure 1).

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• (2) the oxidases glucose oxidase (GOx; 𝛽-d-glucose:oxygen 1-oxidoreductase, E.C. 1.1.3.4) [3]

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• Glucose oxidase catalyzes the oxidation of 𝛽-d-glucose to d-glucono-𝛿-lactone and hydrogen peroxide in the presence of molecular oxygen. d-glucono-𝛿-lactone is sequentially hydrolyzed by lactonase to d-gluconic acid, and the resulting hydrogen peroxide is hydrolyzed by catalase to oxygen and water.

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• fast mechanism of action, high stability and specificity

  Glucose Oxidase, an Enzyme “Ferrari”: Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications - PMC

• A cascade reaction can be described as a reaction where the product of one enzyme is the substrate of another, and the final product is the target. The destruction of hydrogen peroxide to prevent glucose oxidase inactivation, even if it is not a real cascade reaction,212 can be considered as one because hydrogen peroxide is produced by glucose oxidase (enzyme 1), which also produces the target product (d-gluconic acid), while catalase (enzyme 2) destroys the by-product of enzyme 1 to yield only water and oxygen. In these cases, the researchers mainly used co-immobilized enzymes. As will be dis…

  Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)

• Catalases catalyze the decomposition of hydrogen peroxide in water and oxygen without risk of promoting some undesired side reactions. In fact, catalases produce oxygen that can be used again by glucose oxidase, even improving glucose oxidase activity.

  Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)

• Also, Aspergillus terreus was used to produce d-gluconic acid.210 It rapidly metabolized glucose to d-gluconic acid at pH 6.5 (with 70% conversion of d-glucose to d-gluconic acid); however, after using all the d-glucose in the reaction medium, the produced d-gluconic acid was employed as a carbon source. L

  Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)

• Use of whole cell biocatalysts to produce d-gluconic acid from glucose

  Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)

• Aspergillus niger containing glucose oxidase was utilized in the oxidation of glucose employing oxygen-enriched air from 30% to 100% saturation at 1 bar, and a three-fold increase in the enzyme activity was observed.207 At the highest dissolved oxygen concentration, the activity of glucose oxidase increased more than three times, while the production rate of d-gluconic acid increased by a factor of two.

  Enzyme production of d-gluconic acid and glucose oxidase: successful tales of cascade reactions - Catalysis Science & Technology (RSC Publishing)