Massachusetts Institute of Technology. Dept. of Chemistry. Thesis. 1968. Ph.D. / Vita. / Bibliography: leaves 111-113. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. / Includes bibliographical references (leaf 26). / In this study, thermodynamic integration and molecular dynamics methods were used to elucidate the factors affecting stabilities of collagen-like peptides. We proposed to investigate three specific aspects: (1) the stabilizing effect of hydroxyproline (Hyp), (2) the destabilizing effect of replacing Gly, and (3) the role of water mediated hydrogen bonds. A better understanding of the origins of the stabilities of collagens will help in the design of new biomaterials and the treatment of collagen-related diseases. / by Nai-yuan Chang. / S.M.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references (p. 40-41). / by Dean Philipp. / M.S.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. / Vita. / Includes bibliographical references. / Natural products are a rich source of medicinally important molecules. Monoterpene indole alkaloids from plants are an especially important source of therapeutic molecules. Due to the complexity of these molecules, biosynthesis of derivatives is an attractive way of obtaining molecules with potentially new or improved functionality. The rational design of mutants with altered/expanded substrate scope is an important step in engineering organisms to produce such compounds. In monoterpene indole alkaloid biosynthesis, the enzyme strictosidine synthase catalyzes the first committed reaction. This reaction is a Pictet-Spengler coupling between tryptamine and secologanin and produces the biosynthetic intermediate strictosidine, common to all monoterpene indole alkaloids. To better understand the structural features that impart binding selectivity, crystallization studies of this enzyme were performed. The native enzyme and several interesting mutants were studied; co-crystallization experiments with inhibitors and substrates were also performed. Diffraction quality crystals of the native enzyme were obtained following optimization by grid screening, additive screens, and macroseeding. Data on the optimized crystals was collected at the Argonne National Labs synchrotron radiation source. In addition to monoterpene indole alkaloids, the benzylisoquinoline alkaloids are another class of medicinally important plant derived natural products. In a reaction analogous to that catalyzed by strictosidine synthase, the first committed step of benzylisoquinoline biosynthesis is a Pictet-Spengler reaction between 4-hydroxyphenylactetaldehyde and dopamine, catalyzed by the enzyme norcoclaurine synthase. Two different forms of this enzyme have been identified, neither of which shows any homology to strictosidine synthase. / (cont.) Structural information for these enzymes could provide general structural features required for enzymatic Pictet-Spengler reactions. Before crystallization, the enzymes were expressed and tested for activity. Once active preparations of protein were available, crystallization studies were performed and crystals were obtained. / by William C. Hillmann. / S.M.

Thesis (Ph.D.) Massachusetts Institute of Technology. Dept. of Chemistry, 1949. / Vita. / Bibliography: leaves 74-75. / by Telford Grant Maple. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1994. / Includes bibliographical references (leaves 102-112). / by Ellen R. Goldman. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. / Vita. / Includes bibliographical references. / Chapter 1: The Importance of Modeling Diiron Sites in Nature.There are a variety of metalloenzymes that have nearly identical carboxylate-bridged diiron active sites. An example is sMMOH, an enzyme that catalyzes the conversion of methane to methanol. A detailed description of the active site of sMMOH[red] is given and attempts at reproducing its structure in a model complex are discussed. Chapter 2: A Diiron(II) Diaqua Complex: Modeling Water in the Active Site of sMMOH[red]. There are water molecules in the first and second coordination spheres of the diiron centers in sMMOH[red]. A carboxylate-bridged diferrous complex, [Fe₂...(THF)₂], was synthesized to incorporate the presence of water in a model complex and to investigate the function(s) of these water molecules. The synthesis, structural characterization and magnetic properties of this complex are presented. Chapter 3: Ligands for Modeling the Syn Disposition of Nitrogen Atoms in the Active Site of MMOH. The active sites of a variety of carboxylate-bridged diiron metalloenzymes are very similar and feature the syn disposition of two histidine ligands with respect to the iron-iron vector. This orientation has not yet been modeled in a diiron complex with four carboxylate ligands and a stable yet flexible platform. Such geometry may be necessary to replicate the functions of these enzymes. The syntheses of ligands intended to enforce this syn disposition are described and directions for future ligand design are outlined. / by Amy E. Kelly. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Includes bibliographical references. / Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides. Saccharomyces cerevisiae RNR is a class I RNR composed of a dimeric large subunit (RI), containing the active site and allosteric effector sites, and a dimeric small subunit (R2) which houses the diferric tyrosyl radical (Y.) cofactor required for RNR activity. S. cerevisiae has two Rl-like proteins, Y1 and Y3 and two R2-like proteins, Y2 and Y4. In vitro studies have focused on defining the active form of the R2 subunit. As isolated, Y2 and Y4 are homodimers and neither can bind iron to generate the ... cofactor. When mixed, the Y2 and Y4 homodimers rapidly form a heterodimer that can be activated with iron to form the ... cofactor located in the Y2 subunit. While the apo-Y2Y4 protein is capable of undergoing slow exchange of its protomers, loading of iron into the heterodimer prevents this slow reorganization. To define the role of Y4 in vivo, the concentrations of Y2 and ... in the wt and Y4 deletion strain have been determined. Thought deletion of Y4 leads to a >15 fold increase in the concentration of Y2, the concentration of ... is at least 15 fold less than the amount observed in the wt yeast strain. We have concluded form this work and from our work in collaboration with Prof. Amy Rosenzweig's laboratory in which the structures of Y2, Y4 and the heterodimer were determined that Y4 plays an important role in assembly of the diiron cofactor in Y2 through stabilization of a local conformation of Y2 allowing for iron binding and that the active form of yeast R2 is a Y2Y4 heterodimer. These conclusions are supported by in vivo experiments. / (cont.) Using a yeast strain containing an N-terminally tagged Y2 under control of the native promoter, a soluble, active Y2Y4 heterodimer is isolated. This heterodimer contains 0.45±0.08 ..., 1.45±0.05 irons and a specific activity of 2.3±0..5 !Rmolmin' -mg'l. Wt and several deletion strains, including Smll[delta], Rnrl[delta], Rnr4[delta], and Crt 1[delta] strains, have been characterized by Western blotting to quantitate the concentrations of the RNR subunits, by EPR spectroscopy to quantitate the concentration of ... cofactor in vivo and by activity assays with yeast extracts to measure the total amount of RNR activity. These results demonstrate that in vivo every Y2Y4 heterodimer has a diferric-... cofactor and that the activity of Y1 limits RNR activity in vivo. Furthermore, the information acquired has allowed us better understanding how the protein concentration, cofactor generation and subunit localization regulate RNR activity in vivo. / by Deborah Leigh Perlstein. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1997. / Includes bibliographical references (leaves 89-100). / by Kenneth Moore, Jr. / M.S.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrophobic polycations have been shown to completely kill bacterial, fungal, and viral pathogens, on-contact. Herein we describe advances with this technology on two fronts: (1) innovation of a polycationic-derivative that simplifies the labor-intensive covalent-immobilization procedure, and (2) elucidation of the current mechanistic understanding of this phenomenon. First, we developed and characterized a novel polycationic polymer capable of crosslinking to cotton via activation with ultraviolet light. The resultant, covalently-immobilized, Nalkyl polyethylenimine (PEI) demonstrates complete bactericidal activity against S. aureus and E. coli (i.e., representative Gram-positive and Gram-negative bacteria, respectively). In addition, by utilizing light to activate the covalent cross-linking, this immobilization procedure is simpler and more versatile than similar chemically-attached bactericidal polycations. Second, we shed light onto how the coating inactivates microbial pathogens. Gramnegative and Gram-positive bacteria exposed to the polycationic coating revealed substantial structural deformation, which allowed for the leakage of their intracellular contents. Characterization of the enzymes leaked into solution from Gram-negative bacteria indicated a disproportionately greater damage done to the outer-membrane than the inner-membrane. In addition, the quantity of proteins leaked into solution showed striking similarity to results obtained from bacteria subjected to lysozyme/EDTA treatment (i.e., a traditional cell lysis technique that degrades the cellular wall). In total, these results suggest that it is this interaction between the polycation and cellular structure (i.e., outer membrane and cell wall) that ultimately compromises bacterial integrity. Expanding our investigation, we studied the effect of the polycationic coating on another membrane-enclosed microbe: the influenza virus. We found that the viral particles adhere to the polycationic coating, which results in a structural deformation, similar to that borne-out by bacteria. As a consequence, viral genomic material is leaked into solution, revealing the viruses' state of inactivation upon adherence to the coating. / by Bryan Boen Hsu. / S.M.