Lecture 25 (real)

Lecture 25 (real) - Exposed surfaces interact hargedLecture...

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Charged Hydrophobic Charged Exposed surfaces interact with other molecules Lecture 25 A Sequence analysis and Structure Prediction Conserved structures with protein families Evolution of proteins = evolution of genes: Evolution has to happen for selection to happen Selection is not done at the level of DNA but rather done at the level of function You need to therefore go to the level of the protein in order to study evolution of genes What makes the structure of a protein and how is it conserved? Example : hemoglobin Take subunit of hemoglobin and compare it to another iron binding protein myoglobin: Very strong similarities in terms of structure Not identical Alpha-helix and loop present (very similar) Hypothesis : Evolved from the same gene Structure : Important and usually what is conserved Structure is at the core of a protein Cannot conserve what is at the surface without conserving what is responsible for having amino acids exposed at the surface 1 | P a g e
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Evolution of the globin protein family Leghemoglobin originates from the specialized root nodules Can measure the distance in evolution Evolution : Nature has found a nice way to bind heme into the hemoglobin molecule and that way has been kept Sequence comparison 2 | P a g e
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Hard to find out that they are similar by just looking at the sequence Chemical criteria can show that they are similar Usefulness of aligning sequences: Show that they are related Mutations in NF1 makes tumors in peripheral nervous system Ira- GTPase accelerating protein that modulates ras GTPase Yellow : Conserved 3 | P a g e
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Spacing is the same Conclusion : Structure is the same Blue spot: Not conserved but similar Referred to as conservative amino acid exchanges Conservative amino acid exchanges : The mutation that happened at the base pair level has changed the identity of the amino acid but in a way that doesn't perturb the function too much Reason : Between lysine and arganine there is a positive charge (acidic) Convenient way to estimate how this divergence in evolution has potentially modified the chemical properties of the polypeptide You have more criteria to align your sequence in order to see what it looks like Red spot: Phosporylation Interchangeable targets for enzymatic reaction Identification of the transmembrane domain Structure of transmembrane protein: ephrin Structure: 4 | P a g e
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Receptor kinase molecule Kinase domain in cytosol Receptor at the surface Ephrins and Eph are repulsive for neurons Definition : Stretch that is hydrophobic from one end to the other Surrounded by charged ends (locks) Transmembrane domain: Must go through the lipid bilayer and therefore hydrophobic Stretch of 18-26 amino acids Alpha-helix 5 | P a g e
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Don't want the protein to travel back and forth between the membranes: Put charges that lock protein to prevent them from going into the layer Random Summary
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This note was uploaded on 06/05/2011 for the course BIO 200 taught by Professor Thomasebureau during the Fall '07 term at McGill.

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Lecture 25 (real) - Exposed surfaces interact hargedLecture...

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