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Protein Structure Class: 2(b). Secondary - Beta Sheets

Protein Structure Class: 2(b). Secondary - Beta Sheets

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SECONDARY STRUCTURE: GENERAL CHARACTERISTICS
The polypeptide chain begins to assume local 3D conformations of amino acids that are in close proximity with each other in their linear sequence. Here, we address the characteristics of one of the two major types of secondary structure: beta sheets (aka beta pleated sheets).
  • Secondary structure is the conformation of local segments of the polypeptide chain into three-dimensional structure.
  • It specifically involves interactions between residues that are near each other along the polypeptide sequence.
  • Secondary structure includes: alpha helices and beta sheets.
    • Beta sheets are the most prominent secondary structures in proteins because they are the most stable.
  • Amino and carboxy groups of amino acid residues (the backbone of the polypeptide chain) form hydrogen bonds to create secondary structure.
  • Secondary structure involves backbone interaction and not side chain interactions.
beta sheet
  • Comprises two or more beta strands, which are polypeptide chains that hydrogen bond to each other.
  • We show four beta strands as zigzag lines that run in parallel to each other: the side chains of the constituent amino acid residues give each beta strand their zigzag shape, and multiple strands linked together give the beta sheet a pleated shape.
  • Beta sheets were the second secondary structure proposed, thus their name: "beta" sheets.
  • We show both parallel and antiparallel strands in our beta sheet: notice that strands 1 and 2 both run in the same direction (N to C), where as strands 3 and 4 run is opposite directions.
Antiparallel Strands
  • We show the amino and carboxy amino groups for each amino acid group on opposite sides to show that the strands run in opposite direction.
  • We see that in this orientation we have amino groups on one beta strand aligned with the carbonyl group on the other strand.
  • We connect each amino and carboxyl group with dashed lines to represent hydrogen bonds between them.
Parallel Strands
  • We show the carboxyl and amino groups for each amino acid residue both going N terminus to C terminus to show they run in parallel.
  • Although they run in parallel, the carboxy and amino groups on the two strands aren't perfectly aligned.
  • From N to C terminal, we use dashes to connect the amino groups with their closest free carboxyl residue.
  • The lines representing hydrogen bonds create V shapes, unlike in the antiparallel strand where the hydrogen bonds were straight lines that connected to two strands.
The distance between individual amino acids along a beta strand is 3.5 angstroms. Recall from our knowledge of alpha helices that the distance between amino acids in an alpha helix is only 1.5 angstroms [In alpha helices, rise: distance between AA = 1.5 angstroms]. Thus, the amino acid residues in a beta sheet are much more extended, unlike the rigidity of the alpha helix.*
Directionality of beta strand
  • Beta sheets are represented by broad, flat arrows to show directionality.
  • We connect one arrowhead to the tail of the next arrow so that the arrows are connected 1 to 2 to 3 to 4 in order to indicate that beta sheets are often structures on a single polypeptide chain that folds on itself.
Favorable Amino Acids
Amino acids with beta branching include Threonine, Valine and Isoleucine. We can remember these by using their one-letter codes, T, V and I and the phrase "trees, 'Vs' and ice cracks" since all of those entities have branches*. Aromatic amino acids include Tyrosine, Tryptophan and Phenlyalanine. These amino acids all have aromatic rings (ring structures with resonance) as part of their side chains. A mnemonic using their one-letter codes is: Y (tyrosine), W (tryptophan), and F (Phenylalanine): yetis (for Y) with (for W) flowers (for F).
Proline and Glycine
  • Proline and Glycine residues are often found in beta-turns (loops that connect beta sheet or alpha helical segments in a protein's secondary structure).
  • Proline's imino ring structure prevents it from acting as a hydrogen bond acceptor, making it unfavorable within the beta strand, but a good choice for turns.
  • Glycine, which lacks an R-group, is small and flexible and also facilitates turns.

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