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

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.chem.gla.ac.uk/~bernhard/coot/wincoot.html (Windows)

Homework(a.k.a. home education ;-)

Primary (amino acid) sequence of target protein in FASTA format:

>MYSTERY|SEQUENCEDYKDDDAMGQPGNGSAFLLAPNRSHAPDHDVTQQRDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG

Homework(a.k.a. home education ;-)

Helical Wheel