1Super-secondary structuresMotifs&DomainsFigure 8-46abc Schematic diagrams of supersecondary structuresVoet&Voet, Biochemistry, chapter 8alpha/beta beta alpha2Figure 8-46d Schematic diagrams of supersecondary structures.Voet&Voet, Biochemistry, chapter 8Figure 8-19a Polypeptide chain folding in proteins illustrating the right-handed twist of β sheets. (a) Bovine carboxypeptidase A.Voet&Voet, Biochemistry, chapter 83Figure 8-53 Topological diagrams of (a) carboxypeptidase A and (b) the N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase.Voet&Voet, Biochemistry, chapter 8Figure 8-48 The immunoglobulin fold.Voet&Voet, Biochemistry, chapter 84Figure 8-49 Retinol binding protein.Voet&Voet, Biochemistry, chapter 8Motif and Domain structureLarge motifs can be equivalent to domains, i.e. independently folded substructures of proteins.Motif DomainVoet&Voet, Biochemistry, chapter 85The three domains of pyruvate kinase subunitsfrom Richardson and Richardson, p.29Domains are shown separated, but actually form a single polypeptide chain.Amino acid side chains play special roles in protein structuresGlycine – very small side chain volume, confers backbone flexibilityCystein – reactive side chain forming disulfide bonds; binding sites for metal ions like Zn, CuHistidine – pK = 6 makes it a partner in reactions where proton exchange isimportant; binds ions like Zn, Cu, heme (Fe)Proline – alpha helix breaker, hydrophobic turnsSerine – alpha-helix breaker, phosphorylation of proteins6Proline – alpha helix breaker, found in turnsbrokenH-bondsCox, Lehninger Principles in Biochemistry, chapter 5, figure 7Cysteine: a chemically reactive side chainreduced oxidized7Homo-trimer of bacterial maltoporinEach subunit forms a pore across the outer membrane of E.coli cell walls; structure shows diglucose unit inside each subunit channel; the center of the trimer between subunits contains a calcium ion. (PDB accession number 1AF6)Quaternary structureThe four subunits of pyruvate kinase subunitsfrom Richardson and Richardson, p.29Pyruvate Kinase (shown from E. Coli in T-State; PDB code 1PKY) is a tetramericprotein. Each subunit has the three domains shown below:The three domains of pyruvate kinase
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