1. Protein Secondary Structure Lecture 2/19/2003

2. Three Dimensional Protein Structures Confirmation: Spatial arrangement of atoms that depend on bonds and bond rotations. Proteins can change conformation, however, most proteins have a stable “native” conformation. The native protein is folded through weak interactions: a) hydrophobic interaction b) Hydrogen bonds c) Ionic bonds d) Van der Waals attractions

3. A Denatured protein is unfolded, random dangling, and often precipitated (cooking egg whites). The Native conformation is dictated by its amino acid sequence.  primary structure is everything. A one dimensional strand of DNA contains four dimensional data: height width depth life span!!

4. The Amide bond Linus Pauling and Corey determined the structure of the peptide bond by X-ray. 40% double bond character. The amide bond or peptide bond C-N bond is 0.13A  shorter than C  -N bond. The carbonyl bond is.02 A  longer then those for ketones and aldehydes Resonance gives 85 kJmole -1 stability when bond is planar!!

5. Peptide bonds are planar Resonance energy depends on bond angle: 180  is max angle  cis or trans peptide bond. Most peptide bonds are trans, 10% that follow proline may be cis Note: differences between bond angles and bond lengths comparing cis and trans forms.

6. Torsion angles Rotation or dihedral angles C  -N  phi C  -C  psi When a peptide chain is fully extended the angles are defined as 180  or -180 . At 180  one gets a staggered conformation. (all trans) i.e. ethane Note: alternating C=O pointing in opposite directions.

7. When viewed down the N to C terminus axis, rotation to the right or clock wise increases the angle of rotation. Must start with the fully extended form which is defined as 180 o or -180 o Note: this picture and the one in the book is not correct!! The  angle should go the the other direction

8. Rotate clockwise start at -180 o and increase angle Rotate counter clockwise start at +180 o and decrease angle This is C  -carbonyl bond or psi angle,  Start with fully extended protein structure

9. Ethane can exist as staggered or eclipsed conformation Staggeredeclipsed There is a 12 kJmole -1 penalty in energy for an eclipsed geometry Bulky amino acid side chains have a much higher energy penalty. There are a few favored geometries which the protein backbone can fold

10. If all  +  angles are defined then the backbone structure of a protein will be known!! These angles allow a method to describe the protein’s structure and all backbone atoms can be placed in a 3d grid with an x, y, z coordinate.

11. Ramachandran plot If you plot  on the y axis and  on the x axis, you will plot all possible combinations of , . This plot shows which angles are allowed or which angles are sterically hindered for poly-l-alanine

12. Secondary structure can be defined by  and  angles    helix rt handed-57-47  sheet-119113   sheet-139135 3 10 helix-49-26 collagen-51153 Repeating local protein structure determined by hydrogen bonding helices and pleated sheets. 12 proteins except for Gly and Pro

13. Steric hindrance between the amide nitrogen and the carbonyl  = -60 o and  = 30 o