A Protein Interface

Protein

Ribozome

tRNA

mRNA

http://www.wehi.edu.au/education/wehi-tv/dna/Translation.mov

Protein Folding

acetylcholine esterase

Acetylcholine(positive)

Binding Site(Negative)

http://www.scripps.edu/mb/goodsell/interface/interface_images

Amino Acid Sequence ofthe enzyme:

acetylcholine esterase1 mfvnqrtrrp ymsvfvlvlg aavicpaygi idrlvvqtss gpirgrstmv qgrevhvfng 61 vpfakppvds lrfkkpvpae pwhgvldatr lppsciqery eyfpgfagee mwnpntnvse 121 dclylniwvp tktrlrhgrg lnfgsndyfq ddddfqrqhq skgglamlvw iygggfmsgt 181 stldiynaei laavgnviva smqyrvgafg flylapying yeedapgnmg mwdqalairw 241 lkenakafgg dpdlitlfge saggssvslh llspvtrgls krgilqsgtl napwshmtae 301 kalqiaegli ddcncnltml kespstvmqc mrnvdaktis vqqwnsysgi lgfpsaptid 361 gvfmtadpmt mlreanlegi dilvgsnrde gtyfllydfi dyfekdaats lprdkfleim 421 ntifnkasep ereaiifqyt gwesgndgyq nqhqvgravg dhfficptne falglterga 481 svhyyyfthr tstslwgewm gvlhgdevey ifgqpmnasl qyrqrerdls rrmvlsvsef 541 artgnpaleg ehwplytren piffifnaeg eddlrgekyg rgpmatscaf wndflprlra 601 wsvpskspcn lleqmsiasv sstmpivvmv vlvliplcaw wwaikknktp phpqviletr 661 afmh

GenBank Sequence

The Amino Acids

David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6

Proteins Fold by Twisting Peptide Backbone

http://www.itb.uni-stuttgart.de/training/bioinformatics99

Protein Secondary Structure

Tertiary Structure (3-Dimensional Fold)

• Motif– Simple combination of secondary structures– Appears in different proteins

• Domain– More complex combination of secondary

structures– Has a specific function

Predicting Folding

• Fold predictions are made by minimizing free energy

• Hydrogen Bonds Decrease Free Energy

• Some backbone angles are more stable than others