Protein Structure and Function Lecture 2 Notes: Protein Structure Part 2 Protein Structural Hierarchy, Domains and Motifs - Some combinations of a few secondary structure elements occur more frequently. For example, there are recurring arrangements of a-helix and/or ß-sheets in unrelated proteins. These specific geometric arrangements of individual secondary structure elements are referred to as 'motifs'/'super-secondary structure'. Motifs comprise a part of a larger structural assembly and may be associated with a specific function. Defined as combinations of a few secondary structure elements which occur frequently. C helix N - The simplest example is the 'helix-turn-helix' (HTH) motif, which is found in many proteins including: N c "helix-turn-helix": one of the simplest motifs (cylinders represent helices) helix (a) DNA-binding motifs (e.g. transcription factors, regulatory proteins) loop (b) Calcium-binding motifs (proteins regulated by calcium, e.g. parvalbumin, calmodulin, troponin-C) (c) LMW protein toxins (spiders, snakes, snails) N C - All DNA polymerases are structurally similar. Finger and thumb domains wrap around DNA and hold it across the enzyme's active site (primarily in the palm domain). Metal ions are required by all DNA polymerases for activity. All DNA polymerases catalyse the same polymerase reaction. B c D E F A Fingers n m Thumb m - Another protein motif is the 'EF hand', found in parvalbumin, a muscle protein (109 amino acids, side chains of Asp, Asn, Glu and a water molecule). The function of this protein is not clear but it most likely acts as a calcium buffer during muscle relaxation. The HTH motif appears 3 times (2 calcium-binding regions). The EF hand is present in domains 5 and 6 and is comprised of 2 a-helixes and a loop of 12 amino acids (containing 5 oxygen atoms, preferably Asp/Glu), the 6th of which will be glycine (small so maintains structure) and the rest are hydrophobic (forms hydrophobic core). Calcium binds to parvalbumin via the 6 oxygen atoms. Palm Exonuclease lai N helix E Ca - Kretsinger (1973) predicted that more proteins should form similar calcium-binding structural motifs. In 19ff5, this prediction was confirmed by resolving the structure of Troponin (Herzberg & James). Ca loop c helix F
- Troponin-C is found in skeletal and cardiac muscle and causes contraction via binding to Ca2+. Its structure reveals four EF motifs, 2 of which are calcium-binding. - Another common protein motif is the hairpin ß motif. This is folding two adjacent anti-parallel strands joined by a loop. This structure is found in most anti-parallel ß structures (i.e. forms ribbons and/or more complex sheets). The most stable conformation is when two ß strands are adjacent in both primary sequence and structure (i.e. hence it occurs frequently). The length of the loop region varies but is most commonly 2-5 amino acids. The hairpin ß motif appears in bovine trypsin inhibitor and in erabutoxin from snake venom. - The hairpin motif in bovine trypsin inhibitor is part of a ribbon which is formed by two ß strands. The hairpin ß motifs in erabutoxin (acetylcholine receptor inhibitor) is