1. The Three-Dimensional Structure of Proteins

2. Structure Hierarchy
Primary structure
-- only the sequence of the amino acids and the location of –S-S- bonds
Secondary structure
-- bond angles (conformations) or shape of the polypeptide backbone in a folded protein (doesn’t include side chains)
Tertiary structure
-- total 3-dimensional structure of a protein including side chain bond angles
Quaternary structure
-- in a multi-subunit protein: the arrangement of the subunits through non-covalent interactions (sometimes stabilized by –S-S- bonds)

3. N H O The Peptide Bond -- revisited
Resonance structures
Resonance hybrid: 40% double bond character.
No rotation; planar; trans; polar; forms H-bonds

4. (Glycine is the most flexible.)φ ψ φ ψ
Phi bond angle
Psi bond angle
Glycylalanine
(a dipeptide)
Because of steric clashes, only certain phi and psi angles are allowed, depending on the amino acid.
(Glycine is the most flexible.)

5. Proline Gly-Pro H CH2 O H3N C C N C COO _ + α
Reduced double-bond character
Cis & trans possible (1:4)
Phi angle fixed

6. Regular Secondary Structure
Regions of a protein where:
all phi (ϕ) bond angles are equal
all psi (ψ) bond angles are equal
Some Possibilities:
α-helix φ = ─57o ψ = ─47o
β-sheet φ = ─119o ψ = +113o
(parallel)
β-sheet φ = -139o ψ = +135o
(antiparallel)

7. The α-Helix
3.6 amino acids per turn

10. From the X-ray structure of E.coli aminopeptidase P

19. The β-Sheet
Strands can be parallel (both N- to C-terminal directions the same) or antiparallel (opposite).

20. “β-pleated sheet”

32. Tertiary Structure
Side chains, all atoms
Space-filled

33. (Orientation of subunits) A tetramer (4 subunits, non-covalent)
Quaternary Structure
(Orientation of subunits)
A tetramer (4 subunits, non-covalent)
Colored by subunit

34. colored by type of amino acid
Surface Amino Acids:
colored by type of amino acid
Red: ─ charged, Asp, Glu
Blue: + charged, Lys, Arg
Yellow: other polar
Grey: hydrophobic

35. Slice Through the Middle: colored by type of amino acid
Red: ─ charged, Asp, Glu
Blue: + charged, Lys, Arg
Yellow: other polar
Grey: hydrophobic

36. Domains globular; folds independently; spatially separated;
may have specific function

37. Domains are building blocks (modules)
A specific domain can be found in many proteins
Can carry a specific function
Average size: 100 amino acids (<200)
A constituent of multidomain proteins
Protein C

38. α/β-domain fold (central β-barrel)
Secondary Structure of a Domain called a Fold
Fold: specific arrangement of secondary structure elements
Lysozyme
All α-helix globin fold
α/β-domain fold (central β-barrel)
α/β-domain fold
(twisted β-sheet)
All β-domain fold
(β-barrel “jelly role”)
“Superfolds”

39. Amino Acid Sequence Determines Protein Folding
How?
Predicting 3-dimensional structure from amino acid sequence:
Improvements in theory and computation
Homology modeling:
Search X-ray and NMR structure database for a
protein that has a similar amino acid sequence (template)
Do sequence alignment
Use computer programs to “thread” the protein
sequence through the X-ray structure

40. Identity: 33% Similarity: 55%

41. DNA Mutations
Silent: no effect on protein or
Effect on protein structure or function
folding
aggregation
enzyme activity
protein-protein interaction
regulation
size (truncation, deletion, insertion)
gain of function
There are >140,000 disease-associated mutations
80% are in regular secondary structure, tight turns, and bends. They result in decreased stability of the protein structure.

42. Forces Stabilizing Protein Structures
Bond type Bond strength (kcal/mol)
Covalent >50
Non-covalent
hydrogen bonds
ionic bonds (+ - interaction) (internal)
van der Waals <1
hydrophobic interactions

43. van der Waals hydrophobic interactions

44. Forces Stabilizing Protein Structures
Bond type Bond strength (kcal/mol)
Covalent >50
Non-covalent
hydrogen bonds
ionic bonds (+ - interaction) (internal)
van der Waals <1
hydrophobic interactions

45. Motions in Proteins X-ray structure: average structure over time
Proteins move (“jiggle”) over a picosecond time range (10-12 s).
Each atom is in constant motion.
Much larger conformational changes also occur:
Hexokinase + glucose
Hexokinase—glucose complex
Some proteins or portions of proteins are “unstructured,” and only become structured when they interact with another protein.

46. A Fibrous Protein--Collagen
Most abundant protein in humans
(25-30%)
Three-chain superhelix
(triple helix)

47. Glycine 33%; Proline 10%; Hydroxyproline (Hyp) 10%
Partial Amino Acid Sequence of a Collagen Chain
Glycine 33%; Proline 10%; Hydroxyproline (Hyp) 10%
“Derived amino acids.”
Forms “polyproline type II helix”
3 amino acids per turn
Left-handed
2X more extended than α-helix

48. polyproline helix (G - X - Y)n α - chain Gly Pro Hyp
always common common
α - chain