Overview and Themes of Protein Structure

1
Overview and Themes of Protein Structure

• The three-dimensional structure of a protein is
  determined by its primary sequence.
• A proteins function is dictated by its primary
  sequence.
• Any isolated protein of a given primary sequence
  will have a unique or near unique structure.
• There exist common protein structural patterns
• Non-covalent interactions are most important in
  stabilizing protein structure.
• Reading (Chap 6 pp 159-169 Lehninger).

2
Protein Conformation

• Need to distinguish conformation from
  configuration.
• Configuration denotes the geometric possibilities
  for a particular set of atoms. In changing
  configuration, covalent bonds must be broken. A
  particular stereochemistry about a given center
  is considered to be a configuration. The primary
  sequence of a protein is a configuration.
• Conformation denotes the 3-D architecture of a
  protein. It is established by a variety of weak
  forces. In contrast to configuration,a
  conformation can change readily.
• The conformation of a protein is first and
  foremost established by its primary structure
  (amino acid sequence). Its interaction with
  solvent (generally H2O) and the pH and ionic
  composition are also critical in establishing
  and/or maintaining a proteins conformation.

3
Forces that Influence Protein Structure

• Hydrogen bonds - The atoms of the peptide bond
  will tend to form hydrogen bonds whenever
  possible. Amino acid side chains that are
  capable of forming hydrogen bonds will typically
  be found on the surface of proteins, so that they
  may interact with water. Although the energy of
  the hydrogen bond (12 kJ/mol) is fairly weak
  when compared to covalent interactions, they are
  numerous, and together contribute a significant
  amount of energy and stability to protein
  conformation.
• Hydrophobic interactions - The interior of are
  proteins almost exclusively contain amino acids
  with hydrophobic side chains. Well find that
  the need to bury hydrophobic side chains of amino
  acids is what drives a protein to fold into its
  proper conformation.
• Van der Waals interactions - induced electrical
  interactions. Contribute significantly to
  conformational stability in the interior of the
  protein.

4
Electrostatic Interactions

• Charged groups are normally found on the exterior
  of the protein.
• They may interact with oppositely charged
  species.
• The strength of the interaction is dependent on
  the concentration of dissolved salts (dielectric)

5
Structure of the Peptide Bond

• X-ray diffraction studies of crystals of small
  peptides by Linus Pauling and R. B. Corey
  indicated that the peptide bond is rigid, and
  planer.
• Pauling pointed out that this is largely a
  consequence of the resonance interaction of the
  amide, or the ability of the amide nitrogen to
  delocalize its lone pair of electrons onto the
  carbonyl oxygen.
• Because of this resonance, the CO bond is
  actually longer than normal carbonyl bonds , and
  the NC bond of the peptide bond is shorter than
  the NCa bond.
• Notice that the carbonyl oxygen and amide
  hydrogen are in a trans configuration, as opposed
  to a cis configuration. This configuration is
  energetically more favorable because of possible
  steric interactions in the other.

6
The Amide Plane

• As we talked about earlier, because of the
  resonance between the amide nitrogen and the
  carbonyl oxygen, the peptide bond is planar and
  fixed.
• However, rotation around bonds connected to the
  alpha carbon is permitted.
• Angle y corresponds to the angle between alpha
  carbon and carbonyl carbon. It is 0 when the
  amide plane containing the carbonyl bisects the
  alpha carbon in a cis conformation.
• Angle f corresponds to the angle between the
  alpha carbon and the amide nitrogen. It is 0
  when the amide plane containing the nitrogen
  bisects the alpha carbon in a cis conformation.
• Both ? and f are defined as 180C when the
  polypeptide is in its fully extended
  conformation, and all peptide groups are in the
  same plane.

7
Forbidden Conformations
Some f and y combinations are forbidden because
of steric crowding.
8
Ramachandran Diagrams

• G. N. Ramachandran (Madras, India) showed the
  distribution of f and y angles in polypeptides
  containing polyalanine residues.
• The shaded areas represent the areas having the
  most favorable f and y angles.
• Notice that most f and y combinations are in fact
  sterically forbidden (White Space).

9
Secondary Structures

• In almost all proteins, the carbonyl oxygens and
  amide protons of many peptide bonds participate
  in hydrogen bonding.
• The alpha helix is one of two basic secondary
  structures that are stabilized by hydrogen bonds.
• The beta-pleated sheet is the second of the two
  basic structures that are stabilized by hydrogen
  bonds.
• Other important structures include beta turns and
  beta bulges.

10
The alpha-helix

• In the alpha-helix, there are 3.6 amino acid
  residues per turn. This initially perplexed
  Linus Pauling and Max Perutz in their struggle to
  determine the structure. They had supposed that
  there would be an integral number of residues per
  turn.
• There are also 13 atoms along the peptide
  backbone per turn. This standard helical
  conformation is called a 3.613 helix.
• The rise of the helix is 1.5 angstroms per
  residue.
• The pitch is the length of the helix per turn,
  and can be calculated from the rise and the
  number of amino acids per turn.
• The pitch of a standard helix is 5.4 angstroms.
• Ignoring side chains, the helix is about 6
  angstroms in diameter.
• Amino acid residues in an a-helix have
  conformations with j 4550, and f 60.
  This combination of angles prevents steric
  repulsion from R groups.

13
3.6 residues 5.4 Å
10
8
12
11
9
4
7
6
2
3
5
1
Look at first four amides and last four
carbonyls. Cannot hydrogen bond. Therefore, the
helix must be capped by amino acid size chains
that are capable of forming hydrogen bonds.
11
Handedness of a-helix

• The a-helix has a handedness associated with it.
  
• All a helices that are composed of L-amino acids,
  are right-handed helices.
• All a-helices that are composed of D-amino acids,
  are left-handed helices.
• Mixtures of D and L amino acids will not allow
  a-helices to form.
• To determine the handedness of an a-helix, close
  either your left hand or your right hand, and
  point your thumb upwards. If the helix spirals
  up in the same direction as the fingers of your
  right hand, it is a right handed helix. If it
  spirals up in the same direction as the fingers
  of your left hand, then it is a left-handed helix.

12
The Polarity of the Peptide Bond
13
The Helix Dipole

• Each carbonyl of the helix is hydrogen bonded to
  the peptide amide proton four residues farther up
  the chain.
• All hydrogen bonds are parallel to the helix
  axis.
• All carbonyl oxygens point in one direction,
  while all of the amide protons point in the
  opposite direction.
• This gives the helix a macroscopic dipole moment
  from the individual dipoles.
• Negatively charged species will frequently bind
  near the N-terminus of an alpha helix because of
  the positive dipole.

14
Other Helices

• In a typical a-helix containing n residues (amino
  acids), there are n-4 hydrogen bonds. The first
  four amide hydrogens and the last four carbonyl
  hydrogens cannot form helix hydrogen bonds. This
  is because each carbonyl is hydrogen bonded to
  the peptide amide proton four residues farther up
  the chain.
• For backbone amide protons and carbonyl groups
  not involved in helix hydrogen bonding, they are
  frequently capped with H-bonding partners from
  amino acid side chains.
• There are other types of a-helices. One well
  known a-helix is a 310 helix. This means that
  there are 3 residues per turn, and that there are
  10 backbone atoms per turn.

On the above figure, P pitch. N number of
repeating units (amino acids). You should be
able to calculate the rise from the pitch, which
is usually in angstroms, and the number of
repeating units.
15
Helix Stability

• The ability of helices to form is strongly
  dependent upon the nature of a particular stretch
  of amino acids (side chains).
• In studies of stretches of polyamino acids, such
  as poly L, poly K, poly A, poly D, it was found
  that the ability to form helices is strongly
  dependent upon the charge of the amino acid side
  chain.
• Poly L and poly A are strong helix formers. Poly
  D and poly E form random structures at pH 7.0
  because of charge repulsion from the negatively
  charged carboxylates. At low pH, they form
  helices. Poly K forms helices only above pH 11,
  where its side chain is neutral.
• Proline acts as a helix breaker, because of the
  restricted rotation around CaNC. The
  resulting angle, f, does not correspond with the
  values for typical a-helices. Therefore, proline
  gives a destablizing effect on a-helices.
• Glycine occurs infrequently in a-helices as well.
  The reason is that there is more conformational
  flexibility about the peptide bonds that can
  rotate because of lack of an R group. This
  flexibility makes the helix a less rigid
  structure around glycine residues, causing them
  break the helix.

16
Beta-Pleated Sheets

• The b-pleated sheet was also postulated by
  Pauling and Corey in 1951 as an alternative
  structure to a-helices. It was subsequently
  detected in natural proteins.
• In contrast to the a-helix, the peptide backbone
  in b-pleated sheets is in an extended form.
  Also, in contrast to the a-helix, the hydrogen
  bonds are interstrand rather than intrastrand.
• Notice that the hydrogen bonds still occur
  between the backbone amide protons and carbonyl
  oxygens.
• Because of the tetrahedral nature of the alpha
  carbon and the planarity of the peptide bond, the
  extended structure appears pleated.
• Note that the R groups are perpendicular to the
  peptide backbone plane (sheet), and alternate
  from face to face.

Strip
Strip
Strip
Strip
17
Types of b-Pleated Sheets

• Antiparallel b-pleated sheets. The strands that
  are involved in hydrogen bonds run in opposite
  directions. One runs in the C to N direction,
  while the other runs in the N to C direction.
  The distance between residues in the antiparallel
  sheet is 0.347 nm.
• Parallel b-pleated sheets. Both strands that are
  involved in hydrogen bonding run in the same
  direction. Either C to N, or N to C. Notice
  that the hydrogen bonding contacts are not as
  straight (optimal) as in the antiparallel case.
  This places limits on f and y angles that will
  allow an energetically feasible parallel
  structure. This distance between residues in the
  parallel case is 0.325 nm, which is shorter than
  in the antiparallel case. This shorter
  difference is due to a slight bending of the
  chain which is necessary to form decently strong
  hydrogen bonds.
• Since the range of f and y angles in the parallel
  sheet is more restricted, parallel sheets have
  more of a defined or regular structure than
  antiparallel sheets.

Parallel
Antiparallel
18
Depictions from Lehninger of antiparallel and
parallel b sheets (conformations)
19
The Beta-Turn

• Helices and b-pleated sheets are secondary
  structures that run in one direction. For
  globular proteins, it is necessary to change
  directions in order to define the boundaries of
  the protein. This is frequently accomplished
  via a b-turn.
• In a b-turn, a tight loop is formed from hydrogen
  bonding of a carbonyl oxygen of the peptide
  backbone with an amide proton 3 residues away
  along the chain. This results in a 180 turn.
• Two types of b-turns are very common (type 1 and
  type 2). In type 2 turns, glycine is frequently
  found in position 3 of the turn.
• Proline and glycine occur frequently in b-turns.
  Proline can force formation of a b-turn because
  of its fixed f angle. This would promote
  formation of antiparallel strands. Glycine can
  adapt easily to a variety of structures because
  of its absence of a side chain.

20
b-Turn (Lehninger)
glycine
Most peptide bonds not involving proline are in
the trans configuraton (gt99.95). For peptide
bonds involving proline, about 6 are in the cis
configuration. Most of this 6 involve b-turns.
21
1
2
3

• Ramachandran diagram of characteristic psi and
  phi angles for different types of secondary
  structures
• Phi and psi angles for all amino acids in the
  protein pyruvate kinase (glycine is excluded).
• 3. Relative probability of occurrence of a
  particular amino acid in one of three different
  secondary structures.