Initial calculations to be done:

We have the crystal structure of NG domain FtsY (apo, 1FTS.pdb) from Irmi's group for E. coli. However, we have no structure of E. coli Ffh. We can use the NG domain Ffh structures from T. aquaticus and A. ambivalens and the E. coli sequence to model an apo NG domain structure from E. coli.

I submitted both the NG domains and whole protein of the E. coli Ffh to Blast and Swiss Protein and have modelled structures that now I need to examine further and pick one to continue my modeling/computations on. I can evaluate these with Procheck or with the WhatCheck report in WhatIf or on the web.

Then we can dock GTP to the apo-forms of the NG domain Ffh and FtsY from E. coli and compare these results to the GDP and GMPPNP structures available to compare the conforational changes induced by GTP-binding. With the new coordinates from Freymann's group and those form Walter's group, we can compare the conformational differences between the GMPPNP, GDP, and apo forms of Ffh. I have input files from my MM and MD work with InsightII for the discover program.

We can model a SRP/SR complex where both are GTP bound. We should look at the importance of the four Arg residues at the proposed interface in Ffh and FtsY. Irmi is making mutants of these right now and it will be interesting to compare the results of our modelling and her experimental work. Also, many mutants have been made for the SRP and SR in E. coli and this data can be used to guide our work.

I'm compiling these now.

There is also a structure for the 5 subunit signal peptidase enzyme (1B12.pdb, Paetzel, M., Dalbey, R. E., Strynadka, N. C. J. Crystal Structure of a Bacterial Signal Peptidase in Complex with a Beta-Lactam Inhibitor. (1998) Nature. 396:186-190.) with an inhibitor (b-lactam inhibitor, (5S,6S)-6-[(R)ACETOXYETH-2-YL]-PENEM-3-CARBOXYLATEPROPANE) bound. This hydrolase cleaves the signal sequence after the protein is transported through the pore. A comparison should be made between the active site of the signal peptidase and the M-domain of Ffh. (There is a structure for the human SRP M domain also and this could be used to construct the Ffh M domain for this calculation). Both interact with the signal peptide so there should be similarities between the sites of interaction on both of these proteins. An examination of the signal peptidase site could lead to new insights as to exactly how the SRP M-domain interacts with the signal peptide.