Although the native environment of the vast majority of proteins is a complex aqueous solution, like the interior of a cell, many analysis methods for assessing chemical and physical properties of biomolecules require the sample to be aerosolized; that is, transferred to the gas-phase. An important example is electrospray-ionization mass spectrometry, which can provide a wide range of information about e.g. biomolecules. That includes structural features, charged sites, and gas-phase equilibrium constants of reactions. To date much of the microscopic detail about the aerosolization process remains beyond the limits of experimental observation. How is the gas-phase structure of a protein related to the solution-phase structure? How transferable are observations done in the gas phase to solution? On the basis of classical molecular-dynamics simulations this thesis reveals important features of gas-phase biomolecular structure near the end of the the aerosolization process, the relation between gas-phase structure and native structure, microscopic detail about the de-wetting of gas-phase biomolecules, and the impact of temperature and residual solvent on structure preservation. Residual solvent on proteins is shown to have a stabilizing effect on proteins, in part because it allows the scarcely hydrated protein to cool through solvent evaporation, but also because part of the solvent provides structural support by hydrogen bonding to the protein. The gas-phase structure of micellar aggregates is seen to depend on composition, where some types of lipids cause rapid micelle inversion, whereas others maintain much of their collective structure when transferred to the gas phase. The thesis also addresses proton-transfer reactions, which have an impact on the biophysical aspects of proteins, both in the gas phase and in solution. The thesis presents a computationally efficient method for including proton-transfer reactions in classical molecular-dynamics simulations, which expands the range of scientific problems that can be addressed with molecular dynamics.

Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Bridgette Barry; Committee Member: El-Sayed, Mostafa; Committee Member: Fahrni, Christoph; Committee Member: Kröger, Nils; Committee Member: McCarty, Nael. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Abstract Enzymes catalyze chemical changes in biological systems. Therefore, to understand the chemistry of living systems, it is important to understand the enzyme structure and the chemistry of the enzyme's functional groups which are involved in catalysis. In this study, structure and function relationships of two enzymes, (1) α-methylacyl-CoA racemase from Mycobacterium tuberculosis (MCR) and (2) argininosuccinate lyase from Escherichia coli (eASL) have been studied using X-ray crystallography. The main focus of this study has been understanding the structure-function relationship of MCR. The eASL has been crystallized from a highly concentrated sample of purified recombinant α-methylacyl-CoA racemase in which it occurred as a minor impurity. The structure of eASL has been solved using molecular replacement at 2.44 Å resolution. The enzyme is a tetramer, but in this crystal form there is a dimer in the asymmetric unit. Each active site is constructed from loops of three different subunits. One of these catalytic loops, near residue Ser277 and Ser278, has been disordered in the previous structures of active lyases, but is very well ordered in this structure in one of the subunits due to the presence of two phosphate ions in the respective active site cavity. The positions of these phosphate ions indicate a plausible mode of binding of the succinate moiety of the substrate in the competent catalytic complex and therefore this structure has provided new information on the reaction mechanism of this class of enzymes. α-Methylacyl-CoA racemase (Amacr) catalyzes the racemization of α-methyl-branched CoA esters. An Amacr homologue from the eubacteria Mycobacterium tuberculosis, referred to as MCR, was taken as a model protein. MCR was purified, crystallized and the structure of unliganded protein was determined at 1.8 Å resolution using the MIRAS procedure. The structure shows that the enzyme is an interlocked dimer. To understand the reaction mechanism and the mode of substrate binding, several crystallographic binding studies were done using both wild type MCR and mutant H126A MCR crystals. In particular, the structures of the wild type MCR-complexes with (R, S)-ibuprofenoyl-CoA (1.85 Å), (R)-2-methylmyristoyl-CoA (1.6 Å) and (S)-2-methylmyristoyl-CoA (1.7 Å) were important in this respect. These crystal structures show that Asp156 and His126 are the two catalytic residues which are involved in proton donation and abstraction, respectively; when the (S)-enantiomeric substrate is bound in the active site and vice versa when the (R)-enantiomeric substrate is bound. The tight geometry of the active site also shows that His126 and Asp156 are involved in stabilizing the transition state. These crystal structures show that in the active site of MCR, there is one binding pocket for the CoA part and there are two different binding pockets (R-pocket and S-pocket) connected by a hydrophobic methionine rich surface for binding the fatty acyl part of the substrate. After substrate binding, proton abstraction takes place which produces a planar intermediate. Then, donation of a proton to the other side of the planar intermediate changes the configuration at the chiral center. During the stereochemical interconversion of the two enantiomers, the acyl group moves between R-pocket and S-pocket by sliding over the hydrophobic surface connecting these two pockets.

In part 1 of this thesis, the antidiabetic activity of a series of novel oxovanadium(IV) complexes was investigated. A range of bidentate N,O-donor ligands, which partially mimic naturally occurring bioligands, were prepared and reacted with the vanadyl ion to form the corresponding bis-coordinated complexes. Initially, 2-(2ˊ-hydroxyphenyl)-1R-imidazoline (where R = H, ethyl and ethanol) ligands were prepared. The aqueous pH-metric chemical speciation was investigated using glass electrode potentiometry which allowed for the determination of protonation and stability constants of the ligands and complexes, respectively. The species distribution diagrams generated from this information gave an indication of how the complexes might behave across the broad pH range experienced in the digestive and circulatory systems. This information was used to create an improved 2nd generation of ligands that were constructed by combining the imidazole and carboxylic acid functionalities. These corresponding bis[(imidazolyl)carboxylato]-oxovanadium(IV) complexes displayed a broader pH-metric stability. Both sets of complexes improved glucose uptake and reduced coagulation in vitro. In part 2 of this thesis, a range of homogeneous and heterogeneous oxovanadium(IV) catalysts were prepared. Firstly, Merrifield beads were functionalized with ligands from Part 1 and then reacted with vanadyl sulfate to afford the corresponding heterogeneous catalysts. These displayed promising catalytic activity for the peroxide facilitated oxidation of thioanisole, styrene and ethylbenzene as well as the oxidative bromination of phenol red. Smaller imidazole-containing beads with higher surface areas than the Merrifield beads were prepared by suspension polymerization. These beads similarly demonstrated excellent catalytic activity for the oxidation of thioanisole and were highly recyclable. In attempt to increase the exposed catalytic surface area, while retaining the ease of separation achieved in the before mentioned systems, micron to nano sized electrospun fibers containing coordinating ligands were fabricated. The corresponding oxovanadium(IV) functionalized fibers were applied to the oxidation of thioanisole using a continuous flow system. The flexible and porous nature of the fiber mats was well suited to this approach. After optimization of the reactant flow rate and catalyst amount, near quantitative (> 99%) oxidation was achieved for an extended period. In addition, leaching of vanadium was mitigated by modification of the attached ligand or polymer material.

Electrospray ionization mass spectrometry (ESIMS) is widely used to characterize neutral and ionic species in solvents. Typically, electrical, thermal, and pneumatic potentials are applied to create electrosprays from which charged ionic species are ejected for downstream analysis by mass spectrometry. Most recently, ESIMS has been exploited to investigate ambient proton transfer reactions at air-water interfaces in real time. We assessed the validity of these experiments via complementary laboratory experiments. Specifically, we characterized the products of two reaction scenarios via ESIMS and proton nuclear magnetic resonance (1H-NMR): (i) emulsions of pH-adjusted water and isoprene (C5H8) that were mechanically agitated, and (ii) electrosprays of pH-adjusted water that were collided with gas-phase isoprene. Our experiments unambiguously demonstrate that, while isoprene does not oligomerize in emulsions, it does undergo protonation and oligomerization in electrosprays, both with and without pH-adjusted water, confirming that C-C bonds form along myriad high-energy pathways during electrospray ionization. We also compared our experimental results with some quantum mechanics simulations of isoprene molecules interacting with hydronium at different hydration levels (gas versus liquid phase). In agreement with our experiments, the kinetic barriers to protonation and oligomerization of isoprene were inaccessible under ambient conditions. Rather, the gas-phase chemistries during electrospray ionization drove the oligomerization of isoprene. Therefore, we consider that ESIMS could induce artifacts in interfacial reactions. These findings warrant a reassessment of previous reports on tracking chemistries under ambient conditions at liquid-vapor interfaces via ESIMS. Further, we took some high-speed images of electrosprays where it was possible to observe the main characteristics of the phenomena, i.e. Taylor cone, charge separation, and Coulomb fission. Finally, we took the freedom to speculate on possible mechanisms that take place during electrospray ionization that affected our system and possibly may influence other common analytical techniques on ESIMS.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23160号 / 工博第4804号 / 新制||工||1751(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 関 修平, 教授 今堀 博, 教授 梶 弘典 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

In the present work, the abnormal glow discharge at atmospheric pressure was generated in the nitrogen-methane (1 to 5 %) gaseous mixtures related to the atmosphere of Titan. The discharge itself was monitored by optical emission spectrometry that confirmed presence of active nitrogen species and various radicals formed from methane. Besides them, the CN spectral bands were observed. Intensities of all light emitting species were studied in the dependence on applied power and composition of nitrogen-methane mixture. The rotational temperature of about 2000 K was calculated from the second positive nitrogen system. The vibrational temperature also obtained from neutral nitrogen molecule increased nearly directly with methane from 3000 K (1 % CH4) to 3600 K (5 % CH4). In the contrary, vibrational temperature obtained from nitrogen molecular ion decreased with methane in the gaseous mixture and increased with applied discharge power from 3700 K to 4200 K. The same trend showed the vibrational temperature calculated from violet system of CN with value from 4600 K to 5800 K. The stable discharge products were analysed by proton transfer time of flight mass spectrometry of the exhausting gas. Presence of many aliphatic and some aromatic hydrocarbons was confirmed as well as quite a lot of amino and cyano compounds. Increasing concentrations of methane have produced more substances with higher molecular weight and less simple substances that were likely to be consumed on more complex substances. Their relative intensities were determined under the same conditions as optical emission spectra were collected.

6-Chloronicotinic acid was coupled by an amide linkage to Merrifield resin or Jeffamine gel. Nucleophilic displacement of the 6-chloride group by hydroxide gave novel Merrifield resin catalyst 6 or Jeffamine gel catalyst 9 that were successfully used for Henry condensations. The condensation of 4,6-O-benzylidene-β-D-glucopyranose 11 with nitromethane gave 4,6-O-benzylidene-D-glucopyranosyl-l-nitromethane 12; the condensation of 11 with nitroethane gave α-R-(4,6-O-benzylidene-β-D-glucopyranosyl)-1-nitroethane 13 and its diastereomer 15; the condensation of 11 with nitropropane, followed by acetylation, gave α-R-(2,3-di-O-acetyl-4,6-O-benzylidene-β- D-glucopyranosyl)-1 -nitropropane 16 and its diastereomer 17; the condensation of 4,6- O-isopropylidene-β-D-glucopyranose 19 with nitromethane gave 4,6-O-isopropylidene- β-D-glucopyranosyl-1-nitromethane 20; the condensation of 4,6-O-isopropylidene-α- D-mannopyranose 21 with nitromethane gave 4,6-O-isopropylidene-β-D-mannopyranosyl- 1-nitromethane 23. These known compounds were obtained with improved yields compared to protocols with 1,3 proton transfer catalysts that were not bound to polymers. A new monomeric 1,3 proton transfer catalyst, 2,4 (1,3)-quinazolinedione 10, was also introduced.

Final publication is available at http://link.springer.com/article/10.1007/s11060-014-1715-8 / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19605号 / 医博第4112号 / 新制||医||1014(附属図書館) / 32641 / 京都大学大学院医学研究科医学専攻 / (主査)教授 村井 俊哉, 教授 平岡 眞寛, 教授 山田 泰広 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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