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L3 Protein Structure
L3 Protein Structure
Protein structure
alanine valine
H2O
peptide bond
H O H
O
amino H3N C C N C C carboxyl
terminus H O terminus
CH3 CH
( amino group)
H3C CH3
alaninylvaline
Characteristics of the peptide bond
H O H
O
H3N C C N C C
H O
R1 R2
Characteristics of the peptide bond
H O H
O
1. partial double-bond character H3N C C N C C
H O
R1 R2
• due to resonance
O R2 O R2
H H
C C O C C O
C C C
N C N
H 3N H H3N H
H O H O
R1 R1
O R2
H
C C O
C C
N
H3N H
H O
R1
Characteristics of the peptide bond
no rotation around
peptide bond
H O H
O
H3N C C N C C
H O
R1 R2
O
O H
C
Rotation around single bonds H
C C
O
C N R2
H3N
H
R1
O R2
R1
C C O
H
C N C
H
H O
NH3
sigma () bond only = “single bond” rotation possible
O
R2
H
C C O
C C
N
H3N H
O
R1 H
Characteristics of the peptide bond
3. Trans configuration
O R2
H
C C O
C C
N
H3N H
H O
R1
Characteristics of the peptide bond - summary
• partial double bond character
• rigid and planar
• trans configuration
• uncharged but polar
amide
trans plane
config
O R2
H
C C O
C C
N
H3N H
H O
R1
Determination of amino acid composition
1. Acid hydrolysis
• cleaves peptide bonds
• destroys (acidifies) Gln and Asn
• Trp mostly destroyed
2. Chromatography
• separates amino acids based on charge and pH
• resin is negatively-charged
• charge is controlled by pH
O S
C
H2N CH C His Phe Leu Arg COOH + N NH
(CH2)4 C CH
O
NH2 CH3
N-terminal PTH-alanine
lysine
Cleavage of peptide into smaller fragments
Left-hand Right-hand
helix helix
Intrachain Hydrogen Bonding is important in maintaining
secondary protein structure. Here (in the α helix) the carbonyl
oxygen from one amino acid is H-bonded to an alpha nitrogen of
the 4th distant amino acid in the polymer.
Hydrogen
bond
• 3.6 residues per turn
N terminal
C terminal
Structural feature
i i +3
Secondary structure
loop
Structural feature
• corner
• extended super secondary structures are known as
domains:
• barrel
• twisted sheet
porin – barrel
Prion
Tertiary Structure
• Tertiary structure is the 3 dimensional form of a
molecule resulting from distant protein-protein
interactions within the same polypeptide chain
(caused by folding of secondary structures):
Hydrophobic interactions
(Van der Waals forces)
Hydrogen bonds
Hydrophobic interactions
(Van der Waals forces)
Hemoglobin is a
heme-containing
protein comprised of
four subunits: 2β2