Chapter 6: ThreeDimensional Structure of Proteins

1
Chapter 6 Three-Dimensional Structure of Proteins

• 3-D Structure determined by AA sequence
• Function Structure
• Isolated protein has unique or nearly unique
  structure
• Most important stabilizing forces are noncovalent
• Common structural patterns

2
Overview

• Spatial arrangement is called its conformation.
• Any structural state that is achieved without
  breaking covalent bonds.
• Most likely conformation one with the lowest ?G
  (native confirmation)

3
Protein Stability

• Stability tendency to maintain a native
  confirmation
• energy difference between folded and unfolded
  is 20 65 kJ/mol.
• entropy and hydrogen bonding tend to maintain
  unfolded state.
• Bond strength covalent ? 200 460 kJ/mol
• noncovelant ? 4 30 kJ/mol

4
Peptide Bond is Planar and Rigid

• Six atoms of the peptide group lie in a single
  plane.

5
Secondary Structure

• Local conformation of some part of the
  polypeptide.
• a. a-helix
• b. ß-sheet
• Predicted in 1951 by Pauling and Corey 7 years
  before first structure elucidated.

6
Secondary Structure (Contd)

• Hydrogen bonds involving carbonyls and amines.
• e.g. a-keratin regular structure repeats every
  5.15 to 5.2 Angstroms.
• Helix structure is simplest structure rigid
  backbone can achieve.
• each turn roughly 3.6 AAs residues.
• turns always right-handed.
• about ¼ of all AA residues in PPs are found in
  helices.

7
Helices (Contd)

• Optimal use of H-bonds
• With helix, every peptide bond involved in H-bond
• Form with either D or L AAs
• must all be same stereoisomer

8
Stability of Helices

• Affected by AA sequence
• Long block of Glu residues will not form H-bonds
  (repulsive forces) same with Arg or Lys
• Bulk and shape of Asn, Ser, Thr, and Cys tends to
  inhibit helix formation
• Proline rigidity of peptide linkage, lack of
  hydrogen on N
• Gly conformational flexibility polymers of Gly
  tend to form coiled structures different than
  a-helices.

9
5 Factors Affecting Stability of Helices

• Electrostatic attraction or repulsion between
  successive AAs
• Bulkiness of adjacent R groups
• Interactions between residues 3 4 positions
  apart
• Occurrence of Pro and Gly
• Interaction between residues at ends of helix

10
?-Sheets

• Backbone is zig-zag structure instead of helix
• Arranged side by side to form a series of pleats
  held together by H-bonds
• Adjacent sheets can have parallel or
  anti-parallel orientation
• R groups tend to be small (Gly, Ala)

11
ß-Turns

• In globular proteins, 1/3 of AAs are in turns or
  loops where chain reverses direction (connect
  runs of helices or sheets)
• ?-Turns 180o turn involving 4 AAs
• H-bond between carbonyl of 1st and amino of
  4th
• Gly and Pro flexibility imino N of Pro readily
  adopts cis confirmation
• Found near surface, 2 inner residues form H-bond
  with water.
• Table 6-10

12
Tertiary and Quaternary Structures

• Tertiary overall 3-D structure (folding)
• Bend-producing residues Pro, Thr, Ser, and
  Gly
• Quaternary arrangement of protein subunits
• 1. Fibrous proteins arranged in strands or
  sheets
• 2. Globular proteins spherical or globular
  shape.

13
Fibrous and Globular

• Fibrous largely single type of secondary
  structure
• Globular several types of secondary structures
• Fibrous support, shape, and external protections
• Globular enzymes and regulatory functions

14
a-Keratin, Collagen and Silk

• Give strength and flexibility ? single repeating
  element of secondary structure
• Fibrous proteins are insoluble in water
  (hydrophobic residues)

15
a-Keratin

• Hair, wool, nails, claws, quills, horns, hooves
  and much of the outer layer of skin
• Intermediate filament (IF) proteins
• Right-handed helix
• Watson and Pauling predicted coiled coil.
• Two strands oriented parallel
• Helical path of supertwist is left-handed

16
a-Keratin (contd)

• Surfaces that are in contact made up of
  hydrophobic residues (R groups meshed together in
  a regular interlocking pattern)
• Close packing of chains
• Ala, Val, Leu, Ile, Met, and Phe
• Tertiary Structure dominated by alpha helical
  secondary structure with its helical axis twisted
  in a left-handed superhelix.
• Refer to picture on page 171

17
Collagen

• Connective tissue such as tendons, cartilage, the
  organic matrix of bone, and the cornea
• Helix is left-handed and 3 AA residues per turn
• Coiled coil 3 separate PPs (alpha chains)
  supertwisted around each other to form a
  right-handed superhelix

18
Collagen (contd)

• 35 Gly, 11 Ala, and 21 Pro and HyPro
• Gelatin low in essential AAs
• Repeating tripeptide unit Gly-X-Pro or
  Gly-X-HyPro where X can be any residue
• Only Gly fits in tight junctions between
  chains
• Close packing of PP chains
• See picture at bottom of page 173.

19
Collagen (contd)

• Chains cross-linked by unusual types of covalent
  bonds (Lys, HyLys, or His)
• See picture on page 174.
• Typical mammal has more than 30 variants of
  collagen that occur in different tissues.
• Osteogenesis imperfecta abnormal bone formation
  in babies
• Ehlers-Danlos Syndrome loose joints
• Cys or Ser for Gly ? disrupt repeat unit

20
Silk Fibroin

• Produced by insects and spiders in PP chains
  predominantly in the beta conformation
• Rich in Ala and Gly residues (close packing of
  beta sheets and interlocking arrangement of R
  groups).
• See picture on page 174.
• Stabilized by extensive H-bonding between all
  peptide linkages
• does not stretch beta sheets fully extended.
• held together by weak interactions - flexible

21
Globular Proteins

• Enzymes, transport proteins, motor proteins,
  regulatory proteins, etc
• Protein Data Bank (PDB)

22
Myoglobulin

• John Kendrew et al. (1950s)
• Oxygen binding protein in muscle cells
• stores oxygen and facilitates oxygen diffusion
  in rapid muscle movement
• Single PP 153 Aas and single iron
  protoporphyrin (heme)
• Discuss pictures on page 176

23
Myoglobin (contd)

• Abundant in diving mammals (brown muscles)
• Longest helix (23 AAs), shortest (7 AAs)
• gt70 of AAs in helices
• Hydrophobic R groups in interior
• Hydrophilic (polar) on the surface and hydrated

24
Myoglobin (contd)

• All peptide linkages in planar trans conformation
• 3 of 4 Pro residues are at bends
• 4th is in helix ? creates kink for packing
• Ser, Thr, Asn ? in bends
• Fe has two binding sites one to His (93) and one
  to oxygen

25
Common Structural Patterns in Globular proteins

• Supersecondary structures motifs or folds
• particularly stable arrangements of several
  elements of secondary structure.

26
Loss of Protein Structure Results in Loss of
Function

• Loss of 3-D structure sufficient to cause loss of
  function is called denaturation
• See Figure 6-26
• Not necessarily complete unfolding
• Heat (loss of H-bonds) onset is rapid
• Extremes of pH, organic solvents, detergents
• No covalent bonds are broken
• Can be reversible (ribonuclease)

27
Assisted Folding

• Not all PP fold spontaneously ? molecular
  chaperones assist in folding
• Hsp70 cells stressed by high temps.
• chaperoins protein complexes (necessary for
  growth of certain bacterial viruses)
• Protein disulfide isomerase (interchange or
  shifting of disulfide bonds)
• Peptide prolyl cis-trans isomerase (catalyzes
  isomerization of Pro)