MCB110L_lecture21

MCB110L_lecture21 - MCB110L/06/11 Andreas Martin Proteins...

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Unformatted text preview: MCB110L Lecture 21 04/06/11 Andreas Martin Proteins - How does shape define function? - The 3D fold of a protein still cannot be predicted accurately. • Fold into discrete structures and shapes. • Specific shapes → specific functions. • Protein (greek): the most important • protein research: established by Geraldus Mulder (1840) -> demonstrated main elements of proteins: N,S,C,H • assumption back then: proteins = colloids, viscous solutions opinion lingered until beginning of 20 th century (vitalism, life in gelatine) • breakthrough through ultracentrifugation by Svedberg, indication of protein size, complexity • classification into globular (e.g. albumin) and fibrillar proteins (e.g. collagen) Proteins size of proteins Source: Robson & Garnier all amino acids from Lehninger, Chap. 3 and 27 21: Selenocysteine 22: Pyrrolysine Commans-Böck, FEMS Microbiol. Rev. 23 (1999) 335-351 Ambrogelly et al. Nature Chem. Biol. 3 (2007) 29-35 • Protein research strongly developed in the 1950s Linus Pauling and Robert Corey: e- delocalized over the peptide bond -> peptide bond is stiff (partial double-bond character) -> peptide bonds are planar geometry of the peptide bond (derived from high-resolution peptide structures) C ― N: 1.45 Å C ═ N: 1.25 Å C ═ O: 1.21 Å from: Voet & Voet, Fig. 6-2 trans-peptide group Source: The PDZ2 Domain of Syntenin at Ultra-high Resolution: Bridging the Gap Between Macromolecular and Small Molecule Crystallography Beom Sik Kang, Yancho Devedjiev, Urszula Derewenda andZygmunt S. Derewenda* J. Mol. Biol. (2004) 338, 483–493 view along C ― N bond Very high resolution X-ray structure: PDZ-domain at 0.73 Å most bent peptide bond: statistics of all peptide bonds: Ser261-Gly262 ω = 162.2° definition of dihedral angle between atoms A-D ψ = 0°: N i & N i+1 cis ϕ = 0°: C’ i-1 & C’ i cis C=O C=O direction of the chain serine Phi: NH-C α Psi: C α-COO only rotatable angles in the backbone Protein structure • Primary structure (1D) Amino acid sequence. • Secondary structure (2D) Alpha helices, beta sheets, turns, omega loops. 2D arrangement of amino acids in specific conformations, hydrogen bonding mainly defines these topologies. • Tertiary structure (3D) 3D structure of a single polypeptide chain Packing of 2D elements usually mediated by hydrophobic interactions. • Quaternary structure (4D) assembly of multiple chains / proteins predictions based on primary structure: - secondary structure relatively reliable (65-70% probability) - tertiary structure still very difficult, no quantum mechanical calculations (systems too big) energetic aspects of protein structures: - van-der-Waals interactions (1-2 kJ/mol) - hydrogen bonds (10-20 kJ/mol) - hydrophobic interactions - electrostatic interactions (~20 kJ/mol) - disulfide bonds energy contributions relatively hard to determine (amino acid mutations change several interactions at ones) energy of tertiary structure: ~ 80 kJ/mol for unfolding -> disruption of ~ 4 hydrogen bonds (energetically seen) -> proteins are very flexible and relatively instable (Amino-term)-Y-I-S-C-T-(Carboxy-term)...
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MCB110L_lecture21 - MCB110L/06/11 Andreas Martin Proteins...

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