The heroic times of crystallography Kendrew's model of the low-resolution structure of myoglobin shown in three different views. The sausage-shaped regions represent a helices, which are arranged in a seemingly irregular manner to form a compact globular molecule. ca-Prot_Enz

Secondary structure elements Short segments of the sequence (primary structure) spontaneously fold into regular structural elements, reducing the entropy. These elements are stabilized by internal hydrogen bonds between carbonylic oxygen's and amino hydrogen's involved in peptide bonds of the main chain. The H-bonds formed enable most of the main chain to exclude the polar solvent and eventually become buried in the (compact) core of the protein at no energetic cost. Two such elements are (i) the a helix, building ‘internal’ H-bonds, and (ii) the b strand (extended chain), building ‘external’ H-bonds with other b strands, forming b sheets. ca-Prot_Enz

f y The alpha helix The right-handed a helix is one of the major elements of proteins secondary structure. Main-chain N and O atoms are hydrogen- bonded to each other within a helices. Diagram of the path of the main chain in an a helix. 3.6 residues per turn in an a helix, which corresponds to 5.4 Å. Same but with approximate positions for main-chain atoms and hydrogen bonds. Arrow: direction from the N- to the C- terminus. Schematic diagram of an a helix. O and N atoms, H-bonds. Side chains. N C N C ca-Prot_Enz

More on alpha helices (d) A ball-and-stick model of one a helix in myoglobin. The path of the main chain is outlined in yellow; side chains are purple. Main-chain atoms are not colored. (e) One turn of an a helix viewed down the helical axis. The purple side chains project out from the a helix. ca-Prot_Enz

Electronegativities and dipole moment Sd+ Sd- Negatively charged groups frequently bind to the amino ends of a helices. (a) The dipole of a peptide unit. Values are fractional charges of the atoms in the peptide unit. (b) Vectorial sum of aligned dipoles along the a-helical axis, positive at the amino end and negative at the carboxy end. (c) A phosphate group hydrogen-bonded to the NH end of an a helix (dipole moment and H-bond to free NH) . ca-Prot_Enz

Alpha helices position: solvent accessibility 1 3 2 ca-Prot_Enz

The helical wheel or spiral 1 2 Amino acid residues are plotted every 100 degrees around the spiral, following the sequences given in Table 2.1. The following color code is used: green is an amino acid with a hydrophobic side chain, blue is a polar side chain, and red is a charged side chain. The first helix is all hydrophobic, the second is polar on one side and hydrophobic on the other side, and the third helix is all polar 3 1 3 2 ca-Prot_Enz

= S å Hydrophobic moment ) cos ( sin ( ú û ù ê ë é × + = n H q m 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 10 1 3 4 5 7 8 11 12 14 15 2 6 9 13 q = 100 ° a Helix (wheel) 2 3 4 5 6 1 1 2 3 4 5 6 S i=1 6 = ca-Prot_Enz

Antiparallel beta sheets f y Antiparallel beta sheets Beta sheets are the second major element of secondary structure in proteins. (a) The extended conformation of a b strand. Side chains are shown as purple circles. A b strand is schematically illustrated as an arrow, from N to C terminus. (b) Schematic illustration of the hydrogen bonds pattern in an antiparallel b sheet. Main-chain NH and O atoms within a b sheet are hydrogen bonded to each other. ca-Prot_Enz

Antiparallel beta sheets- cont f y Antiparallel beta sheets- cont (c) A ball-and-stick version of (b). Oxygen atoms are red; nitrogen atoms are blue. The hydrogen atom in N-H...O is white. The carbon atom in the main chain, Ca, is black. Side chains are illustrated by one purple atom. The orientation of the b strands is different from that in (a). (d) Illustration of the pleat of a b sheet. Two antiparallel b strands are viewed from the side of the b sheet. Note that the directions of the side chains, R (purple), follow the pleat, which is emphasized in yellow. ca-Prot_Enz

Parallel beta sheets f y ca-Prot_Enz

f y Mixed beta sheets ca-Prot_Enz

= = å Hydrophobic moment ) cos ( sin ( ú û ù ê ë é × + = n H q m 2 6 ° 1 ) cos ( sin ( ú û ù ê ë é × + = å n H i q m = Strand (sheet) 1 2 3 5 6 4 b q = 180 ° = ca-Prot_Enz

Topology diagrams for b-sheets Rules The beta strands are consecutively numbered from N- to C-terminal. Neighboring strands and often those at the ends are most likely linked by H-bonds. Connecting loops and a helices (often out of the virtual plane) are geometrically inconsistent in topology diagrams. ca-Prot_Enz

Motives of secondary structures Consecutive elements of secondary structure can assemble together and form recurring or frequently found structures in protein folds (=tertiary structure). These special assemblies are called motives and represent supra-secondary elements, often associated with special structural or functional properties. In a motif, a helices and/or b strands are linked together by loops of variable lengths; the main chain of the latter is devoid of regular structure. The atom density in an assembled motif is generally higher than that before the assembly. ca-Prot_Enz