lec04 - MIT OpenCourseWare http:/ocw.mit.edu 7.88J Protein...

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MIT OpenCourseWare http://ocw.mit.edu 7.88J Protein Folding Problem Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
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7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding Problem Professor Gossard – “Retrieving, Viewing Protein Structures from the Protein Data Base” Helix helix packing Packing of Secondary Structures One of the determinants of the shapes of proteins and the folds is the packing of the units of secondary structure against each other. In trying to interpret fibrous diffraction patterns from muscle, Frances Crick Model: surface of helices composed of knobs and holes. Orientation angles of +20 and -70 yield good contact. With the accumulation of solved protein structures - However these helices very long, not interrupted by turns, loops or beta strands: What is distribution and organization of helices in globular proteins: Helical Protein Subset; T With the accumulation of solved protein structures "Helix to Helix Packing in Proteins" Cyrus Chothia, Michael Leavitt and Doug Richardson (1981) J. Mol. Biol 145, 215- 250. Analyzed the actual packing of helices against each other in a set of globular proteins. Analyzed 50 contacts, 100 surfaces. Helices ranged from 6 to 23 residues long, mean of 15. The intersections of the helix surfaces – interfaces had between 3 and 7 residues in van der waal’s contact, mean 4.7. How many contacts in coiled coil stretch of 10 amino acids? Depends on helix length; from packed helices independent of helix length! If one plots the angle, defined thusly…
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lec04 - MIT OpenCourseWare http:/ocw.mit.edu 7.88J Protein...

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