BETA STRAND Prof. Alejandro Hochkoeppler Department of Pharmaceutical Sciences and Biotechnology University of Bologna
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1 Prof. Alejandro Hochkoeppler Department of Pharmaceutical Sciences and Biotechnology University of Bologna
2 C-ter NH and CO groups: right, left, right (plane of the slide) R groups: Front, back, front... (plane of the slide) N-ter
3 Intra-strand hydrogen bonds are hampered by the extended conformation of beta strands. Inter-strand hydrogen bonds are favoured.
4 C-terminus By convention, the N-ter side of a beta strand is represented as the base of an arrow. The C-ter side is depicted as the head of an arrow. N-terminus
5 Beta strands can mutually interact, forming a beta sheet. The orientation of strands can be parallel or anti-parallel.
6 Antiparallel beta-sheet Hydrogen bonds in beta-sheets Parallel beta-sheet
7 i+2 Two beta strands can be connected via a type-one turn. Hydrogen bond between i and i+3 residues. i+1 i i+3 Any of the 20 amino acids can reside at i and i+2 sites. Type-1 beta turn Carbon C of i+1 residues and R-group of i+2 amino acid are directed toward opposite directions (C of i+1 down, and R of i+2 up, respectively). Clash between i+1 carbonyl and i+2 R is avoided.
8 Type-2 beta turn i+2 Two beta strands can be connected via a type-two turn. Hydrogen bond between i and i+3 residues. i+1 i i+3 Glycine must reside at i+2 site. Carbon C of i+1 residue and R-group of i+2 amino acid are directed toward the same direction. Clash between i+1 carbonyl and i+2 R is avoided by the presence of glycine.
9 Helix Periodicity: 3 residues/turn The groove contains 10 atoms Narrower than alpha helix BETA STRAND
10 Beta turn Structural motif two contiguous antiparallel beta strands connection by a loop present in proteins also containing alpha helices (isolated beta turn) repetition of the beta turn yields a sheet
11 Retinol-binding protein Binding and transport of vitamin A Antiparallel strands forming two sheets. n strand connected to n+1, n+1 to n+2 The two sheets form a barrel. The barrel cavity binds retinol. The beta strands are connected by: two small alpha helices turns Turns can be of two types: type-1 beta-turns type-2 beta turns (contain glycine)
12 Hydrophobic residues fill the cavity Charged residues on the surface
13 Bovine gamma-crystallin Antiparallel strands forming two sheets. n strand connected to n+3 The barrel is crossed by the connection between stands. n n+3 This structural motif is denoted as greek key.
14 The connection between n and n+3 strand is not a beta-turn n+2 n+1 n n+3 The cavity of the barrel is crossed by the connection between strands n and n+3
15 AraC protein of Escherichia coli Barrel formed by antiparallel beta-sheets. Transcriptional regulator arabinose The N-terminal domain binds arabinose. The C-ter domain binds DNA. AraC is a dimer. Free AraC represses genes of arabad operon. When AraC is bound to arabinose, arabad genes are transcribed.
16 Jelly Roll motif: the barrel is crossed 4 times by connections between strands. The motif resembles a jelly roll, an english candy decorated in a typical way. Greek key motif: the barrel is crossed 1 time by connections between strands.
17 Jelly Roll: 8 beta strands 2 antiparallel sheets the barrel is crossed by 2-3, 3-4, 6-7, and 7-8 loops Greek key: 4 beta strands 8 1 antiparallel sheet 3 the barrel is crossed by 3-4 loop two greek keys can 5 4 form a barrel
18 4 1 Generation of a Greek-key motif from an extended conformation Folding β-strands 1-4: contiguous in the secondary structure non-contiguous in the tertiary structure 5 4 1
19 5 4 Generation of a Jelly-Roll motif from an extended conformation 6 3 Folding Connections 2-3 and 6-7: cross the bottom of the barrel 5 4 Connections 3-4 and 7-8: cross the top of the barrel 1
20
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