MBM2

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MBM2

• Protein structure and folding A

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Learning Goals for MBM 2

• Understand what is meant by primary structure
• The nature of the peptide bond
• The main elements of secondary structure
• Principles of protein folding
• Common tertiary structure folds

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Levels of protein structure

• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

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Primary structure

• The covalent linkage, e.g. insulin
• Notation for proteins. Written from N-terminus to
  C-terminus.

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Disulphide bond formation
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Peptide bond formation
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The peptide bond resonates
O
R2
O
Backbone
C
C
H3N
C
N
C
O
Side-chains
H
R1
-
O
R2
O

C
C
H3N
C
N
C
O
H
R1
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Partial double bond restricts conformation
O
R2
O
O
C
N
C
C
N
C
C
N
C
x
H
H
H
R3
R1
x
No rotation about this partial double bond
Free rotation about this bond
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Only two angles cis and trans allowed at the
peptide bond
O
H
O
R2
C
N
C
C
C
N
C
C
H
R1
R2
R1
cis Unfavourable, except where R2 Proline
trans Energetically favourable
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Backbone is otherwise highly flexible
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Secondary structures result from

• Non-covalent interactions
• No new chemical bonds are formed
• Stabilised by regular hydrogen-bonds
• Can be local (i.e. amino acids clustered in the
  primary structure)
• Can bring distant regions of the primary
  structure closer together

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The a-helix I dimensions

• Ribbon-like
• Right-handed thread
• 0.54 nanometres/turn
• 3.6 amino acids/turn

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The a-helix II hydrogen bonds

• Each residue H-bonded to the one four amino acids
  along
• All H-bonds point the same direction
• Helix has a dipole.
• Net positive at the N-terminus

d-
d
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The a-helix III side-chains

• Side-chains protrude from centre
• 100 degrees per
• side-chain
• Centre excludes water

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The b-sheet I - architecture

• ß-sheets comprised of at least 2 ß-strands
• Pleated rather than a flat appearance
• Each strand consists of consecutive amino-acid
  residues
• Sheets can be parallel or anti-parallel.

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The b-sheet II hydrogen bonds

• Hydrogen bonds between adjacent strands
• Adjacent strands need not be close in the primary
  sequence

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The b-sheet III side-chains

• Side-chains protrude away from the plane of the
  sheet.
• Above and below the sheet

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The b-turn

• Regular structures, 4-7 amino acids
• Easiest way to connect 2 secondary structural
  elements
• e.g. b-strand b-turn b-strand

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Loops/Random Coil/Disordered

• No regular pattern of hydrogen bonding
• No regular conformation
• Frequently important in enzyme mechanisms
• e.g. calcium binding EF-hand motif

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Tertiary structure

• Describes the packing of the secondary structural
  elements
• Defines the overall fold of the protein
• Inextricably linked to function
• Stable, active conformation of the protein

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Catchphrase Time - 1

• 4-helix bundle
• All a-helical structure
• Anti-parallel nature
• Classical cytokine structure

is an a-helix
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Catchphrase Time - 1

• All b-sheet structure
• 4-stranded sheet and a 3-stranded sheet
• Anti-parallel
• Classic immunoglobulin fold.
• Present in virtually all proteins of the immune
  recognition system
• Specificity of interaction in the loops

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Catchphrase Time - 1

• Mixed a/b structure
• 8 b-strands in a single sheet
• 8 a-helices around the periphery
• Structural order a-b-a-b-a-b-a-b-a-b-a-b-a-b-a-b
• TIM barrel (triose phosphate isomerase)

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Summary

• The primary structure describes the peptide bonds
  linkage and the disulphide bond pattern.
• Proteins have 2 predominant secondary structural
  motifs, stabilized by H-bonds.
• The a-helix
• The b-sheet
• Tertiary structure