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Revision as of 07:48, 21 October 2009

Histamine Sensor

During the allergic response, the concentration of histamine in the extracellular fluid of the nasal cavity increases. To initiate a response, therefore, a histamine sensor is necessary.

Because natural histamine receptors exist only in eukaryotic cells as G-coupled protein receptors, they are unusable for our prokaryotic system. Therefore we have set out to engineer our own receptor. This novel receptor will sense extracellular concentrations of histamine and initiate an intracellular cascade, signaling cells to respond appropriately to the increase in histamine concentration.

To engineer a novel histamine receptor, we are mutating two existing prokaryotic chemoreceptors so that they bind histamine rather than their wild type ligands.

Chemoreceptor #1: Ribose Binding Protein

We modified ribose binding protein (RBP), which normally binds ribose in the periplasmic space of Escherichia coli, to bind histamine. Our computational approach to accomplish this task was modeled after that taken in Looger et al., "Computational design of receptor and sensor proteins with novel functions" (2003). Using Rosetta macromolecular modeling software, we modified the program's existing Enzyme Design Function (such as that used in Röthlisberger et al "Kemp elimination catalysts by computational enzyme design" (2008)) to enable the re-design of RBP, a non-enzymatic protein. The successful modification of RBP would result in its ability to bind histamine.

How we designed the protein:

1) Took the PDB file for the crystal structure of RBP cocrystallized with ribose (2DRI). Removed water molecules and added missing hydrogens.

2) Used UCSF Chimera to geometrically search for all van der Waals interactions between ribose and RBP in the crystal structure. Identified the amino acids responsible for these interactions as those most likely present in the ligand binding pocket of RBP.

3) Used UCSF Chimera to mutate all the identified residues in RBP to alanine (which has neutral chemical properties, and almost no side chains), thereby effectively creating a "blank" version of RBP, one that has no specific binding pocket for any ligand (removing its binding affinity for ribose).

4) Used Rosetta's Ligand Docking mode on a cluster of 100 servers to replace ribose in the alanine-mutated RBP (polyala RBP) with a 3D structure for histamine.

5) To isolate histamine's lowest energy conformation in RBP, used Monte Carlo minimization to find the relative orientations of both components that minimize steric contacts while still keeping histamine roughly within the original ligand binding pocket. Generated 10000 PDB files of histamine docked to the polyala RBP.

6) Sorted the 10000 docked PDB files by their interface energies between ligand and protein. Selected the top 2500.

7) Took the top 2500 and input them into the Rosetta Enzyme Design mode. Specified the residues mutated to alanine as those to re-design. Used Rosetta Design’s probabilistic simulated annealing algorithm to find the particular residues that minimize total energy between protein and ligand (minimized energy indicates a stable state, favoring binding). Final designs are not guaranteed to yield the lowest possible energy conformations. However, by doing thousands of designs in parallel, we increased the likelihood of isolating mutations that result in histamine binding.

8) Sorted through the output designs using several criteria: predicted interface energies between the protein and histamine, amount of hydrogen bonding between the protein and histamine (H-bonds are very good for ligand binding), and predicted folding ability of protein.

The DNA for the top design was synthesized by GeneArt AG. We are in the process of testing the protein’s ability to bind histamine.

In normal E. coli cells, ribose binding to RBP forms a ribose-RBP complex that interacts with the periplasmic domain of Trg, which in turn activates an intracellular cascade that induces chemotaxis. To link activation of Trg to induction of gene expression, we created a fusion between Trg periplasmic receptor domain and the EnvZ intracellular kinase domain by stitching the two intracellular domains at a shared NdeI restriction site. (as done in Baumgartner JW, et al. “Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor EnvZ” (1994)). EnvZ phosphorylates the transcription factor OmpR, which causes transcription of DNA regulated by OmpC promoter.

Chemoreceptor #2: Tar Receptor

In parallel, we modified the receptor Tar, which normally binds aspartate in the periplasmic space of E. coli, to bind histamine.

Loren Looger at the Howard Hughes Medical Institute's Janelia Farm campus used his protein design software Chameleon to calculate mutations that would transform Tar’s aspartate binding pocket to a histamine binding pocket. His algorithm gave us the top 16 receptor designs and we are currently in the process of creating this library of mutants. We have designed primers for each of these designs and are introducing these mutations by both the “Round the Horn Site-Directed Mutagenesis” protocol on OpenWetWare and Strategene’s Quikchange Mutagenesis II Kit.

In normal E. coli cells, binding of Aspartate to Tar initiates an intracellular cascade that signals chemotaxis. Dr. Masayori Inouye et al, using the same methodology as that which created the Trg-EnvZ chimera, fused the intracellular domain of Tar to the kinase domain of EnvZ. Thus, activation of the Tar receptor domain will cause its EnvZ domain to phosphorylate the transcription factor OmpR, which will subsequently activate the transcription of DNA under the OmpC promoter.

Assay to Test Histamine Sensitivity and Signaling Cascade Functionality

Our assay to test these receptors’ affinities for histamine is based on fluorescence. Because the intracellular cascades of both Trg-EnvZ and Tar-EnvZ induce transcription of DNA under the OmpC promoter, we have constructed a cassette from the registry that places the OmpC promoter over the gene for RFP. With this OmpC-RFP reporter cassette, we can test the functionality of the intracellular cascade.

We have tested this signaling cascade by performing a series of transformations. The E. coli strain RU1012 was used, because it is an EnvZ knockout strain. Results indicate that signal transduction is effective.

RU1012 with no plasmid

RU1012 with OmpC-RFP

RU1012 with Tar-EnvZ

RU1012 with Trg-EnvZ

RU1012 with OmpC-RFP + Tar-EnvZ

RU1012 with OmpC-RFP + Trg-EnvZ

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