C to C Phi φ N to NPsi ψ

15
C to C Phi φ N to N Psi ψ Takes 4 atoms to define rotation about a bond! vs. Cis peptide bonds , carbonyl oxygen is on opposite side of peptide bond from amide hy Fischer & Sumner Proteins have regular structure Hydrophobic effect elices (, 3 10 , π) n to n+4, n to n+3, n to n+5 has 3.6 residues/turn, 1.5Å rise/residue ets parallel, antiparallel, mixed 3.5Å (C - C) urns Must connect secondary structure somehow – usually not regular structure so backbone exposed

description

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 Phi φN to N Psi ψ

Takes 4 atoms to define rotationabout a bond!

Trans vs. Cis peptide bondsTrans, carbonyl oxygen is on opposite side of peptide bond from amide hydrogen

Fischer & Sumner Proteins have regular structure

Hydrophobic effect

Helices (, 310, π) n to n+4, n to n+3, n to n+5 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

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

Where might you guess is the active site??

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

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