Lecture 8 - Monday, September 11, 2006 Lecture 8...

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Monday, September 11, 2006 Lecture 8 Announcements: 1. Do LG problems 10 - 17 for this week. RasMol Assignment #3, Structural Domains. 2. Make-up exam for midterm: probable date Fri 10/21. Prof will meet in a few weeks with students who have a conflict to choose a time. 3. For all the scripted RasMol assignments (i.e. except for the Tour of the Protein Data Bank): Open RasMol. Then, in the Command Line, type script index.spt 4. Any student who has just added this class: Meet Prof right after lecture to discuss how to catch up. Friday’s Lecture: collagen structure structural domains, superfamilies, families multidomain proteins Today's lecture: Repeated domains Quaternary structure (IV) Protein stability Repeated domains occur pp. 62-63 Not only do some proteins have more than one structural domain within a single polypeptide chain, but also some proteins have the same domain repeated along the chain, sometimes together with many other domains, all in the same chain. This is one of the ways that larger proteins are built-up from the folding units. Stable Quaternary Structure : p. 64 IV structure is defined as the packing of more than 1 polypeptide chain. The average protein inside a cell has IV structure! What holds these polypeptide chains together: steric and chemical fit of surfaces is the key general principle that describes how the chains are joined. The most important driving force to form IV structure is usually the hydrophobic interaction , i.e. the nonpolar residues on different chains match up and are driven out of water. (But some are still on the outside of the protein exposed to water, along with the charged and polar AA). All the interactions (pp.44-45) can come into play: H-bond partners are found; electrostatic repulsions are minimized, attractions maximized. For some quaternary structures, disulfide bonds hold the chains together.
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There are many examples of proteins that consist of more than one polypeptide chain. For example: Hemoglobin has 4 polypeptide chains, 2 of one type, 2 of another: α 2 β 2 RNA polymerase has 12 subunits ribosomes have 30 - 40 separate polypeptide chains viruses can have 100s of polypeptides muscle filaments many enzymes histones in chromatin Is it significant that many proteins have IV structure? 1. There are "protein machines" e.g. ribosomes, that have complex function, and require more than one polypeptide chain to perform their several tasks. 2.
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This note was uploaded on 02/13/2008 for the course BIOBM 3310 taught by Professor Feigenson,gw during the Fall '07 term at Cornell University (Engineering School).

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Lecture 8 - Monday, September 11, 2006 Lecture 8...

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