Lecture 6. Thursday, September 14. Membrane Proteins. Sequence-Structure Relationships.

Lecture 6. Thursday, September 14. Membrane Proteins. Sequence-Structure Relationships.

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Unformatted text preview: Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 1 John Kuriyan: University of California, Berkeley Chem 130/MCB 100, Lecture 6, Fall 2006. Stretches of hydrophobic residues in soluble proteins are short (7-10 residues). This contrasts with membrane proteins, in which a distance of ~30 40 has to be spanned by a contiguous hydrophobic segment. Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 2 A hydrophobicity scale Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 3 Such hydrophobicity scales help predict the locations of transmembrane segments within proteins. The membrane is highly impernious to ions, including protons. An important class of membrane proteins are pumps, that move ions against a concentration gradient. Ions that are stored in a concentration gradient can be released to generate energy, as we shall see later. E.g., Coupling light energy to pumping protons. Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 4 Reaction cycle of bacterio rhodopsin Net effect is to pump protons uphill against a proton gradient. Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 5 When a protein molecule folds up:- the backbone is in a low energy conformation (ref: Ramachandran diagram)- all sidechain torsions are also in low energy conformations- all buried hydrogen-bonding groups are satisfied- Thus: the conformation is without strain.- Thus: the conformation is without strain....
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Lecture 6. Thursday, September 14. Membrane Proteins. Sequence-Structure Relationships.

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