Bi1_2009_Lecture5_full

Bi1_2009_Lecture5_full - Tertiary Structure: An Example of...

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Unformatted text preview: Tertiary Structure: An Example of an All-Alpha Protein, Hemoglobin Subunit Rotated 90 Degrees Tertiary Structure: An Example of an All-Beta Protein, Flu Virus Neuraminidase 1) Rotate 90 Degrees Tertiary Structure: An Example of an Alpha/ Beta Protein, Triose Phosphate Isomerase 1) Rotate 90 Degrees Tertiary Structure: An Example of an Alpha + Beta Protein, TATA Binding Protein 1) Rotate 90 Degrees From Tertiary to Quaternary Structure: Hemoglobin as an Example • • • Quaternary structure -- the relative arrangement of two or more individual polypeptide chains Protein assemblies can contain one type of polypeptide (homo-oligomer) or multiple types (hetero-oligomer) Example: Hemoglobin (oxygen carrier in blood) • Hemoglobin is a hetero-tetramer composed of two alpha subunits and two beta subunits Hemoglobin, Tertiary Structure Hemoglobin, Quaternary Structure Tetrameric Hemoglobin Single Subunit PyMol Molecular Viewer Will be used for PS2 and other sets throughout the course Tutorial on Bi1 website Demo by Toni Lee on Friday, April 10 4-6pm Here: (119 Kerckhoff) Structure of GCN4 bound to DNA Grasps DNA like a pair of chopsticks Ellenberger et al., 1992, Cell 71: 1223-1237 Leucine zippers • Leucine region arranged as parallel coiled coil. • Only basic region interacts with DNA. Leucine repeat is a dimerization motif that allows two molecules to dimerize. • Formation of different Leu zipper homo- and heterodimers allows combinatorial action of gene regulatory proteins. • Advantages of binding as a dimer: Doubles DNA contact area Tightly associated dimers can bind at more dilute concentrations than monomers. Zinc fingers Conserved residues circled. Zinc coordinated by two Cys, two His. Zinc finger/DNA complex • • Each finger contacts 3 bp in major groove. Fingers are similar (0.45 Å to 0.87 Å rmsd). Pavletich & Pabo, 1991, Science 252: 809-816. Zinc fingers bind as modules to adjacent sites on DNA Model of HIV protease http://mgl.scripps.edu/projects/tangible_models/movies ...
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