Unnatural amino acids in the synthesis and semisynthesis of metalloprotein motifs

The design, synthesis, and characterization of two novel metalloprotein motifs is presented. The first project involved the design and construction of a protein motif which was programmed to form a tetradentate metal complex upon the addition of metal cations. The overall structure of the motif was based on a ββ super-secondary structure consisting of a flexible peptide sequence flanked by metal binding regions located at the carboxy and amino termini. The metal binding region near the amino terminus was constructed from a reverse turn motif with two metal ligating residues, (2R, 3R)-β-methyl-cysteine and histidine. Selection of the peptide sequence for this region was based on the conformational analysis of a series of tetrapeptides designed to form reverse turns in solution.

The stereospecific syntheses of a series of novel bipyridyl- and phenanthrolylsubstituted amino acids was carried out to provide ligands for the carboxy terminus metal binding region. These residues were incorporated into peptide sequences using solid phase peptide synthesis protocols, and metal binding studies indicated that the metal binding properties of these ligands was dictated by the specific regioisomer of the heteroaromatic ring and the peptide primary sequence.

Finally, a peptide containing optimized components for the metal binding regions was prepared to test the ability of the compound to form the desired intramolecular peptide:metal cation complexes. Metal binding studies demonstrated that the peptide formed monomeric complexes with very high metal cation binding affinities and that the two metal binding regions act cooperatively in the metal binding process. The use of these systems in the design of proteins capable of regulating naturally occurring proteins is discussed.

The second project involved the semisynthesis of two horse heart cytochrome c mutants incorporating the bipyridyl-amino acids at position 72 of the protein sequence. Structural studies on the proteins indicated that the bipyridyl amino acids had a neglible effect on the protein structure. One of the mutants was modified with Ru(bpy)_2^(+2) to form a redox-active protein, and the modified protein was found to have enhanced electron transfer properties between the heme and the introduced metal site.

Hatchery construction and its feasibility in the Nigerian economy

Aquaculture drive in the Niger Delta has necessitated the springing up of various forms of hatcheries in Nigeria in the area. The hatchery level is high as most fish farmers now want to produce their own fingerlings for the stocking of their production ponds for culture to market (table) size. The paper shows that there is a lot of market in the Niger-Delta for fresh fish. Majority of the numerous fish farmers are not well empowered to breed and produce fish seeds especially species most loved and eaten. The rising cost of materials in the Nigerian economy has become a bottleneck in the construction of more fish hatcheries for fingerling production. However, the assistance of multinationals has become very necessary to enhance its feasibility to encourage better involvement in the fish hatchery works. One remarkable area where assistance is being felt by the communities in the Niger-Delta is in fish farming and more so in the supply of fish fingerling to top fish farmers by The Shell Petroleum Development Company of Nigeria Limited (SPDC), a multinational oil company in the area. Few fish farmers have benefited from this. If more hatcheries are available to service and provide the needed fingerlings to stock the available water bodies such as, home backyard ponds, the 0.74 million hectares of brackish water, 1.01 million hectares of perennial swamps, and other marginal land available for aquaculture and properly managed, it will yield between 2.5 and 10 metric tones of fish depending on the species stocked and bred

Beyond the blur: Construction and characterization of the first autonomous AO system and An AO survey of magnetar proper motions

Adaptive optics (AO) corrects distortions created by atmospheric turbulence and delivers diffraction-limited images on ground-based telescopes. The vastly improved spatial resolution and sensitivity has been utilized for studying everything from the magnetic fields of sunspots upto the internal dynamics of high-redshift galaxies. This thesis about AO science from small and large telescopes is divided into two parts: Robo-AO and magnetar kinematics.

In the first part, I discuss the construction and performance of the world’s first fully autonomous visible light AO system, Robo-AO, at the Palomar 60-inch telescope. Robo-AO operates extremely efficiently with an overhead < 50s, typically observing about 22 targets every hour. We have performed large AO programs observing a total of over 7,500 targets since May 2012. In the visible band, the images have a Strehl ratio of about 10% and achieve a contrast of upto 6 magnitudes at a separation of 1′′. The full-width at half maximum achieved is 110–130 milli-arcsecond. I describe how Robo-AO is used to constrain the evolutionary models of low-mass pre-main-sequence stars by measuring resolved spectral energy distributions of stellar multiples in the visible band, more than doubling the current sample. I conclude this part with a discussion of possible future improvements to the Robo-AO system.

In the second part, I describe a study of magnetar kinematics using high-resolution near-infrared (NIR) AO imaging from the 10-meter Keck II telescope. Measuring the proper motions of five magnetars with a precision of upto 0.7 milli-arcsecond/yr, we have more than tripled the previously known sample of magnetar proper motions and proved that magnetar kinematics are equivalent to those of radio pulsars. We conclusively showed that SGR 1900+14 and SGR 1806-20 were ejected from the stellar clusters with which they were traditionally associated. The inferred kinematic ages of these two magnetars are 6±1.8 kyr and 650±300 yr respectively. These ages are a factor of three to four times greater than their respective characteristic ages. The calculated braking index is close to unity as compared to three for the vacuum dipole model and 2.5-2.8 as measured for young pulsars. I conclude this section by describing a search for NIR counterparts of new magnetars and a future promise of polarimetric investigation of a magnetars’ NIR emission mechanism.

Biological electron transfer in copper proteins

Nature has used a variety of protein systems to mediate electron transfer. In this thesis I examine aspects of the control of biological electron transfer by two copper proteins that act as natural electron carriers.

In the first study, I have made a mutation to one of the ligand residues in the azurin blue copper center, methionine 121 changed to a glutamic acid. Studies of intramolecular electron transfer rates from that mutated center to covalently attached ruthenium complexes indicate that the weak axial methionine ligand is important not only for tuning the reduction potential of the blue copper site but also for maintaining the low reorganization energy that is important for fast electron transfer at long distances.

In the second study, I begin to examine the reorganization energy of the purple copper center in the CuA domain of subunit II of cytochrome c oxidase. In this copper center, the unpaired electron is delocalized over the entire binuclear site. Because long-range electron transfer into and out of this center occurs over long distances with very small driving forces, the reorganization energy of the CuA center has been predicted to be extremely low. I describe a strategy for measuring this reorganization energy starting with the construction of a series of mutations introducing surface histidines. These histidines can then be labeled with a series of ruthenium compounds that differ primarily in their reduction potentials. The electron transfer rates to these ruthenium compounds can then be used to determine the reorganization energy of the CuA site.

On the Construction of Higher étale Regulators

We present three approaches to define the higher étale regulator maps Φ^r,n_et : H^r_et(X,Z(n)) → H^r_D(X,Z(n)) for regular arithmetic schemes. The first two approaches construct the maps on the cohomology level, while the third construction provides a morphism of complexes of sheaves on the étale site, along with a technical twist that one needs to replace the Deligne-Beilinson cohomology by the analytic Deligne cohomology inspired by the work of Kerr, Lewis, and Müller-Stach. A vanishing statement of infinite divisible torsions under Φ^r,n_et is established for r > 2n + 1.

Construction of the refractive index profiles for few-mode planar optical waveguides

We present a nondestructive technique to predict the refractive index profiles of isotropic planar waveguides, on which a thin gold film is deposited to as the cladding. The negative dielectric constant of the metal results in significant differences of effective indices between TE and TM modes. The two polarized modes and a surface plasmon resonance (SPR) with abundant information of the surface index can be used to construct the refractive index profiles of single-mode and two-mode waveguides at a fixed wavelength. (c) 2005 Elsevier B.V. All rights reserved.