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- 2013/2014 - 3D Structures of Biological Macromolecules Exercise: Membrane Proteins. Jürgen Sühnel [email protected] Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany.

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J rgen s hnel jsuehnel fli leibniz de

- 2013/2014 -

3D Structuresof Biological Macromolecules

Exercise: Membrane Proteins

Jürgen Sühnel

[email protected]

Leibniz Institute for Age Research, Fritz Lipmann Institute,

Jena CentreforBioinformatics

Jena / Germany

Supplementary Material: http://www.fli-leibniz.de/www_bioc/3D/


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Cell Membrane


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Membrane Structural Components


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Lipids


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Cholesterol, a ConstituentoftheCell Membrane

Without cholesterol, cell membranes would be too fluid, not firm enough, and too permeable to some molecules. In other words, it keeps the membrane from turning to mush.

Cholesterol is an amphipathic molecule, meaning, like phospholipids, it contains a hydrophilic and a hydrophobic portion. Cholesterol's hydroxyl (OH) group aligns with the phosphate heads of the phospholipids. The remaining portion of it tucks into the fatty acid portion of the membrane.


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Membrane Proteins

  • Integral membrane proteins (penetrating the lipid bilayer; permanently attached)

    [Insulin receptor, rhodopsin, …]

    • Integral polytopic membrane proteins (transmembrane proteins)

    • Integral monotopic membrane proteins

  • Peripheral membrane proteins (external bound with non-covalent bonds; temporarily attached)

    [Enzymes: phospholipase …]

  • Lipid-anchored proteins (external bound with covalent bonds)

    [G proteins …]


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Integral Polytopic Membrane (Transmembrane) Proteins

  • Schematicrepresentationoftransmembraneproteins:

  • a singletransmembraneα-helix (bitopicmembraneprotein)

  • a polytopictransmembraneα-helicalprotein

  • a polytopictransmembraneβ-sheetprotein


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Integral Monotopic Membrane Proteins

  • Schematicrepresentationofthe different typesofinteractionbetweenmonotopicmembraneproteinsandthecellmembrane:

  • interactionby an amphipathicα-helix parallel tothemembrane plane (in-plane membranehelix)

  • interactionby a hydrophobicloop

  • interactionby a covalentlyboundmembranelipid (lipidation)

  • electrostaticorionicinteractionswithmembranelipids (e.g.through a calciumion)


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The First 3D Membrane Protein Structure


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Membrane Protein Databases

http://blanco.biomol.uci.edu/mpstruc/listAll/list


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Membrane Protein Databases

http://blanco.biomol.uci.edu/mpstruc/listAll/list


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Membrane Protein Databases

www.mpdb.tcd.ie


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Membrane Protein Databases

opm.phar.umich.edu


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Membrane Protein StructureClasses

January 2013

January 2014


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Protein Orientation in Membranes


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Transmembrane Protein (Halorhodopsin)

alpha-helical polytopic


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Transmembrane Protein (Halorhodopsin)

alpha-helical

1e12


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Transmembrane Protein (Halorhodopsin)

alpha-helical

1e12


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Transmembrane Protein (Outer Membrane Protein A)

beta-barrel


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Transmembrane Protein (Outer Membrane Protein A)

beta-barrel

1qjp


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Monotopic Membrane Protein


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1bhp


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Transmembrane Helix Prediction Server

www.cbs.dtu.dk/services/TMHMM/


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FASTA Format

>sp|P16102|BACH_HALSA Halorhodopsin OS=Halobacterium salinarium (strain ATCC 700922)

MSITSVPGVVDAGVLGAQSAAAVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPR

LIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMIL

LALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALV

TDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVF

AKYVFAFILLRWVANNERTVAVAGQTLGTMSSDD


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Transmembrane Helix Prediction Server (1e12)

www.cbs.dtu.dk/services/TMHMM/


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Transmembrane Helix Prediction Server (1e12)

www.cbs.dtu.dk/services/TMHMM/


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Split Server

split.pmfst.hr/split/4/


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Split Server Prediction (1e12)

split.pmfst.hr/split/4/


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Split Server Prediction (1qjp)

split.pmfst.hr/split/4/


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Other Tools for Membrane Protein StructurePrediction

http://www.stats.ox.ac.uk/~kelm/medeller/


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iMembranePrediction (1e12)


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iMembranePrediction (1e12)


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Transmembrane Prediction Sites

http://expasy.org/tools/


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Transmembrane Prediction Sites

http://www.sacs.ucsf.edu/Links/transmem.html


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