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Biochemistry of Proteins
Biochemistry of Proteins
Stryer
Biochemistry
Proteins: Polymers of Amino Acids
amino R acid
NH2 Ca COOH
H
R1
NH2 Ca COOH R1 R2
H R2 NH2 Ca CO NH Ca COOH
NH2 Ca COOH H H
Also titratable
Note the axes groups in side chain
Amino Acids with Aliphatic R-Groups
Glycine Gly - G 2.4 9.8
Primary Structure
The order of amino acids: Protein sequence
Secondary Structure
Local conformation, depends on sequence
Tertiary/Quaternary Structure
Overall structure of the chain(s) in full 3D
Beyond Primary Structure:
The Peptide Bond
Partial double-bond:
H H
-
-
-C - N- -C = N-
-
O O-
Peptide bond
Resonance structures
Implications of Peptide Planes
f R H
Ca
Ca Ca
H R
Peptide planes
f R H
Ca
Ca Ca
H R H R
H-bond
Secondary Structure- b Sheet
3 4
2 1
helix
Domain
EGF
Protease
Kringle
Ca-binding
Tertiary Structure
Definition: Overall 3D form of a molecule
Organization of the secondary structures/
motifs/domains
Optimization of interactions between residues
A specific 3D structure is formed
h-CaM A T V R L L E W E D L
b-CaM A T V R L L E Y K D L
5 10
conservative non-conservative
Proteins Fold To Their
Native Structure
Folded proteins are only marginally stable!!
~0.4 kJ•mol-1 required to unfold (cf. ~20/H-bond)
Balance loss of entropy vs. stabilizing forces
Stabilizing
Inter-strand
H-bonds
Gly-Pro-Pro Repeat
Extracellular
Membrane-
spanning
Intracellular
(cytoplasmic)
1. Steric access
2. Shape
3. Hydrophobic
accessible surface
4. Electrostatic surface
Calmodulin
Ca2+
Target
SequenceStructureFunction
Many sequences can give same structure
Side chain pattern more important than
sequence
When homology is high (>50%), likely to have same
structure and function (Structural Genomics)
Cores conserved
Surfaces and loops more variable
Heme
Thioredoxin