Protein Structure

1. Protein Structure BL4010 09.26.06

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 57 47 left-handed alpha helix 3-10 Helix -49 -26 right-handed. π helix -57 -80 right-handed. Type II helices -79 150 left-handed helices formed by polyglycine and polyproline. Collagen -51 153 right-handed coil formed of three left handed helicies.

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

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