Iron Nitrosyl Complexes

Nitric oxide (NO) is an endogenously produced bioregulatory agent that also is toxic. Disturbances in NO production and regulation are known to cause central nervous system disorders and asthma among many other diseases. Iron nitrosyl complexes help to balance the beneficial effects of NO against its potentially fatal effects. This document reviews the literature devoted to structural and chemical characteristics of iron nitrosyl porphyrin complexes, bimetallic iron containing nitrosyl complexes, dinitrosyl complexes, iron nitrosyl cluster complexes, and non-heme nitrosyl complexes prepared between 1992 and 2002

Copper active sites in biology

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Transient protein interactions: the case of pseudoazurin and nitrite reductase

Nuclear Magnetic Resonance study of the structural and dynamic characteristics of the transient complex between pseudoazurin and nitrite reductase.UBL - phd migration 201

Investigating Electrostatics and Dynamics in Confinement and Constructs Using Two-Dimensional Infrared Spectroscopy and Molecular Simulations.

Understanding the ultrafast dynamics of enzymes is required to fully explain what makes them such efficient catalysts. Two-dimensional infrared (2D-IR) spectroscopy along with molecular modeling helps provide a more complete description of the environment of enzyme active sites and other related systems. A carbonyl-labeled copper site in a de novo peptide exhibits vibrationally driven nonequilibrium dynamics when characterized using 2D-IR spectroscopy. The source of the dynamics is found to be the coupling of the CO stretching mode to the CuCO bending mode, enhanced by distortions to the histidine side chains binding the copper. QM/MM calculations show the source of the distortions to be primarily from electrostatic interactions with the peptide. Using similar calculations, but with a refined sampling of starting structures, other de novo peptides are modeled to identify a candidate that will show different nonequilibrium dynamics from the original metalloenzyme. The selected enzyme is more catalytically active, and calculations predict a smaller coupling between the CO stretching and CuCO bending modes. This prediction is confirmed using 2D-IR, where the nonequilibrium dynamics have a smaller amplitude, but occur on the same time scale. Several thiocyanate salts in the Hofmeister series are studied in neat D2O and with alpha-cyclodextrin (a-CD). In neat D2O, 2D-IR shows slightly faster spectral diffusion for kosmotropes and slower spectral diffusion for chaotropes. When a-CD is introduced to the system, an additional slowly decaying component of the FFCF is found. The presence of the slower dynamics indicates the nitrogen in thiocyanate is not solvent exposed, but embedded in the interior of the a-CD. A combination of 2D-IR and molecular modeling was also needed to characterize the structure of a labeled crown either with a nearby sodium thiocyanate contact ion pair. The spectral diffusion of the metal carbonyl label shows dynamics occurring on a slower time scale than the vibrational lifetime of the probe. DFT calculations show that two different conformations of the thiocyanate ion around the crown ether have similar energies, but produce different CO frequencies. The time to sample these states is longer than the vibrational lifetime of the metal carbonyl.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120712/1/amwhi_1.pd

Structure based reaction mechanism studies on periplasmic nitrate reductase

The Periplasmic Nitrate Reductase (Nap) from Cupriavidus necator (Cn) belongs to the Dimethyl Sulfoxide (DMSO) Reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit containing the Mo active site and one [4Fe-4S] cluster (NapA, 91kDa), and a small diheme c-type cytochrome subunit (NapB, 17kDa). In the present dissertation, the reaction mechanism of the Periplasmic Nitrate Reductase from Cupriavidus necator is studied by X-Ray Crystallography and complementary techniques like Thermal Shift Assays (TSA), Isothermal Titration Calorimetry (ITC) and Microscale Thermophoresis (MST). In the first crystallographic studies of Nap from Desulfovibrio desulfuricans (Dd), it was established that in the active site, the Mo atom was coordinated by two cis-dithioline groups, a sulfur from a cysteine side chain and a water/hydroxo ligand. Recently published crystal structures of Nap, particularly the structure of the heterodimeric Cn NapAB solved at high resolution (1.5 Å) and Dd NapA with bound ligands demonstrated that the sixth ligand is in fact a sulfur atom, contrary to the previous believed water/hydroxo ligand. Also, a partially reduced NapAB Cn crystal structure was obtained, where the coordinating Mo Cys thiolate is partially occupying a new conformation. The sixth sulfur ligand seems to have a partial disulfide bond with the Cys thiolate group, blocking nitrate from interacting directly with the Mo atom unless some rearrangement occurs during catalysis. Various crystal structures of NapAB from Cn co-crystallized with ligands are presented in this dissertation complemented by TSA, ITC and MST results. The results corroborate the existence of an alternate conformation of the coordinating Mo Cys thiolate and pave the way for more studies about the reaction mechanism of nitrate reductases