1. Protein Structure BL

2. The relationship of structure and function
Desirable conformations will be at energy minima
1° structure: amino acid sequence
2° structure: structures localized to certain short stretches of the polypeptide chain - form wherever possible - stabilized by large numbers of H-bonds
3° structure: overall folding of the entire polypeptide
4° structure: overall structure for multimeric proteins (several polypeptides)

3. The peptide bond

4. The Peptide Bond
0.133 nm (1.33 Å) - shorter than a typical single bond but longer than a double bond
40% double bond character
the six atoms of the peptide bond group are planar (C,C=O,N-H, C)
Rotation in the polymer occurs at C
Inherent dipole (N partially positive; O partially negative)

6. Limited Rotation about Peptide Bond
Two degrees of freedom per residue for the peptide chain
Backbone and side groups limited free rotation

8. Further conformational restriction

9. Backbone Torsion Angles
ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl pi electrons and nitrogen lone pair
φ and ψ are flexible, therefore rotation occurs here
However, φ and ψ of a given amino acid residue are limited due to steric hindrance
Only 10% of the {φ, ψ} combinations are generally observed for proteins
First noticed by G.N. Ramachandran

10. Computed Ramachandran Plot
Plot of φ vs. ψ
The computed angles which are sterically allowed fall on certain regions of plot
White = sterically disallowed conformations (atoms come closer than sum of van der Waals radii)
Blue = sterically allowed conformations

11. Experimental Ramachandran Plot
X-ray crystallography

12. Secondary Structure
Repeating values of φ and ψ along the chain result in regular structure
The ability to do this is dependent on steric considerations...i.e. secondary structure is dependent to some degree on primary structure (sequence)

13. Secondary Structure - alpha helix
For example, repeating values of φ ~ -57° and ψ ~ -47° give a right-handed helical fold (the alpha-helix) e.g. cytochrome c, an alpha helical protein

14. Secondary Structure - beta sheet
Similarly, repetitive values in the region of φ = -110 to –140 and ψ = +110 to +135 give beta sheets. Plastocyanin is composed mostly of beta

17. Note more allowed regions due to less steric hindrance - Turns

18. Note less allowed regions due to structure rigidity

19. Name φ ψ Structure
alpha-L left-handed alpha helix
3-10 Helix right-handed.
π helix right-handed.
Type II helices left-handed helices
formed by polyglycine
and polyproline.
Collagen right-handed coil formed
of three left handed
helicies.

20. And Secondary Structure
Hydrogen Bonding
And Secondary Structure
alpha-helix
beta-sheet

21. Alpha helix

22. Alpha helix Residues per turn: 3.6 Rise per residue: 1.5 Angstroms
Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms
The backbone loop that is closed by any H-bond in an alpha helix contains 13 atoms
phi = -60 degrees, psi = -45 degrees
The non-integral number of residues per turn was a surprise to crystallographers

23. Beta sheet

24. Beta sheet Postulated by Pauling and Corey (1951)
Strands may be parallel or antiparallel
Rise per residue:
3.47 Angstroms for antiparallel strands
3.25 Angstroms for parallel strands
Each strand of a beta sheet may be pictured as a helix with two residues per turn

25. Beta turn allows the peptide chain to reverse direction
carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away
proline and glycine are prevalent in beta turns

26. Turns & Random Coils Loops & Turns ( turns) 1/3 globular protein
Mostly at surface of protein
allows the peptide chain to reverse direction
C=O H-bonded to the NH three residues away
proline and glycine
Random coil
can't assign 2° structure, adopts multiple conformations depending on conditions but not random - energy minima
flexible linkers, hinges

27. Structure Stabilizing Interactions
Noncovalent
Van der Waals forces (transient, weak electrical attraction of one atom for another)
Hydrophobic (clustering of nonpolar groups)
Hydrogen bonding
Covalent
Disulfide bonds

28. Disulfide Bonds
Side chain of cysteine contains highly reactive thiol group
Two thiol groups form a disulfide bond
Contribute to the stability of the folded state by linking distant parts of the polypeptide chain 

29. Other factors that affect 2° structure
Prosthetic groups
Coenzymes
Cations
Intramolecular/Intermolecular bonds
disulfides
dityrosine
aldol cross-linking

30. Tertiary Structure
The backbone links between elements of secondary structure are usually short and direct
Proteins fold to make the most stable structures (make H-bonds and minimize solvent contact

31. Protein classification
Structural motif
Biochemical function

32. Protein evolution Divergent evolution Similar sequence
Different function
Convergent evolution
Different sequence
Similar function