the peptide bond has a rigid, planar structure.
The rigid, planar structure is a consequence of the resonance interactions that give the peptide bond ~40% double bond character.
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Term
Peptide bonds – trans vs cis
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Definition
The 2 amino acids that make up the peptide bond are almost always trans to each other; that is, successive α C’s ( and R groups) are on opposite sides of the peptide bond connecting them.
A planar, fully extended all-trans conformation would appear to be optimum for proteins to minimize steric interactions.
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Term
Trans and Cis conformations of Proline
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Definition
A few peptide bonds will have a cis configuration, especially when the peptide bond is followed by a Pro.
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Term
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Definition
the bonds on either side of the peptide bond are regular single bonds and they are capable of twisting.
These 2 bonds are known as:
C α – C bond -
psi torsion angle (ψ)
N - C α bond –
phi torsion angle (φ)
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Term
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Definition
psi and phi angles are defined as +180° when the polypeptide chain is in its planar, fully extended all-trans conformation and all peptide groups are in the same plane.
•If psi or phi angles rotate clockwise, there is an increase in their ψ or φ values.
•If psi or phi angles rotate counterclockwise, there is an decrease in their ψ or φ values.
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Term
| Role of Steric Interference |
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Definition
However, only certain combinations of ψ and φ will work because other combinations produce steric interference.
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Term
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Definition
| The plot shows ψ and φ angles and the combinations of these angles that will not cause groups to invade each other’s van der Waals space |
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Term
| Main Types of Secondary Structure |
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Definition
Regular
A regular structure occurs when ψ and φ angles remain the same or nearly the same throughout the segment.
Nonrepetitive
A nonrepetitive structure has varying ψ and φ angles
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Term
| Characteristics of Secondary Structure |
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Definition
Secondary structures elements are rarely associated with specific functions
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Term
| Most Common Regular Structure: Helices |
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Definition
| a polypeptide chain is twisted by the same amount about each of its αC atoms, it assumes a helical conformation |
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Term
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Definition
distance the helix rises per turn
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Term
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Definition
number of amino acids per helical turn
Positive n – right-handed helix
Negative n – left-handed helix |
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Term
| Properties of Probable Helices |
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Definition
•must be allowed on the Ramachandran plot
•must allow for maximum bonding interactions
•must allow for H bonding between the
–NH of a backbone amino acid and the C=O of another amino acid.
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Term
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Definition
The α-helix is the only helical polypeptide conformation which has both:
• an allowed conformation
• a favorable H bonding pattern
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Term
| α-Helix for L-amino acids |
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Definition
Most common type of secondary structure. Is found in both globular and fibrous proteins.
Characteristics:
Is right-handed
ψ = - 47°, φ = - 57° (note: angles are both negative, so peptide chain continuously circles)
n = 3.6 residues per turn
p = 5.4 Å
Each –C=O hydrogen bonds to the –NH four amino acids away.
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Term
R Groups of Alpha Helicies
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Definition
R groups all project out and backwards, perpendicular to the helix axis, at 100° intervals.
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Term
| Properties of an average α-helix |
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Definition
Inglobular proteins, the average stretch of α-helix has:
~12 residues
3 helical turns
length of 18Å
In actual proteins, and ψ and φ angles may deviate slightly from the theoretical values. This produces important subtle bends and kinks.
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Term
| Propensity of amino acids to be part of an α-helix |
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Definition
Depends on the R group:
Ala – greatest tendency
Leu, Lys, Met – strong helical formers
Ile, Gln, Glu– pretty good
Asn, Ser, Thr, Cys - bulk and shape destabilize α-helix – too much crowding
Gly and Pro – the worst
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Term
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Definition
α-helices are found within protein structures, often buried within the protein.
They are common in the lipid bilayers of membranes.
Approximately 20 amino acids in an α-helix formation are needed to span a membrane.
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Term
| α-Helix for D-amino acids |
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Definition
All properties are opposite from the α-helix with L-amino acids:
• Left-handed
• ψ = + 57° φ = + 47°
• n = - 3.6 residues per turn
• p = 5.4 Å
Is very rare since D-amino acids are very rare.
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Term
| Left-handed α-helix with L-amino acids |
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Definition
Left-handed α-helices are occasionally seen in proteins.
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Term
| Stability of an α-helix depends on |
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Definition
a.Intrinsic propensity of amino acids to form an α-helix
b.Interactions between R groups
c.Bulkiness of R groups
d.Occurrence of Pro and Gly
e.Interactions of groups at C- and N-termini of helix
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Term
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Definition
nm helices:
n = number of residues / turn
m = number of atoms, including H, in the ring that is closed by the H bond
An α-helix is 3.613
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Term
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Definition
Right-handed
n = 2.2 residues per turn
Φ and ψ combinations are forbidden in the Ramachandran plot. Has strongly forbidden conformation angles.
Has never beenobserved |
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Term
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Definition
Right-handed
n = 3.0 residues per turn
p = 6.0 Å (thinner than α-helix; rises steeply)
R groups are not well staggered and experience some interference
Only occasionally observed in proteins.
Most 310 helices often occur as a single-turn transition at one end of an α-helix.
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Term
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Definition
There is no H on the Nof the peptide bond. (No H bonding occurs.)
The cyclic pyrrolidone side chains cause conformational constraints.
Polyproline I is an all cis right-handed conformation. It is very compact.
Polyproline II is an all trans, left-handed conformation. It is very extended and much more favorable.
Ψ = 150°
Φ = -79°
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Term
| All Trans Polyproline Helix |
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Definition
Left-handed
n = -3.0 residues per turn
p = 9.4 Å
The pitch is very large. The extended conformation permits Pro side chains to avoid each other.
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Term
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Definition
Since glycine has no side chain, polyglycinecan assume ψ, φ angle combinations that no other polypeptide can tolerate.
The helix can be either right-handed or left-handed.
The type II helix is trans, n = 3,
p = 9 Å
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Term
| Where are the helices on the Ramachandran Plot? |
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Definition
α = α helix
αL = left-handed α helix
3 = 310 helix
2 = 2.27 ribbon
π = π helix
II = left-handed polyglycine II and polyproline II helices
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Term
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Definition
The ψ and φ angle combinations in β structures are in an allowed region of the Ramachandran plot.
They also fully utilize the H binding capacity of the –NH and O of peptide bonds
H bonding is not within the immediate chain
Each individual segment of the polypeptide chain is referred to as a β strand.
β strands H bonded to one another to form βsheets
itself, but between neighboring polypeptide chains (H bonds are perpendicular to helical axis).
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Term
| Two Types of β-Pleated Sheets |
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Definition
Antiparallel
Neighboring H bonded chains run in opposite directions
Carbonyl oxygens and amine groups are optimally aligned
Parallel
Neighboring H bonded chains extend in the same direction.
Parallel and antiparallel strands can be mixed within a sheet.
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Term
| Characteristics of polypeptide strands in β-pleated sheets |
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Definition
Parallel: ψ = 113° φ = -119°
Antiparallel: ψ = 135° φ = -139°
Two residue distance is 7.0 Å (antiparallel) and 6.5 Å (parallel).
Amino acids are in trans configuration
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Term
| Where are β Sheets on the Ramachandran Plot? |
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Definition
↑↓ Antiparallel β sheets
↑↑ Parallel β sheets
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Term
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Definition
In 3-D structures of proteins, each β strand is shown as a ribbon with an point.
The arrow points from N-terminus to C-terminus.
For parallel sheets, arrows point in the same direction. For antiparallel strands, arrows point in opposite directions.
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Term
Display of β strands and α helices
Bovine carboxypeptidase A |
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Definition
β-pleated sheets in globular proteins usually have a right-handed helical twist.
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