Algorithmic Combinatorics on Words REU
July 11 - July 17, 2005 (Week 6) Schedule

All events are in room 335, Bryan Building, unless otherwise noted.

Monday, July 11

9:30 am team meetings
10:00 am Guest speaker: Stacy Duncan, Ph.D. Candidate, Iowa State University

Characterization of the finger loop domain of Ffh by random sequence libraries and sequence analysis


Although the role of the function of the signal recognition particle (SRP) from Escherichia coli in targeting of proteins to the cytoplasmic membrane is known, details of many of its structural features require further study. The finger loop region of the Ffh protein is essential for SRP function and likely forms part of the binding site for hydrophobic membrane targeting sequences. To investigate the sequence and structural features of this domain important for its function, we have developed a genetic system to screen a random aptamer library for sequences that restored function to a finger loop deletion mutant. About 1% of random sequences can replace the wild type finger loop. Analysis of the random sequences, as well as targeted mutagenesis, shows the importance of hydrophobicity in finger loop function. All functional sequences also lack extensive secondary structural consistent with the role of the finger loop in binding a variety of ligands. Continued isolation and analysis of random sequences should provide new insights into how the finger loop functions in membrane protein targeting.

11:30 am lunch at Lucky 32 restaurant
1:00 pm team meetings

Tuesday, July 12

9:30 am team meetings

Wednesday, July 13

9:30 am team meetings

Thursday, July 14

9:30 am team meetings

Friday, July 15

9:30 am team meetings

Saturday, July 16

9:30 am team meetings