C to C Phi φ N to NPsi ψ

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C to C Phi φ N to NPsi ψ. Takes 4 atoms to define rotation about a bond!. Trans vs. Cis peptide bonds Trans, carbonyl oxygen is on opposite side of peptide bond from amide hydrogen. Fischer & SumnerProteins have regular structure. Hydrophobic effect. - PowerPoint PPT Presentation

Transcript of C to C Phi φ N to NPsi ψ

  • C to C PhiN to NPsiTakes 4 atoms to define rotationabout a bond!Trans vs. Cis peptide bondsTrans, carbonyl oxygen is on opposite side of peptide bond from amide hydrogenFischer & SumnerProteins have regular structureHydrophobic effectHelices (, 310, ) n to n+4, n to n+3, n to n+5 has 3.6 residues/turn, 1.5 rise/residue-sheetsparallel, antiparallel, mixed 3.5 (C - C)TurnsMust connect secondary structure somehow usually not regular structure so backbone exposed

  • Sequence preference for helices, sheets, turns(loops)Helices usually are amphipathic, so are sheets! Where do the sidechains point?MotifsH-L-H, -H-, -hairpin, Greek keyRamachandran diagrams 3 major regions (B, A, L)Staggaered conformation of sidechains (rotomers)Supersecondary structureDomains, mosaic proteinsTertiary, Quaternary structure structures, structures, / structures, + structures

  • Where might you guess is the active site??

  • A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchangeKent L. Rossman,1 David K. Worthylake,2 Jason T. Snyder,1 David P. Siderovski,2,3 Sharon L. Campbell,1,3 and John Sondek1,2,3,4

  • Nature Reviews Molecular Cell Biology 6, 167-180 (2005);