Protein Chemistry & Structure
Levels of Protein Structure
Primary structure = order of amino
acids in the protein chain
Anatomy of an amino acid
Non-polar amino acids
Polar, non-charged amino acids
Negatively-charged amino acids
Positively-charged amino acids
Charged and polar R-groups tend
to map to protein surfaces
Non-polar R-groups tend to be
buried in the cores of proteins
Myoglobin
Blue = non-polar
R-group
Red = Heme
Some R-groups can be ionized
The Henderson-
Hasselbalch
equation allows
calculation of the
ratio of a weak acid
and its conjugate
base at any pH
General protein pK’ values
	

 	

 	

 Approximate pK'	

Group	

 	

 	

In a “Typical” Protein	

α-carboxyl (free) 	

3 (C-terminal only)	

β-carboxyl (Asp) 	

4	

γ-carboxyl (Glu) 	

4	

imidazole (His) 	

6	

sulfhydryl (Cys) 	

8	

1˚α-amino (free) 	

8 (N-terminal only)	

ε-amino (Lys)	

 	

10	

hydroxyl (Tyr)	

 	

10	

2˚α-amino (Pro)(free)	

9 (N-terminal only)	

guanido (Arg)	

 	

12	

Some R-groups can modified
Amino Acids Are Joined By
Peptide Bonds In Peptides
- α-carboxyl of one amino acid is joined to
α-amino of a second amino acid (with
removal of water)
- only α-carboxyl and α-amino groups are
used, not R-group carboxyl or amino
groups
Chemistry of peptide bond formation
The peptide bond is planar
This resonance
restricts the number
of conformations in
proteins -- main
chain rotations are
restricted to φ and ψ.	

Primary sequence reveals important
clues about a protein
DnaG E. coli	

 ...EPNRLLVVEGYMDVVAL...	

DnaG S. typ	

 ...EPQRLLVVEGYMDVVAL...	

DnaG B. subt	

 ...KQERAVLFEGFADVYTA...	

gp4 T3	

 ...GGKKIVVTEGEIDMLTV...	

gp4	

 T7	

 ...GGKKIVVTEGEIDALTV...	

:	

 *	

:	

 :	

:	

 *	

 *	

 :	

 :	

small hydrophobic	

large hydrophobic	

polar	

positive charge	

negative charge	

• Evolution conserves amino acids that are important to protein
structure and function across species. Sequence comparison
of multiple “homologs” of a particular protein reveals highly
conserved regions that are important for function.
• Clusters of conserved residues are called “motifs” -- motifs
carry out a particular function or form a particular structure that
is important for the conserved protein.
motif
Secondary structure = local folding
of residues into regular patterns
The α-helix
• In the α-helix, the carbonyl
oxygen of residue “i” forms a
hydrogen bond with the
amide of residue “i+4”.
• Although each hydrogen
bond is relatively weak in
isolation, the sum of the
hydrogen bonds in a helix
makes it quite stable.
• The propensity of a peptide
for forming an α-helix also
depends on its sequence.
The β-sheet
• In a β-sheet, carbonyl
oxygens and amides form
hydrogen bonds.
• These secondary
structures can be either
antiparallel (as shown) or
parallel and need not be
planar (as shown) but can be
twisted.
• The propensity of a peptide
for forming β-sheet also
depends on its sequence.
β turns
• β-turns allow the protein backbone to make abrupt turns.
• Again, the propensity of a peptide for forming β-turns depends
on its sequence.
Which residues are common for αhelix,
β-sheet, and β-turn elements?
Ramachandran plot -- shows φ and ψ
angles for secondary structures
Tertiary structure = global folding of
a protein chain
Tertiary structures are quite varied
Quaternary structure = Higher-order
assembly of proteins
Example of tertiary and quaternary
structure - PriB homodimer
Example is PriB replication protein solved at UW: Lopper, Holton, and Keck
(2004) Structure 12, 1967-75.
Example of tertiary and quaternary
structure - Sir1/Orc1 heterodimer
Example is Sir1/Orc1 complex solved at UW: Hou, Bernstein, Fox, and Keck
(2005) Proc. Natl. Acad. Sci. 102, 8489-94.
Examples of other quaternary
structures
Tetramer Hexamer Filament
SSB DNA helicase Recombinase
Allows coordinated Allows coordinated DNA binding Allows complete
DNA binding and ATP hydrolysis coverage of an
extended molecule
Classes of proteins
Functional definition:
Enzymes: Accelerate biochemical reactions
Structural: Form biological structures
Transport: Carry biochemically important substances
Defense: Protect the body from foreign invaders
Structural definition:
Globular: Complex folds, irregularly shaped tertiary structures
Fibrous: Extended, simple folds -- generally structural proteins
Cellular localization definition:
Membrane: In direct physical contact with a membrane; generally
water insoluble.
Soluble: Water soluble; can be anywhere in the cell.