Lecture 16: Membrane Proteins - Biophysical Society...For alpha-helical membrane proteins, you can...
Transcript of Lecture 16: Membrane Proteins - Biophysical Society...For alpha-helical membrane proteins, you can...
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Lecture 16: Membrane Proteins
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Membrane proteins:1) Overview: Types and Properties
2) Getting into the Membrane3)What Membrane Proteins Do--
examples3) Working with Membrane Proteins
4) Pymol/Chimera Tutorial
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Membrane Overview
Membrane proteins are 25-35% of the genome.
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Beta-Barrel
Alpha Helix
Amphipathic Helix
Fatty acid Chain
GPI-Anchored
Peripheral
Orientation of N and C termini
Size
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Beta-Barrel Proteins
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Hydropathy Plots for Alpha Helical Proteins: Classic Method
For alpha-helical membrane proteins, you can use hydropathy plots to predict the probability that a segment will be within the membrane. These are generated by measuring, for each amino acid, its partition coefficient between water and a non-interacting, isotropic phase such as Ethanol, and calculating from that partition coefficient a transfer free energy.
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Hydropathy Plots: More Realistic Method
Von Heijne, Biochem Soc. Trans. 2011
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Membrane proteins:1) Overview: Types and Properties
2) Getting into the Membrane3)What Membrane Proteins Do--examples
3) Working with Membrane Proteins4) Pymol/Chimera Tutorial
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Getting into the Membrane: Destination Matters!
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SRP Dependent Protein Targeting
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Ribosome Nascent Chain Translocon Complex!
Frauenfeld et al., NSMB 2011,
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Getting into the Membrane: The Lateral Gate
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Getting into the ER: Single N-terminal TM Segment
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Getting into the ER: Positive Inside Rule
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Getting into the ER: the Special Case of Tail-Anchored Proteins
Hegde RS, Keenan RJ Nature Reviews cell Biology 2011.
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Extra Players in Prokaryotic Protein Targeting: YidC
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Chloroplasts and Mitochondria Have Their Own Genome but Most Proteins are Made in the Cytosol and Imported.
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Trafficking to Mitochondrial Membranes
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Membrane proteins:1) Overview: Types and Properties
2) Getting into the Membrane3)What Membrane Proteins Do--examples
4) Working with Membrane Proteins5) Pymol/Chimera Tutorial
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Functions of Membrane Proteins:
SignalingTransportersEnzymesAnchors
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Signaling: IRE1 and the Unfolded Protein Response
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Signaling: IRE1 and the Unfolded Protein Response
Kawaguchi and NG, Science 30 September 2011
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Transporters: Aquaporins
Gonen et al., Nature 2005
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Enzymes: FtsH, a Membrane Bound Protease
Krzywda et al., Structure 2002 and Bieniossek et al., PNAS 2009
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Membrane proteins:1) Overview: Types and Properties
2) Getting into the Membrane3)What Membrane Proteins Do--examples
4) Working with Membrane Proteins5) Pymol/Chimera Tutorial
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Working with Membrane Proteins: Pick Detergents Wisely
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Proteoliposomes
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Hegde RS, Keenan RJ Nature Reviews cell Biology 2011.
Not Many Membrane Protein Crystal Structures Solved
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Lipidic Cubic Phase for Membrane Proteins
Ehud M. Landau and Jürg P. Rosenbusch, PNAS 1996, and Nollert et al., FEBS Letters 2001
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Electron Crystallography: An Example (Wza)
Nesper et al.,JBC 2003
Neg. Stain Diffraction Pattern
2-D crystals Class averages of single particles
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Electron Crystallography: Aquaporin
Gonen et al., Nature 2005
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Electron Crystallography: Solved Structures
Wisedchaisri et al., Nature 2005
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Membrane proteins:1) Overview: Types and Properties
2) Getting into the Membrane3)What Membrane Proteins Do--examples
4) Working with Membrane Proteins5) Pymol/Chimera Tutorial