C to C Phif

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C to C Phi f N to N Psi ?
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 Sumner Proteins have regular structure
Hydrophobic effect
Helices (?, 310, p) n to n4, n to n3, n to
n5 ? has 3.6 residues/turn, 1.5Å rise/residue
?-sheets parallel, antiparallel, mixed 3.5Å (C?
- C?)
Turns Must connect secondary structure somehow
usually not regular structure so backbone
exposed
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Sequence preference for helices, sheets,
turns(loops)
Helices usually are amphipathic, so are sheets!
Where do the sidechains point?
Motifs H-L-H, ?-H-?, ?-hairpin, Greek key
Ramachandran diagrams 3 major regions (B, A, L)
Staggaered conformation of sidechains (rotomers)
Supersecondary structure
Domains, mosaic proteins
Tertiary, Quaternary structure
? structures, ? structures, ?/? structures, ? ?
structures
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Where might you guess is the active site??
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A crystallographic view of interactions between
Dbs and Cdc42 PH domain-assisted guanine
nucleotide exchange Kent 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
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Nature Reviews Molecular Cell Biology 6, 167-180
(2005)