CH 4
CH 4
CH 4
1 2
3 4
2˚ Structure -Helix
• 2˚ of proteins is hydrogen-bonded arrangement of • Coil of the helix is clockwise or right-handed
backbone of the protein • There are 3.6 amino acids per turn
• Two bonds have free rotation: • Repeat distance is 5.4Å
• Each peptide bond is s-trans and planar
1) Bond between -carbon and amino nitrogen in
• C=O of each peptide bond is hydrogen bonded to the
residue N-H of the fourth amino acid away
2) Bond between the -carbon and carboxyl carbon of • C=O----H-N hydrogen bonds are parallel to helical
residue axis
• See Figure 4.1 • All R groups point outward from helix
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1
-Helix (Cont’d) -Helix (Cont’d)
• Several factors can disrupt an -helix
• proline creates a bend because of (1) the restricted
rotation due to its cyclic structure and (2) its -amino
group has no N-H for hydrogen bonding
• strong electrostatic repulsion caused by the proximity
of several side chains of like charge, e.g., Lys and Arg
or Glu and Asp
• steric crowding caused by the proximity of bulky side
chains, e.g., Val, Ile, Thr
7 8
9 10
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2
Schematic Diagrams of Supersecondary
-Helices and -Sheets
Structures
• Supersecondary structures: the combination of -
and -sections, as for example
• unit: two parallel strands of -sheet connected by
a stretch of -helix
• unit: two antiparallel -helices
• -meander: an antiparallel sheet formed by a series of
tight reverse turns connecting stretches of a
polypeptide chain
• Greek key: a repetitive supersecondary structure
formed when an antiparallel sheet doubles back on
itself
• -barrel: created when -sheets are extensive enough
to fold back on themselves
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15 16
17 18
3
3˚ Structure Forces in 3˚ Structure
• The 3-dimensional arrangement of atoms in the • Noncovalent interactions, including
molecule. • hydrogen bonding between polar side chains, e.g., Ser
and Thr
• In fibrous protein, backbone of protein does not fall • hydrophobic interaction between nonpolar side chains,
back on itself, it is important aspect of 3˚ not specified e.g., Val and Ile
by 2˚ structure. • electrostatic attraction between side chains of opposite
charge, e.g., Lys and Glu
• electrostatic repulsion between side chains of like
• In globular protein, more information needed. 3k charge, e.g., Lys and Arg, Glu and Asp
structure allows for the determination of the way
helical and pleated-sheet sections fold back on each • Covalent interactions: Disulfide (-S-S-) bonds
other. between side chains of cysteines
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21 22
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4
Myoglobin The Structure of Myoglobin
• A single polypeptide chain of 153 amino acids
• A single heme group in a hydrophobic pocket
• 8 regions of -helix; no regions of -sheet
• Most polar side chains are on the surface
• Nonpolar side chains are folded to the interior
• Two His side chains are in the interior, involved with
interaction with the heme group
• Fe(II) of heme has 6 coordinates sites; 4 interact with
N atoms of heme, 1 with N of a His side chain, and 1
with either an O2 molecule or an N of the second His
side chain
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27 28
29 30
5
Quaternary Structure Oxygen Binding of Hemoglobin (Hb)
• Quaternary (4°) structure: the association of • A tetramer of two -chains (141 amino acids each)
polypepetide monomers into multisubunit proteins and two -chains (153 amino acids each); 22
• dimers • Each chain has 1 heme group; hemoglobin can bind
• trimers up to 4 molecules of O2
• tetramers • Binding of O2 exhibited by positive cooperativity;
when one O2 is bound, it becomes easier for the next
• Noncovalent interactions O2 to bind
• electrostatics, hydrogen bonds, hydrophobic • The function of hemoglobin is to transport oxygen
• The structure of oxygenated Hb is different from that
of unoxygenated Hb
• H+, CO2, Cl-, and 2,3-bisphosphoglycerate (BPG)
affect the ability of Hb to bind and transport oxygen
31 32
33 34
35 36
6
Predicting Protein Structure Hydrophobic Interactions
• Hydrophobic interactions are major factors in protein
folding
• Folds so that nonpolar hydrophobic side chains tend
to be on inside away from water, and polar side chains
on outside accessible to aqueous environment
• Hydrophobic interactions are spontaneous
37 38
39 40