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Lecture 5

BIOC12Fall2012 Lecture Week 5 Notes.docx

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University of Toronto Scarborough
Biological Sciences
Rongmin Zhao

BIOC12Fall2012 Lecture Week 5: Protein Structures and Analysis (Chapter 6) Supersecondary structures/Motifs Tertiary Structure: supersecondary structure/motifs  Motif/supersecondary structure: a common grouping of secondary structural elements  Structural motifs usually consist of just a few elements  Most motifs contain only a few conserved amino acids  βαβ motif: combination of alpha helix, 2 beta strands and connecting loops  an alpha helix is connecting 2 consecutive parallel beta strands  β hair pin motif: antiparallel β-strands with tight reverse turns  figure b shows 2 hairpins  αα motif: antiparallel α helices are packed together  the side chains contact with each other  greek key motif: β-hairpin is folded over to form a 4 stranded anti-parallel β sheet  topology: in protein structural biology, the topology represents the way secondary structures are connected  helix bundle: often occurs in membrane proteins  forms transmembrane fragments  β sandwich: β strands or β sheets stack on top of each other = 2 layers of β sheets  usually no H bonds between the 2 layers  Tertiary Structure  Overall conformation of a polypeptide chain  3D structure  Depending on the size of the polypeptide chain, the tertiary structure can be either simple or complicated Globular Proteins Mediate Cellular Function  Globular proteins (not exactly spheres) are more numerous than fibrous proteins  The diversity of protein structures in nature reflects the remarkable variety of functions they perform  Functional diversity derives from: o The large number of folded structures that polypeptides can adopot o The varied chemistry of the side chains of the 20 common amino acids Globular Proteins Properties 1  Helices and b-sheets make up the core of most globular proteins  Most polar residues face the outside of the protein and interact with solvent  Most hydrophobic residues face the interior of the protein and interact with each other  Packing of residues is close  However ratio of van der Waals volume to total volume is only 0.72-0.77  empty space exists  The empty space is in the form of small cavities Why does the protein core consist of primarily a-helices and b-sheets?  The protein core is predominantly hydrophobic  The highly polar N-H and C=0 moieties of the peptide backbone must be neutralized in the hydrophobic core  The extensively H-bonded nature of a-helices and b-sheets is ideal for this purpose  The surfaces of proteins are ideally suited to form multiple H bonds with water molecules  stabilizes the protein structure Domain structures (equivalent to global protein) The structural and functional unit of proteins: Domain/Fold  A globular cluster of protein in the view of 3D structure  Structurally independent  Usually contains 40-200 amino acids  Contains 2 or more layers of secondary structures  Often has a specific function Small Proteins usually contain only One Domain  E.coli cytochrome b562  made up of 106 residues  Composed of an up-down-up-down four-helix bundle  Classified as alpha protein (containing only alpha helices) Showing the topology  Rossmann Fold  N-terminal fragment of dogfish lactate dehydrogenase (163 aa)  6 stranded parallel b-sheet in which the crossovers between b-strands all contain an a-helix  the fold was first described by Michael Rossmann and therefore named as Rossmann fold  appears in different hydrogenases which require NAD+ as coenzyme (a factor that is required to work together with enzyme) 2  topology: b-a-b-a-b-a… Immunoglobulin fold  Human immunoglobulin N-terminal fragment Fab (103 residues)  A b-sandwich composed of 2 antiparallel b-sheet (one in four and one in 3 strands)  Classified as B-protein (containing only b-strands)  α/β -barrels often appear in enzyme structures  this is the structure for chicken muscle triose phosphate isomerase  8 parallel b-strands surrounded by 8 parallel a-helices  this is also called a/b proteins  10% of known enzymes have this barrel structure  Large proteins are composed of individual domains  Glyceraldehyde-3-phosphate dehydrogenase (GPD)  Contains 2 structurally independent parts (orange and blue) – domains  Blue (N-terminal): contains βαβαβ unit which bind the dinucleotide NAD+ (nicotinamide adenine dimucleotide) 3  Many proteins are composed of several distinct domains  Multidomain proteins typically possess the sum of dunctional properties and behaviors of their constituent domains  Proteins consisting of multiple domains probably evolved by the fusion of genes that once coded for separate proteins  About 90% of domains in proteins have been duplicated in other proteins  Many proteins even contain multiple copies of the same domain  A large domain consisting of 2 sequences in
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