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46907-GB4
Development of Peptide Based Biocatalysts for the Desulfurization of Dibenzothiophene
Chad D. Tatko, Calvin College
The combustion of sulfur generates sulfur oxyacids that contribute to deforestation and
cardiopulmonary disease. The current technology for reducing sulfur content in
fuels, hydrodesulfurization, cannot eliminate
recalcitrant aromatic sulfur compounds. Discovery of bacteria that metabolize
aromatic sulfur heterocycles has led to significant
interest in biocatalytic desulfurization. However,
meeting the aqueous environment needed by the organism, while effectively
removing sulfur from fuel stocks has not been achieved.
In the biological metabolism of DBT usas
DszB, a desulfurase, and is
thought to involve a number of flavodoxins, or
related enzymes. The crystal structure of DszB, from Rhodococcus erythropolis,
was recently solved, revealing that binding occurs from contact with six
primary residues, three of which display an edge-face aromatic interaction. Flavodoxin binding to flavin
commonly involves aromatic residues as well. Favorable electrostatic
interactions arise from the proximity of the electron rich centroid
of the ring and the electron poor hydrogens. The
ubiquitous presence of aromatic interactions in enzymatic action on DBT has
biased design of a molecular receptor.
The peptide biocatalyst includes a number of essential
features: a regular structure, modifiable sidechains
and aromatic residues to interaction with DBT. Progress towards peptide
receptor exploration has resulted in four possible sequence designs, cyclic and
acyclic versions of diagonal and lateral sidechains.
Initially, in order to guarantee structural rigidity all peptides were macrocyclized with a disulfide bond from terminal cystine residues. However, many peptides demonstrated
sufficient stability to consider eliminating the disulfide bond to allow for
greater positional freedom. The shift from random coil of the Ha resonances are typically between 0.05 and
0.7 ppm with more than a 0.1 ppm
shift considered an indication of structure. Disulfide bonds are still used in
the event that a peptide is not sufficiently folded. In this manner greater
conformational flexibility is available to maximize interactions with a
substrate.
The positioning of the aromatic sidechains
has been varied to determine the impact on binding site. Initially the aromatic
residues were positioned diagonally (i, j-2) within the
peptide. A number of peptides were synthesized and characterized utilizing this
structural motif (RFVKVNGOFIKQ, RWVTVNGOWITQ, RWVKVNGOWIKQ, and RWVKVNGOWIFQ).
All of these peptides were well folded (greater than 60%) and have been
characterized. A number of technical problems have been found from early
investigations into the binding potential of these peptides. The excitation
band for Trp is altered within the diagonal geometry
such that it overlaps with the DBT absorbance band. As such binding data cannot
be obtained from fluorescence spectroscpoy. Anaylsis with NMR based binding studies in much slower and
ongoing. The phenylalanine containing peptides are expected to bind the
weakest, but could be amenable to fluorescence analysis and will be
investigated. The aromatic rings are not sufficiently close to interaction with
one another, but can bind to an intercalated substrate in a sandwich motif.
While this offers an efficient method for packing it appears to confer only
offset stacked geometries.
To diversify the accessible geometries for interacting with
substrates a variation is being explored. Laterally disposed aromatic residues
(i, j) are sufficiently close to interact
with each other, which seems to preclude them from subsequent substrate
interactions. However, our studies indicate that the lateral interaction occurs
predominantly through one or two hydrogens via an edge-face geometry. The
shift of specific aromatic resonances from random coil, when laterally
positioned with a phenylalanine, are between 0 and 1.4 ppm. What is interesting
from a design perspective is that 1-naphthylalnine and tryptophan have very
similar trends with the 7, 8 and 4, 5 hydrogens, respectively, the most upfield shifted. This suggests
that these two rings adopt similar geometries. A subtle shift in the point of
attachment to 2-naphthylalanine gives a very different set of shifts, wher the
1, 3 positions are most shifted. For both 1- and 2-naphthylalanine the majority
of the aromatic ring is not involved in a lateral aromatic interaction. A
preliminary geometry suggests that the aromatic rings are edge-face with a
cleft for edge-face type interactions with a substrate.
Future direction: Analysis of the binding of peptide to DBT
and DBTO2 with the diagonal aromatic residues is ongoing. A computational
structure will be generated for the lateral polycyclic aromatic peptides from
NOE restraints. Binding data will then be generated with the lateral aromatic
peptides. After this initial round of diagonal and lateral structural and
binding analysis an investigation into the redox
potential of DBT and perturbations from binding will begin.
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