Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c

Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.

Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.

Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c

A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.

A measurement of the proton elastic form factors for 1 ≤ Q^2 ≤ 3 (GeV/c)^2

We report measurements of the proton form factors, G^p_E and G^p_M, extracted from elastic electron scattering in the range 1 ≤ Q^2 ≤ 3 (GeV/c)^2 with uncertainties of <15% in G^p_E and <3% in G^p_M. The results for G^p_E are somewhat larger than indicated by most theoretical parameterizations. The ratio of Pauli and Dirac form factors, Q^2(F^p_2/F^p_1), is lower in value and demonstrates less Q^2 dependence than these parameterizations have indicated. Comparisons are made to theoretical models, including those based on perturbative QCD, vector-meson dominance, QCD sum rules, and diquark constituents to the proton. A global extraction of the form factors, including previous elastic scattering measurements, is also presented.

Comparative studies of Vulva development in C. briggsae

As evolution progresses, developmental changes occur. Genes lose and gain molecular partners, regulatory sequences, and new functions. As a consequence, tissues evolve alternative methods to develop similar structures, more or less robust. How this occurs is a major question in biology. One method of addressing this question is by examining the developmental and genetic differences between similar species. Several studies of nematodes Pristionchus pacificus and Oscheius CEW1 have revealed various differences in vulval development from the well-studied C. elegans (e.g. gonad induction, competence group specification, and gene function.)

I approached the question of developmental change in a similar manner by using Caenorhabditis briggsae, a close relative of C. elegans. C. briggsae allows the use of transgenic approaches to determine developmental changes between species. We determined subtle changes in the competence group, in 1° cell specification, and vulval lineage.

We also analyzed the let-60 gene in four nematode species. We found conservation in the codon identity and exon-intron boundaries, but lack of an extended 3' untranslated region in Caenorhabditis briggsae.

Synthesis and matrix isolated photolysis of 2,3-dimethylbicyclo [2.2.0]hexa-2,5-diene-1,4-dicarboxylic acid anhydride: a potential percursor to 2,3-dimethyl-1,4-dehydrobenzene

The synthesis of the first member of a new class of Dewar benzenes has been achieved. The synthesis of 2,3- dimethylbicyclo[2.2.0]hexa-2,5-diene-1, 4-dicarboxylic acid and its anhydride are described. Dibromomaleic anhydride and dichloroethylene were found to add efficiently in a photochemical [2+2] cycloaddition to produce 1,2-dibromo- 3,4-dichlorocyclobutane-1,2-dicarboxylic acid. Removal of the bromines with tin/copper couple yielded dichloro- cyclobutenes which added to 2-butyne under photochemical conditions to yield 5,6-dichloro-2,3-dimethylbicyclo [2.2.0] hex-2-ene dicarboxylic acids. One of the three possible isomers yielded a stable anhydride which could be dechlorinated using triphenyltin radicals generated by the photolysis of hexaphenylditin.

Photolysis of argon matrix isolated 2,3-dimethylbicyclo [2.2.0]hexa-2, 5-diene-1,4-dicarboxylic acid anhydride produced traces whose strongest bands in the infrared were at 3350 and 600 cm^(-1). This suggested the formation of terminal acetylenes. The spectra of argon matrix isolated E- and Z- 3,4-dimethylhexa-1,5-diyne-3-ene and cis-and trans-octa- 2,6-diyne-4-ene were compared with the spectrum of the photolysis products. Possibly all four diethynylethylenes were present in the anhydride photolysis products. Gas chromatograph-mass spectral analysis of the volatiles from the anhydride photolysis again suggested, but did not confirm, the presence of the diethynylethylenes.

The streaming of 1.3-2.3 MeV cosmic-ray protons during periods between prompt solar particle events

The anisotropy of 1.3 - 2.3 MeV protons in interplanetary space has been measured using the Caltech Electron/Isotope Spectrometer aboard IMP-7 for 317 6-hour periods from 72/273 to 74/2. Periods dominated by prompt solar particle events are not included. The convective and diffusive anisotropies are determined from the observed anisotropy using concurrent solar wind speed measurements and observed energy spectra. The diffusive flow of particles is found to be typically toward the sun, indicating a positive radial gradient in the particle density. This anisotropy is inconsistent with previously proposed sources of low-energy proton increases seen at 1 AU which involve continual solar acceleration.

The typical properties of this new component of low-energy cosmic rays have been determine d for this period which is near solar minimum. The particles have a median intensity of 0.06 protons/ cm^(2)-sec-sr-MeV and a mean spectral index of -3.15.The amplitude of the diffusive anisotropy is approximately proportional to the solar wind speed. The rate at which particles are diffusing toward the sun is larger than the rate at which the solar wind is convecting the particles away from the sun. The 20 to 1 proton to alpha ratio typical of this new component has been reported by Mewaldt, et al. (1975b).

A propagation model with κ_(rr) assumed independent of radius and energy is used to show that the anisotropy could be due to increases similar to those found by McDonald, et al. (1975) at ~3 AU. The interplanetary Fermi-acceleration model proposed by Fisk (1976) to explain the increases seen near 3 AU is not consistent with the ~12 per cent diffusive anisotropy found.

The dependence of the diffusive anisotropy on various parameters is shown. A strong dependence of the direction of the diffusive anisotropy on the concurrently measured magnetic field direction is found, indicating a κ_⊥ less than κ_∥ to be typical for this large data set.

Excitation energies and decay properties of T = 3/2 states in ^(17)O, ^(17)F and ^(21)Na

The two lowest T = 3/2 levels in ²¹Na have been studied in the ¹⁹F(³He, n), ²⁰Ne (p,p) and ²⁰Ne (p,p’) reactions, and their excitation energies, spins, parities and widths have been determined. In a separate investigation, branching ratios were measured for the isospin-nonconserving particle decays of the lowest T = 3/2 levels in ¹⁷O and ¹⁷F to the ground state and first two excited states of ¹⁶O, by studying the ¹⁵N(³He,n) ¹⁷F*(p) ¹⁶O and ¹⁸O(³He, α)¹⁷O*(n) ¹⁶O reactions.

The ¹⁹F(³He,n) ²¹Na reaction was studied at incident energies between 4.2 and 5.9 MeV using a pulsed-beam neutron-time-of-flight spectrometer. Two T = 3/2 levels were identified at excitation energies of 8.99 ± 0.05 MeV (J > ½) and 9.22 ± 0.015 MeV (J ^π = ½⁺, Γ ˂ 40 keV). The spins and parities were determined by a comparison of the measured angular distributions with the results of DWBA calculations.

These two levels were also obsesrved as isospin-forbidden resonances in the ²⁰Ne(p,p) and ²⁰Ne(p,p’) reactions. Excitation energies were measured and spins, parities, and widths were determined from a single level dispersion theory analysis. The following results were obtained:

E_x = 8.973 ± 0.007 MeV, J ^π = 5/2 ⁺ or 3/2⁺, Γ ≤ 1.2 keV,

^Γp_o = 0.1 ± 0.05 keV; E_x = 9.217 ± 0.007 MeV, J^π = ½ ⁺,

Γ = 2.3 ± 0.5 keV, ^Γp_o = 1.1 ± 0.3 keV.

Isospin assignments were made on the basis of excitation energies, spins, parities, and widths.

Branching ratios for the isospin-nonconserving proton decays of the 11.20 MeV, T = 3/2 level in ¹⁷F were measured by the ¹⁵N(³He,n) ¹⁷ F*(p) ¹⁶O reaction to be 0.088 ± 0.016 to the ground state of ¹⁶O and 0.22 ± 0.04 to the unresolved 6.05 and 6.13 MeV levels of ¹⁶O. Branching ratios for the neutron decays of the analogous T = 3/2 level, at 11.08 MeV in ¹⁷O, were measured by the ¹⁶O(³He, α)¹⁷O*(n)¹⁶O reaction to be 0.91 ± 0.15 to the ground state of ¹⁶O and 0.05 ± 0.02 to the unresolved 6.05 and 6.13 MeV states. By comparing the ratios of reduced widths for the mirror decays, the form of the isospin impurity in the T = 3/2 levels is shown to depend on T_z.

Photosensitized CIS-TRANS isomerization of 2,3-diphenylbutene-2 investigation of anomalous sensitizers for substituted Stilbene isometrization

The behavior of the photosensitized cis-trans isomerization of 2,3-diphenylbutene-2 was studied as a function of sensitizer energy by previously established methods. In addition, certain sensitizers for which parameters other than energy transfer are operative in inducting isomerizations, were studied in more detail. Sensitization of various stilbenes and substituted stilbenes by triphenylene is discussed in terms of excited state complex formation with stilbene. Sensitization by quinones, halogen-containing aromatics and 1,2-diketones is discussed in terms of attack by photolytically produced free radicals, either by addition to and elimination from the double bond, or in the cases of 1,2-diphenylpropene and 2,3-diphenylbutene-2, by hydrogen abstraction from one of the methyl groups and reversible abstraction by the allylic radical to produce cis-trans isomerized substrate and the structurally isomerized products, 2,3-diphenylpropene and 2,3-diphenylbutene-1.

I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

Photodisintegration of helium-3 at energies between 200 and 600 MEV

We have measured differential cross-sections for the two-body photodisintegration of Helium-3, ɣ + He³ → p + d, between incident photon energies of 200 and 600 MeV, and for center of mass frame angles between 30° and 150°. Both final state particles were detected in arrays of wire spark chambers and scintillation counters; the high momentum particle was analyzed in a magnet spectrometer. The results are interpreted in terms of amplitudes to produce the ∆(1236) resonance in an intermediate state, as well as non-resonant amplitudes. This experiment, together with an (unfinished) experiment on the inverse reaction, p + d → He³ + ɣ, will provide a reciprocity test of time reversal invariance.