Download Protein Structure Peptide bonds Polypeptides

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Protein Structure
Stryer Short Course
Chapter 4
Peptide bonds
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Amide bond
Primary structure
N‐ and C‐terminus
Condensation and hydrolysis
Polypeptides
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Drawing Peptides
• Sidechains
• Stereochemistry
• Ionization states
• Example: Draw the peptide AHSCVE at pH 8.
• Steps
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–
–
–
Backbone
Stereochemistry
Sidechains
Check ionization
Example: Draw the peptide AHSCVE at pH 8.
Step 1
O
O
H
N
O
H
N
H3N
H
N
N
H
N
H
O
O
O
Step 2
O
O
O
H
N
O
H
N
H3N
H
N
N
H
N
H
O
O
O
O
Step 3
OH
CH3
O
O
H
N
O
H
N
H3N
H
N
N
H
N
H
H
N
O
O
O
O
SH
pKa 6
pKa 4
HO
N
O
Step 4
OH
CH3
O
O
H
N
O
H
N
H3N
H
N
N
H
H
N
O
N
H
O
O
O
SH
pKa 6
N
pKa 4
O
O
Disulfide bond formation
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Primary Structure •
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Protein defined by unique primary sequence
Structure defined by primary sequence
Function dictated by structure
Basis of understanding mutation
Basis of Secondary Structure
• Polarity
• Rigidity
• Planarity
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Cis and Trans Peptide Bonds
• Double bond character
• Slowly interchangeable
• Trans heavily favored—steric interactions
Conformational Constraint
NOT cis/trans
Ramachandran Plots
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Alpha Helix
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•
•
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Right handed
Polarity
n and n + 4
Gly and Pro
Helical Wheel
• The sequence of a domain of the gp160 protein(HIV) is shown below using one‐letter codes for the amino acids. Plot this sequence on the helical wheel. What do you notice about the amino acid residues on either side of the wheel? MRVKEKYQHLWRWGWRWG
W
Q
M
R
E
R
K
W
H
G
R
W
Y
G
K
V
L
W
Beta Sheets
• Parallel
• Antiparallel
• mixed
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Amphipathic Sheets
• Alternating sidechains can lead to amphipathic sheets
Irregular Secondary Structure
• Nonrepeating loops and turns
• Change of direction
• Turns have about 4 residues
• Internal H‐bonds
• Gly, Pro 6
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Tertiary Structure
• Too many shapes to memorize
• But not an infinite number of possibilities
• Take away the ability to read a paper
– Discussions of motifs and why important
– Discussion of domains and why important
Motifs (Super Secondary Structure)
• Recognizable combinations of helices, loops, and sheets
• Match
– Helix‐turn‐
helix
– Helix bundle
– Hairpin
– ‐sandwich
Studying Motifs
• Some Motifs are highly studied
• Know the lingo
– Leucine zipper
– Zinc finger
• Often have recurring applications
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Structural and Functional Domains
• Discrete, independently folded unit (may maintain shape when cleaved on loop)
• May have separate activities: “ATP binding domain” or “catalytic domain”
• Similar activity = similar structure across many proteins
• Binding pockets at interfaces
How many domains?
Common Domains
Quaternary Structure
• Multiple subunits: Oligomers
• Homodimer, heterotetramer
• Advantages
2
3
2 2
– Economy
– Stability
– regulation
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Protein Structure
• Fibrous Proteins
– Keratin—coiled coil
– Collagen—triple helix
• Globular Proteins
– Myoglobin
Collagen
• Repeating Gly
and Pro
• Hyp: hydroxyproline
– Oxidized form
– Requires vitamin C
– Scurvy
Collagen
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Myoglobin
• Globular Protein
• Hydrophobic effect
• Helix bundle
• Polar loops
• Nonpolar core
Protein Folding
• Native vs denatured states
• G might be 40 kJ/mol for small protein (about 2 H‐bonds)
• Classic Anfinsen experiments show folding info contained in primary sequence (in many cases)
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Thermodynamics and Kinetics
• Levinthal’s paradox: not random sampling of all possible conformations
• Energy funnel
• Series of irreversible steps
• Entropy traps
More than one fold
• Traditionally, one protein = one fold
• Intrinsically Unstructured Proteins (IUPs) are more common than originally thought
• Metamorphic proteins
– Cytokine with equilibrium of two structures with necessary function
Misfolding Pathology
• Amyloidoses
– Alzheimer, Parkinson, Huntington, prion
• Mad Cow Disease: prions as the infectious agent
• Formation of amyloid fibers
– The less stable protein form accumulates into a nucleus, which grows to a fibril
– Aggregations cause damage—oxidation??
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