November 2001 Research Report- Kelly Elkins

I created a model of a structure for the E.coli SRP Ffh using Swiss Model at http://www.expasy.org. I performed a WhatCheck report on this model and am using that to determine weak parts of the model and to find residues with poor WhatCheck values. I then submitted all of the crystal structures (1FFH.pdb, 1FTS.pdb, 1J8M.pdb, 1J8Y.pdb, 1NG1.pdb, 2FFH.pdb, 2NG1.pdb, 3NG1.pdb (details of these are in the document outline srp.doc)) used for the model to WhatCheck and Procheck to determine weak parts of the original structures on which the model is based. I am in the process of reviewing all of these reports.

I have also compiled most all of what is known in relation to the bacterial SRP and SRP receptor and with references. I have also included information about the human SRP when it correlates to the bacterial system and information on Ras, another GTP binding protein, noting exact amino acid atom hydrogen bonds to the GTP.

Upon completion of checking the structure reports, I will perform a UHBD electrostatic calculation on the E. coli Ffh model. Then using the information I have compiled from the literature, I will be able to dock the FtsY (1FTS.pdb crystal structure that is known for E. coli FtsY for Irmi's lab) and Ffh model to form a protein-protein complex, either before or after GTP is also docked in each protein as this is still ambiguous in the literature.