Understanding orchestrated chemical reactions in toluene/o-xylene monooxygenase from pseudomonas sporium OX1

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2011.Vita. Cataloged from PDF version of thesis.Includes bibliographical references.Chapter 1. Geometric and Functional Versatility of Carboxylate-Bridged Nonheme- Diiron Motifs: sMMO and ToMO. Several metalloenzymes utilize a carboxylate-bridged non-heme diiron motif for dioxygen activation. Despite their conserved diiron active site structures and mechanisms of dioxygen activation, they catalyze a wide range of chemical transformations. These observations suggest that diiron-containing enzymes have distinct active sites and secondary/tertiary environments that are tuned for their dedicated biological functions. Detailed studies of two diiron-containing enzymes in the family of bacterial multicomponent monooxygenases (BMMs), soluble methane monooxygenase (sMMO) and toluene/o-xylene monooxygenase (ToMO), are described. The functions and structures of the three or four components of sMMO and ToMO are summarized. Distinctly different dioxygen activation chemistry and hydrocarbon specificity is observed for these two enzymes. A comparison of these two enzymes provides insight into the evolution of diironcontaining enzymes as well as their differing chemical mechanisms of catalysis. Chapter 2. Role of an Active Site Threonine in the Determination of Distinctive Dioxygen Reactivity in Toluene/o-Xylene Monooxygenase Hydroxylase. Dioxygen activation of toluene/o-xylene monooxygenase hydroxylase (ToMOH) exhibits the formation of a diiron(III) intermediate having unprecedented spectroscopic properties. To evaluate whether an active site threonine plays a role in the determination of the dioxygen chemistry in ToMOH, a T201S variant was prepared by site-directed mutagenesis. We reported the observation of a novel intermediate in the reaction of reduced ToMOH T201 S variant with dioxygen in the presence of its cognate regulatory protein (ToMOD). This species, T201 peroxo, is the first oxygenated intermediate of any toluene monooxygenase to display an optical band. The optical and M6ssbauer spectroscopic properties of the intermediate allowed us to assign it as a peroxodiiron(III) species, similar to Hperoxo in soluble methane monooxygenase hydroxylase (sMMOH). This result indicates that mutation of the T201 to serine altered the dioxygen chemistry of ToMOH in part to be more similar to that of sMMOH. Computational studies suggest that the T201 mutation can greatly perturb the energetics of the enzyme, which might be responsible for the distinct dioxygen reactivity of sMMOH and ToMOH. Structures of the oxygenated intermediates of ToMOH are proposed. Chapter 3. Role of an Active Site Threonine in the Kinetics of Dioxygen Activation in Toluene/o-Xylene Monooxygenase Hydroxylase. To elucidate the role of a strictly conserved T201 residue during dioxygen activation of toluene/o-xylene monooxygenase hydroxylase (ToMOH), T201S, T201G, T201C, and T201V variants of this enzyme were prepared by site-directed mutagenesis. X-ray crystal structures of all variants were obtained. Steady-state activity, regiospecificity, and single-turnover yields were also determined for the T201 mutants. Dioxygen activation by the reduced T201 variants was monitored by stopped-flow UV-vis and M6ssbauer spectroscopy. These studies demonstrated that the same dioxygen activation mechanism is preserved in the T201S, T201C, and T201G variants; however, both formation and decay kinetics of a peroxodiiron(III) intermediate, T201peroxo, were greatly altered, revealing that the T201 residue is critically involved in dioxygen activation. Rate-limiting steps in dioxygen activation of the T201S, T201C, and T201G variants were identified, revealing that T201 plays a major role in proton transfer, which is required to generate the peroxodiiron(III) intermediate. The role of the active site threonine residue in ToMOH is analogous to that of cytochrome P450 monooxygenases, suggesting it as a general threonine-dependent process in Nature to control proton transfer.(cont.) Chapter 4. Mechanistic Studies of Reactions of Peroxodiiron(III) Intermediates in the T201 Variants of Toluene/o-Xylene Monooxygenase Hydroxylase. Site-directed mutagenesis studies of a strictly conserved T201 residue in the active site of toluene/oxylene monooxygenase hydroxylase (ToMOH) revealed that a single mutation can facilitate kinetic isolation of two distinct peroxodiiron(III) species, designated T201peroxo and ToMOHperoxo, during dioxygen activation. In Chapter 2 and 3, we characterized both oxygenated intermediates by UV-vis and M6ssbauer spectroscopy, proposed structures from DFT and QM/MM computational studies, and elucidated chemical steps involved in dioxygen activation through the kinetic studies of T201peroxo formation. In Chapter 4, we investigated the kinetics of T2 0lperoxo decay to explore the reaction mechanism of the oxygenated intermediates following 02 activation. The decay rates of T201 peroxo were monitored in the absence and presence of external (phenol) or internal (tryptophan residue in I100W variant) substrates under pre-steady-state conditions. Three possible reaction models for the formation and decay of T201perX0 were evaluated, and the results demonstrate that this species is on the pathway of arene oxidation and appears to be in equilibrium with TOMOHperoxo. Chapter 5. Tracking a Defined Route of 0 2-Migration in a Dioxygen-Activating Diiron Enzyme, Toluene/o-Xylene Monooxygenase Hydroxylase. For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/oxylene monooxygenase hydroxylase (ToMOH) is a dioxygen-activating carboxylatebridged nonheme-diiron enzyme. Structural analyses of the resting state enzyme suggest two possible pathways for dioxygen to access the c-subunit diiron center, a series of hydrophobic cavities or long solvent-exposed channel. To distinguish which pathway is utilized for dioxygen transfer, the dimensions of the cavities and channel were varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate of dioxygen access to the active site was monitored by measuring the formation rate of an oxygenated intermediate (T 2 01peroxo), a process that is dependent on 02 concentration. Altering the dimensions of the cavity but not the channel drastically changed the rate of dioxygen activation by the reduced enzyme. These results explicitly reveal that the cavities in the ToMOH a-subunit are not merely artifacts of protein packing/folding but rather programmed routes of dioxygen movement through the protein matrix. This conclusion indicates that conformational changes are required during catalysis to form a dioxygen trajectory and that the temporary opening/closing of the cavities control dioxygen transfer. Given that the cavities are present in all BMMs, the breathing motion presumably controls dioxygen consumption in all BMMs. This study represents the first approach to track kinetically a defined transient pathway by which a small gaseous molecule gains access to a diiron enzyme.(cont.) Appendix A. Insights into the Different Dioxygen Activation Pathways of Methane and Toluene Monooxygenase Hydroxylases. The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, Hperoxo, Q and Q* in MMOH, and ToMOHperoxo in toluene/o-xylene monooxygenase hydroxylase (ToMOH), are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss the differences that give rise to the distinct behavior of dioxygen reactivity in sMMOH and ToMOH. In particular, analysis of multiple crystal structures reveals that T213 of MMOH and analogous T201 of TMOH, located in the immediate vicinity of the active site, have different rotamer configurations. We study the rotation energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to whether T201 and T213 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed M6ssbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the regulatory protein (ToMOD), which is essential for oxygenated intermediate formation and the protein functioning in the ToMO system, is advanced. Appendix B. Multiple Roles of Component Proteins in Bacterial Multicomponent Monooxygenases: Phenol Hydroxylase and Toluene/o-Xylene Monooxygenase from Pseudomonas sp. OX1. Phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) from Pseudomonas sp. OXI require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. In this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate consumption and product generation. Single-turnover experiments revealed that only complete systems containing all three or four protein components are capable of oxidizing phenol, a major substrate for both enzymes. Under ideal conditions, the hydroxylated product yield was -50% of the diiron centers for both systems, suggesting that these enzymes operate by half-sites reactivity mechanisms. Single-turnover studies indicated that the PH and ToMO electron-transfer components exert regulatory effects on substrate oxidation processes taking place at the hydroxylase active sites, most likely through allostery. Steady state NADH consumption assays showed that the regulatory proteins facilitate the electron-transfer step in the hydrocarbon oxidation cycle in the absence of phenol. Under these conditions, electron consumption is coupled to H20 2 formation in a hydroxylase-dependent manner. Mechanistic implications of these results are discussed.by Woon Ju Song.Ph.D

Trichilemmal Carcinoma of the Upper Eyelid: A Case Report

We report a very rare case of trichilemmal carcinoma (TLC) involving the upper eyelid. To the best of our knowledge, this is the first report of trichilemmal carcinoma of the upper eyelid in Korea. A 51-year-old man presented to our hospital complaining of a bloody discharge from his left upper eyelid. He had a soft and lobulated mass on the palpebral conjunctiva. An incisional biopsy revealed trabecular growth of tumor cells with clear cytoplasm, prominent nucleoli, frequent mitoses, and foci of trichilemmal keratinization. Immunohistochemically, the lesion was positive for p53 and negative for CD 34. A diagnosis of TLC was made, and total excision of the mass and reconstruction of the eyelid were performed. Trichilemmal carcinoma is a rare malignant tumor, though it appears to be an indolent neoplasm with no metastatic potential. The treatment of choice for trichilemmal carcinoma of the eyelid is complete excision with tumor-free margins due to the locally invasive nature of the lesion

Combined effects of aerobic exercise and 40-Hz light flicker exposure on early cognitive impairments in Alzheimer’s disease of 3×Tg mice

Alzheimer’s disease (AD) is a progressive degenerative brain disease and the primary cause of dementia. At an early stage, AD is generally characterized by short-term memory impairment, owing to dysfunctions of the cortex and hippocampus. We previously reported that a combination of exercise and 40-Hz light flickering can protect against AD-related neuroinflammation, gamma oscillations, reduction in Aβ, and cognitive decline. Therefore, we sought to extend our previous findings to the 5-mo-old 3×Tg-AD mouse model to examine whether the same favorable effects occur in earlier stages of cognitive dysfunction. We investigated the effects of 12 wk of exercise combined with 40-Hz light flickering on cognitive function by analyzing neuroinflammation, mitochondrial function, and neuroplasticity in the hippocampus in a 3×Tg-AD mouse model. Five-month-old 3×Tg-AD mice performed 12 wk of exercise with 40-Hz light flickering administered independently and in combination. Spatial learning and memory, long-term memory, hippocampal Aβ, tau, neuroinflammation, proinflammatory cytokine expression, mitochondrial function, and neuroplasticity were analyzed. Aβ and tau proteins levels were significantly reduced in the early stage of AD, resulting in protection against cognitive decline by reducing neuroinflammation and proinflammatory cytokines. Furthermore, mitochondrial function improved, apoptosis was reduced, and synapse-related protein expression increased. Overall, exercise with 40-Hz light flickering was significantly more effective than exercise or 40-Hz light flickering alone, and the improvement was comparable to the levels in the nontransgenic aged-match control group. Our results indicate a synergistic effect of exercise and 40-Hz light flickering on pathological improvements in the hippocampus during early AD-associated cognitive impairment

Microglandular Adenosis

Microglandular adenosis (MGA) of the breast is a very rare and benign proliferative lesion. Most patients complain of a palpable breast mass that may arouse a clinical suspicion of breast cancer. Histopathologically, it is hard to distinguish MGA from breast cancer because of the lack of a myoepithelial layer and infiltrative proliferation. Several studies have reported a strong relationship between MGA and carcinoma arising in MGA, so the mass should be excised completely in cases of MGA determined from a core needle biopsy rather than observation. A 72-years-old woman presented with a palpable breast mass. On physical examination, a mass was palpable in the right upper outer quadrant area and somewhat fixed to the surrounding tissues and pectoralis major muscle. We could not detect any mass or dense lesion on mammography because of a grade 4 dense breast. Ultrasonographic findings revealed a low echoic lesion with indistinct margins. The result of a core needle biopsy was MGA, which was confirmed by excision. We report one case of MGA, which was believed to breast cancer clinically

Sirolimus- Versus Paclitaxel-Eluting Stents for the Treatment of Coronary Bifurcations Results From the COBIS (Coronary Bifurcation Stenting) Registry

ObjectivesWe aimed to compare the long-term clinical outcomes of patients treated with sirolimus-eluting stents (SES) or paclitaxel-eluting stents (PES) for coronary bifurcation lesions.BackgroundThere are limited data regarding comparisons of SES and PES for the treatment of bifurcation lesions.MethodsPatients who received percutaneous coronary intervention for non-left main bifurcation lesions were enrolled from 16 centers in Korea between January 2004 and June 2006. We compared major adverse cardiac events (MACE [cardiac death, myocardial infarction, or target lesion revascularization]) between the SES and PES groups in patients overall and in 407 patient pairs generated by propensity-score matching.ResultsWe evaluated 1,033 patients with bifurcation lesions treated with SES and 562 patients treated with PES. The median follow-up duration was 22 months. Treatment with SES was associated with a lower incidence of MACE (hazard ratio [HR]: 0.53, 95% confidence interval [CI]: 0.32 to 0.89, p < 0.01) and target lesion revascularization (HR: 0.55, 95% CI: 0.31 to 0.97, p = 0.02), but not of cardiac death (HR: 2.77, 95% CI: 0.40 to 18.99, p = 0.62) and cardiac death or myocardial infarction (HR: 0.97, 95% CI: 0.38 to 2.49, p = 0.94). After propensity-score matching, patients with SES still had fewer MACE and target lesion revascularization incidences than did patients with PES (HR: 0.52, 95% CI: 0.30 to 0.91, p = 0.02, and HR: 0.48, 95% CI: 0.25 to 0.91, p = 0.02, respectively). There was no significant difference in the occurrences of stent thrombosis between the groups (0.7% vs. 0.7%, p = 0.94).ConclusionsIn patients with bifurcation lesions, the use of SES resulted in better long-term outcomes than did the use of PES, primarily by decreasing the rate of repeat revascularization. (Coronary Bifurcation Stenting Registry in South Korea [COBIS]; NCT00851526

Physiological impact of nanoporous acupuncture needles: Laser Doppler perfusion imaging in healthy volunteers

Background Recently, porous acupuncture (PA), which is anodized to increase its surface area for higher stimulation intensity, was developed and showed significantly improved therapeutic effects with more comfort as compared with original acupuncture (OA) in vivo. However, the impact of PA on the change of local blood flow as well as its efficacy and acceptability has not yet been confirmed in a clinical trial. In a randomized, controlled crossover clinical trial, we investigated the effects of PA on the change in local blood flow using laser Doppler perfusion imaging and considered the sensation of pain intensity and discomfort severity using a visual analogue scale (VAS) to explore its physiological impact and the possibility of PA in clinical use. Methods Twenty-one healthy participants were randomly treated with PA or OA on one side of Zusanli (ST36) and each participant served as his or her own control. Baseline local blood flow and galvanic skin response (GSR) were obtained for 5 min and acupuncture interventions were subsequently performed. Next, local blood flow and GSR were subsequently obtained for 10 min after insertion, 10 min after manipulation, and 5 min after the withdrawal of acupuncture. At the end of the experiment, participants were asked to indicate the sensation of pain intensity at each session of insertion, retention, manipulation, and withdrawal as well as the overall pain intensity and discomfort severity. Results PA significantly increased the local blood flow as compared with OA and there was no significant difference in GSR between patients treated with PA versus OA in each phase of insertion and manipulation. No significant difference in pain intensity or discomfort severity was found during manipulation, retention, or withdrawal of acupuncture. Conclusions These results indicate that PA increases local blood flow, which can be closely related to the observed enhanced performance, without any associated discomfort or pain, suggesting its applicability in clinical practice. © 2019 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.1

Exendin-4 Protects Oxidative Stress-Induced β-Cell Apoptosis through Reduced JNK and GSK3β Activity

Oxidative stress induced by chronic hyperglycemia in type 2 diabetes plays a crucial role in progressive loss of β-cell mass through β-cell apoptosis. Glucagon like peptide-1 (GLP-1) has effects on preservation of β-cell mass and its insulin secretory function. GLP-1 possibly increases islet cell mass through stimulated proliferation from β-cell and differentiation to β-cell from progenitor cells. Also, it probably has an antiapoptotic effect on β-cell, but detailed mechanisms are not proven. Therefore, we examined the protective mechanism of GLP-1 in β-cell after induction of oxidative stress. The cell apoptosis decreased to ~50% when cells were treated with 100 µM H2O2 for up to 2 hr. After pretreatment of Ex-4, GLP-1 receptor agonist, flow cytometric analysis shows 41.7% reduction of β-cell apoptosis. This data suggested that pretreatment of Ex-4 protect from oxidative stress-induced apoptosis. Also, Ex-4 treatment decreased GSK3β activation, JNK phosphorylation and caspase-9, -3 activation and recovered the expression of insulin2 mRNA in β-cell lines and secretion of insulin in human islet. These results suggest that Ex-4 may protect β-cell apoptosis by blocking the JNK and GSK3β mediated apoptotic pathway

Clinical Benefit of Low Molecular Weight Heparin for ST-segment Elevation Myocardial Infarction Patients Undergoing Primary Percutaneous Coronary Intervention with Glycoprotein IIb/IIIa Inhibitor

The efficacy of low molecular weight heparin (LMWH) with low dose unfractionated heparin (UFH) during percutaneous coronary intervention (PCI) with or without glycoprotein (Gp) IIb/IIIa inhibitor compared to UFH with or without Gp IIb/IIIa inhibitor has not been elucidated. Between October 2005 and July 2007, 2,535 patients with ST elevation acute myocardial infarction (STEMI) undergoing PCI in the Korean Acute Myocardial Infarction Registry (KAMIR) were assigned to either of two groups: a group with Gp IIb/IIIa inhibitor (n=476) or a group without Gp IIb/IIIa inhibitor (n=2,059). These groups were further subdivided according to the use of LMWH with low dose UFH (n=219) or UFH alone (n=257). The primary end points were cardiac death or myocardial infarction during the 30 days after the registration. The primary end point occurred in 4.1% (9/219) of patients managed with LMWH during PCI and Gp IIb/IIIa inhibitor and 10.8% (28/257) of patients managed with UFH and Gp IIb/IIIa inhibitor (odds ratio [OR], 0.290; 95% confidence interval [CI], 0.132-0.634; P=0.006). Thrombolysis In Myocardial Infarction (TIMI) with major bleeding was observed in LMHW and UFH with Gp IIb/IIIa inhibitor (1/219 [0.5%] vs 1/257 [0.4%], P=1.00). For patients with STEMI managed with a primary PCI and Gp IIb/IIIa inhibitor, LMWH is more beneficial than UFH