Motifs, Motifs, Motifs...

Table of Contents

{1} Motifs, Motifs, Motifs...

{2} A closer look at the alpha-helix and its interactions.

{3} “Standard pitch” is 3.6 residues/turn

{4} 3.6/turn is not just one phi/psi pair

{5} Where is this line on the Ramachandran plot?

{6} at 3.6/turn, residue 19 is over residue 1, an 18-mer repeat

{7} Other phi/psi combinations… 3.0 residues/turn

{8} Other phi/psi combinations… 4.0 residues/turn

{9} Other phi/psi combinations… 3.5 residues/turn

{10} Other phi/psi combinations… 3.667 residues/turn

{11} Helical wheels for various numbers of residues/turn

{12} Helix-Helix Interactions:

{13} So two helical dipoles can interact...

{14} A heptad repeat in sequence confers “sidedness”

{15} Hydrophobic sides form complexes...

{16} 1,4,5,7 repeat found in some other coiled-coils

{17} When the complete turn is not 3.5 residues...

{18} Coiled-coil motifs are formed

{19} Close topographical interactions

{20} Another way to pack two helices is at ~20 degree angle

{21} More complex motifs constructed from helix-helix packing

{22} Consider the interactions in a Lectin (1afb)

{23} Barrel and Barrel-like Motifs

{24} Simple Geometries can combine to form barrel-like structures

{25} Linked Hairpins in Adipocyte lipid-binding protein

{26} A More Complex Pattern in GFP

{27} Two Greek key motifs form a barrel like structure in gamma-crystallin

{28} A Greek key combines with an extended hairpin in gamma-chymotrypsin A

{29} Another barrel-like motif is the “jellyroll”

{30} Barrel and Barrel-like Motifs

{31} The TIM Barrel is formed from a repeating sequence

{32} The LuxF Gene Product is a mix ...

{33} Thermitase has a complex structure.

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C. Cohen & D. A. D. Parry (1990) Proteins, Structure, Function and Genetics 7, 1-15.

T. E. Creighton (1993), Proteins, Structure and Molecular Properties, W. H. Freeman & Company, New York.

IUPAC-IUB Commission on Biochemical Nomenclature (1970), Biochemistry 9, 3471-3479.

E. J. Milner-White (1997) The Partial charge of the nitrogen atom in peptide bonds, Protein Science 6, 2477-2482.

G. N. Ramachandran & V. Sasisekharan (1968), Adv. Protein Chem. 23, 283-437.

D. Voet & J. G. Voet (1995), Biochemistry, John Wiley & Sons, Inc., New York. pp. 141-190.