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Protein Structure
BL4010 09.26.06
The relationship of structure and function
Desirable conformations will be at energy minima
1° structure: amino acid sequence
2° structure: structures localized to certain short stretches
of the polypeptide chain - form wherever possible stabilized by large numbers of H-bonds
3° structure: overall folding of the entire polypeptide
4° structure: overall structure for multimeric proteins
(several polypeptides)
The peptide bond
The Peptide Bond
• 0.133 nm (1.33 Å) - shorter than a typical
single bond but longer than a double bond
• 40% double bond character
• the six atoms of the peptide bond group are
planar (C,C=O,N-H, C)
• Rotation in the polymer occurs at C
• Inherent dipole (N partially positive; O partially
negative)
Limited Rotation about Peptide Bond
• Two degrees of
freedom per residue
for the peptide chain
• Backbone and side
groups limited free
rotation
Further conformational
restriction
Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º trans) due to delocalization of carbonyl pi
electrons and nitrogen lone pair
• φ and ψ are flexible, therefore rotation occurs here
• However, φ and ψ of a given amino acid residue
are limited due to steric hindrance
• Only 10% of the {φ, ψ} combinations are
generally observed for proteins
• First noticed by G.N. Ramachandran
Computed Ramachandran Plot
Plot of φ vs. ψ
The computed angles which are
sterically allowed fall on certain
regions of plot
White = sterically disallowed
conformations (atoms come
closer than sum of van der
Waals radii)
Blue = sterically allowed
conformations
Experimental Ramachandran Plot
X-ray crystallography
Secondary Structure
• Repeating values of φ and ψ along the chain result
in regular structure
• The ability to do this is dependent on steric
considerations...i.e. secondary structure is
dependent to some degree on primary structure
(sequence)
Secondary Structure - alpha helix
•For example, repeating values of φ ~ -57° and ψ ~
-47° give a right-handed helical fold (the alphahelix) e.g. cytochrome c, an alpha helical protein
Secondary Structure - beta sheet
Similarly, repetitive values in the region of φ = -110 to
–140 and ψ = +110 to +135 give beta sheets.
Plastocyanin is composed mostly of beta
Note more allowed regions due to less steric hindrance - Turns
Note less allowed regions due to structure rigidity
Name
φ
ψ
Structure
------------------- ------- ------- --------------------------------alpha-L
57
47
left-handed alpha helix
3-10 Helix
-49 -26
right-handed.
π helix
-57 -80
right-handed.
Type II helices -79 150
left-handed helices
formed by polyglycine
and polyproline.
Collagen
-51 153 right-handed coil formed
of three left handed
helicies.
Hydrogen Bonding
And Secondary Structure
alpha-helix
beta-sheet
Alpha helix
Alpha helix
•Residues per turn: 3.6
•Rise per residue: 1.5 Angstroms
•Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms
•The backbone loop that is closed by any H-bond in
an alpha helix contains 13 atoms
•phi = -60 degrees, psi = -45 degrees
•The non-integral number of residues per turn was a
surprise to crystallographers
Beta sheet
Beta sheet
•Postulated by Pauling and Corey (1951)
•Strands may be parallel or antiparallel
•Rise per residue:
•
–3.47 Angstroms for antiparallel strands
–3.25 Angstroms for parallel strands
–Each strand of a beta sheet may be pictured
as a helix with two residues per turn
Beta turn
•allows the peptide chain to reverse direction
•carbonyl C of one residue is H-bonded to the
amide proton of a residue three residues away
•proline and glycine are prevalent in beta turns
Turns & Random Coils
• Loops & Turns ( turns)
– 1/3 globular protein
– Mostly at surface of protein
– allows the peptide chain to
reverse direction
– C=O H-bonded to the NH three
residues away
– proline and glycine
• Random coil
– can't assign 2° structure,
adopts multiple
conformations depending on
conditions but not random energy minima
– flexible linkers, hinges
Structure Stabilizing Interactions
• Noncovalent
– Van der Waals forces (transient, weak electrical
attraction of one atom for another)
– Hydrophobic (clustering of nonpolar groups)
– Hydrogen bonding
• Covalent
– Disulfide bonds
Disulfide Bonds
• Side chain of cysteine contains highly reactive
thiol group
• Two thiol groups form a disulfide bond
• Contribute to the stability of the folded state by
linking distant parts of the polypeptide chain
Other factors that affect 2° structure
• Prosthetic groups
– Coenzymes
– Cations
• Intramolecular/Intermolecular
bonds
– disulfides
– dityrosine
– aldol cross-linking
Tertiary Structure
• The backbone links between elements
of secondary structure are usually short
and direct
• Proteins fold to make the most stable
structures (make H-bonds and minimize
solvent contact
Protein classification
• Structural motif
• Biochemical function
Protein evolution
•
Divergent evolution
– Similar sequence
– Different function
•Convergent evolution
–Different sequence
–Similar function