Download Peptide bonds and side chains Peptide bonds

Protein physics, Lecture 5
Peptide bonds: resonance structure
Properties of proteins:
Peptide bonds and side chains
Proteins are linear polymers
However, the peptide binds and side chains
restrict conformational possibilities
How do the peptide backbone and the amino acid side chains influence
protein structure?
Planar
Peptide bond
Peptide bonds are ‘stiff’
Planarity of the peptide bonds is due to:
• Partial double bond character
• Large dipole moment that inhibits rotation
Resonance forms of a typical peptide group. The uncharged, single-bonded
form (typically ~60%) is shown on the left, whereas the charged,
double-bonded form (typically ~40%) is on the right.
Dihedral angles
Rotation around a bond
Planarity of bond means that
‘cis’ and ‘trans’ forms are possible
Trans form is much more common
due to less steric hindrance
Cis form is most common in Proline
residues
Compare with bond angle
Dihedral angles
Dihedral angles
CE
In general there are 4 dihedral angles
involved in describing protein structure
F
Side chain
\
CD
CE
F
\
CD
N
N
I
Z
C
Z
O
I
C
Backbone
Peptide bond
Planar
O
I and \ are flexible
And account for freedom
One amino acid
of protein structure
Carbonyl
group
Z= 0 or 180
Protein conformation can be described in terms of the amino
acid sequence and dihedral angles: Ii, \i, Fi for each amino
acid residue
Flexibilty of the polypetide chain is restricted by
• Stiff peptide bond
• Steric hindrance – (ie avoiding overlap of atoms)
Ramachandran et al
GN Ramachandran (1922-2001)
Ramachandran plot for glycine
• G.N. Ramachandran (1963) used computer models of small
polypeptides to systematically vary and with the objective of
finding stable conformations
• For each conformation, the structure was examined for close
contacts between atoms
• Atoms were treated as hard spheres with dimensions
corresponding to their van der Waals radii
• Therefore, and angles which cause spheres to collide
correspond to sterically disallowed conformations of the
polypeptide backbone
Ramachandran plot
• Allowed regions are in the 4 corners of the plot
• Prohibitive contacts are indicated
• Note that glycine has no side chain and is
therefore the most flexible
•Plot of vs. •The computed angles which are sterically allowed fall on
certain regions of plot
Can improve using potential energy function rather than hard sphere model.
Just the crosshatched regions
Ramachandran plot for with CE
Ramachandran plot for with CE
Allowed regions correspond to angles that yield
E sheet
D helix
Left hand helix
Repeating values of and along the chain result in regular structure
Experimental Ramachandran plot
, distribution from over 80,000 AA
residues from high-resolution protein
structures (x-ray crystallography)
Prediction using potential
energy function
• About 5% of observed conformations fall in ‘forbidden regions’
• Flexibility of peptide bond needs to be taken into account to improve this
• Deviations of 5o bond angle; 0.05Å bond length or 12o torsion angle (Z)
increases the potential energy by about 1/kcal/mol each
Protein structure example
The structure of cytochrome C shows many segments of helix and
the Ramachandran plot shows a tight grouping of , angles near
-50,-50
alpha-helix
cytochrome C
Ramachandran plot
Protein structure example
Similarly, repetitive values in the region of = -110 to –140 and =
+110 to +135 give beta sheets. The structure of plastocyanin is
composed mostly of beta sheets; the Ramachandran plot shows
values in the –110, +130 region:
Side chain properties
How do the side chains influence protein structure?
Glycine
• Side chain is just H
• Increases side chain flexibility (see Ramachandran plot)
• Can fit chain into small spaces
• Frequency restricted – too much would render
chains to flexible and lose 3D shape
Alanine
• Has one methyl group as side chain
• Smallish – nonpolar
• No real preference for inside or surface of protein
beta-sheet
• Very abundant (due to simplicity and availability?)
plastocyanin
Ramachandran plot
Side chain properties
Side chain properties
Polar side chains
Branched side chains are stiffer
• Cys, Ser, Thr, Asn, Gln, Tyr
• Can form hydrogen bonds
• Often on surface of protein
• Val, Ile, Leu
• Reduce possibilities for chain folding
Cysteine
• Has unique property:
only side chain with exposed S atom
Aromatic residues
• Phe, Trp, Tyr, His
• Can form disulfide bond with another
• Contain one methylene group ’spacer’
Cys further along the chain
• Without this severe steric hinderance
• Used to maintain a given structure of the protein
or to respond to oxidation
• Would make chain too stiff
•Intrinsically fluorescent – particularly Trp
Large non-polar residues
• Leu, Ile, Phe, Pro, Trp
• Predominantly found in the interior of the molecule
Disulfide bond
Side chain properties
Side chain properties
Negative charged side chains
Proline
• Back bone is part of the cyclic group
• Backbone section has a bend
• Invokes bends in the protein chain or kinks in helices
• Asp, Glu
• Negative charge at physiological pH (lose an H+)
• Usually found on protein surface
Positive charged side chains
• Lys, Arg
Histidine
• Positive charge at physiological pH (gain an H+)
• Side chain has pK value of 6.0
• Can be charged or uncharged in the
physiological pH range
• Two readily available states – useful as a catalyst
• Involved in the active site of most enzymes
• Usually found on protein surface
Hydrophobicity
• Folding process of polypetide chain depends
on hydrophobicity (non-polarity) of side chains
• Formation of hydrophobic core is an essential
driving force in protein folding