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  • Ch13c Motifs

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    Parijat Banerjee
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    The document discusses various super-secondary protein structures including alpha/beta motifs, beta barrels, and alpha helical bundles. It provides examples of specific protein structures that exhibit these motifs such as cytochrome 5562 which forms a 4-helical bundle and immunoglobulin domains which form beta sandwiches. It also discusses structural features of these motifs such as how anti-parallel beta sheets form amphipathic structures and how hydrophobic contacts stabilize alpha helical bundles.

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    The document discusses various super-secondary protein structures including alpha/beta motifs, beta barrels, and alpha helical bundles. It provides examples of specific protein structures that exhibit these motifs such as cytochrome 5562 which forms a 4-helical bundle and immunoglobulin domains which form beta sandwiches. It also discusses structural features of these motifs such as how anti-parallel beta sheets form amphipathic structures and how hydrophobic contacts stabilize alpha helical bundles.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    3 views6 pages

    Ch13c Motifs

    Uploaded by

    Parijat Banerjee
    The document discusses various super-secondary protein structures including alpha/beta motifs, beta barrels, and alpha helical bundles. It provides examples of specific protein structures that exhibit these motifs such as cytochrome 5562 which forms a 4-helical bundle and immunoglobulin domains which form beta sandwiches. It also discusses structural features of these motifs such as how anti-parallel beta sheets form amphipathic structures and how hydrophobic contacts stabilize alpha helical bundles.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
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    of 6

    Super-secondary structures (motifs)

    alpha/beta

    beta

    alpha

    Voet, Fundamentals, 2nd

    4-helical bundle Cytochrome 5562

    beta sandwich immunoglobulin domain

    6-stranded / cross-over lactate dehydrogenase

    Ribbon diagram

    Topology diagram

    Voet, Fundamentals, 2nd

    Beta barrels 8-stranded beta-barrel Retinol binding protein Jelly role Asparagine amidase F / barrel Triose phosphate isomerase

    Voet, Fundamentals, 2nd

    A two-stranded anti-parallel beta-pleated sheet drawn to emphasize its pleated appearance. If all even numbered residues are hydrophilic and all odd numbered residues hydrophobic, the beta sheet will have amphipathic properties.
    Note: there must be at least two strands to form a sheet.
    R1 N-term R2 7.0 R4 R6 R3 R5 R7 C-term

    anti-parallel NC CN

    parallel NC NC

    Voet&Voet, Biochemistry, chapter 8

    Bacterial porin a -barrel outer membrane protein (OMP)


    Top view of homotrimer Side view of monomer

    X-ray structure of maltoporin trimer (OmpC) with di-glucose unit in each subunit [from Protein Data Bank, accession number 1AF6]

    The X-ray structure of a subunit of E. coli maltoporin in complex with a maltodextrin of 6 glucosyl units (Glc6).
    Voet, Fundamentals, 2nd

    Top: Projection map of 16-strand barrel of a porin monomer showing aligned aromatic side chains anchoring the protein in the phospholipid bilayer (white surface residues in trimer space filling model). Left: X-Ray crystal structure of the E. coli OmpF porin. A space-filling model of the trimer. Box = membrane spanning domain
    Voet, Fundamentals, 2nd

    Why are super-secondary structures stable? Alpha helical bundle; helix-helix interaction stabilizes helical structures in solution

    Hydrophobic contacts stabilize helix-helix contacts in water

    Voet, Fundamentals, 2nd

    Amphipathic alpha helix giving rise to coiled-coils

    Voet, Fundamentals, 2nd

    Helical wheel representation of an amphipathic alpha helix


    15 8 1 4 11 9 7 14 13 3 10 6 2 hydrophilic 12 5 hydrophobic

    n + 3,4 rule
    Determines distribution of polar and non-polar residues

    Amino acid side chains with special roles secondary structures Glycine: very small side chain volume, confers backbone flexibility Proline: alpha helix breaker, hydrophobic turns Serine: alpha-helix breaker, phosphorylation of proteins

    broken H-bonds

    Proline alpha helix breaker

    Voet, Fundamentals, 2nd

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