1. BioSci M160 / MolBio255 Structure-Function Relationships of Integral Membrane Proteins Homework Hartmut “Hudel” Luecke Biochemistry, Biophysics & Computer Science Email: hudel@uci.edu http://bass.bio.uci.edu/~hudel http://bass.bio.uci.edu/~hudel

2. 1) Use amino acid sequence on next slide to predict: transmembrane segments secondary structure (helix, strand, turn) hydrophilic & hydrophobic face of predicted helices (if any) using helical wheel analysis 2) Only once you have done 1) above, find & use the PDB (3D structure) file to evaluate accuracy of predictions (helix boundaries, hydrophobic faces etc.) Coot: http://www.ysbl.york.ac.uk/~emsley/coot/ http://www.ysbl.york.ac.uk/~emsley/coot/ http://www.chem.gla.ac.uk/~bernhard/coot/wincoot.html (Windows)http://www.chem.gla.ac.uk/~bernhard/coot/wincoot.html Homework (a.k.a. home education ;-)

3. Primary (amino acid) sequence of target protein in FASTA format: >MYSTERY|SEQUENCE DYKDDDAMGQPGNGSAFLLAPNRSHAPDHDVTQQRDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFIT SLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVI ILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIF EMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKL KPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFC LKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRS SLKAYGNGYSSNGNTGEQSG Homework (a.k.a. home education ;-)

4. Helical Wheel