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Protein Basics

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Protein conformation framework. Dihedral angles. Ramachandran plots ... Three repeating torsion angles along protein backbone: ?, f, ?. Backbone Torsion Angles ... – PowerPoint PPT presentation

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Title: Protein Basics


1
Protein Basics
  • Protein function
  • Protein structure
  • Primary
  • Amino acids
  • Linkage
  • Protein conformation framework
  • Dihedral angles
  • Ramachandran plots
  • Sequence similarity and variation

2
Protein Function in Cell
  • Enzymes
  • Catalyze biological reactions
  • Structural role
  • Cell wall
  • Cell membrane
  • Cytoplasm

3
Protein Structure
4
Protein Structure
5
Hemoglobin Quaternary Structure
Two alpha subunits and two beta subunits (141 AA
per alpha, 146 AA per beta)
6
Hemoglobin Tertiary Structure
One beta subunit (8 alpha helices)
7
Hemoglobin Secondary Structure
alpha helix
8
Hydrogen Bonding
9
Hemoglobin Primary Structure
NH2-Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-T
hr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- G
ly-Gly-Glu-..
beta subunit amino acid sequence
10
Protein Structure - Primary
  • Protein chain of amino acids joined by peptide
    bonds

11
Protein Structure - Primary
  • Protein chain of amino acids joined by peptide
    bonds
  • Amino Acid
  • Central carbon (Ca) attached to
  • Hydrogen (H)
  • Amino group (-NH2)
  • Carboxyl group (-COOH)
  • Side chain (R)

12
General Amino Acid Structure
H
COOH
H2N
Ca
R
13
General Amino Acid Structure
14
Amino Acids
  • Chiral

15
Chirality Glyceraldehyde
L-glyderaldehyde
D-glyderaldehyde
16
Amino Acids
  • Chiral
  • 20 naturally occuring distinguishing side chain

17
20 Naturally-occurring Amino Acids
18
Amino Acids
  • Chiral
  • 20 naturally occuring distinguishing side chain
  • Classification
  • Non-polar (hydrophobic)
  • Charged polar
  • Uncharged polar

19
Peptide Bond
  • Joins amino acids

20
Peptide Bond Formation
21
Peptide Chain
22
Peptide Bond
  • Joins amino acids
  • 40 double bond character
  • Caused by resonance

23
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24
Peptide bond
  • Joins amino acids
  • 40 double bond character
  • Caused by resonance
  • Results in shorter bond length

25
Peptide Bond Lengths
26
Peptide bond
  • Joins amino acids
  • 40 double bond character
  • Caused by resonance
  • Results in shorter bond length
  • Double bond disallows rotation

27
Protein Conformation Framework
  • Bond rotation determines protein folding, 3D
    structure

28
Protein Conformation Framework
  • Bond rotation determines protein folding, 3D
    structure
  • Torsion angle (dihedral angle) t
  • Measures orientation of four linked atoms in a
    molecule A, B, C, D

29
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30
Protein Conformation Framework
  • Bond rotation determines protein folding, 3D
    structure
  • Torsion angle (dihedral angle) t
  • Measures orientation of four linked atoms in a
    molecule A, B, C, D
  • tABCD defined as the angle between the normal to
    the plane of atoms A-B-C and normal to the plane
    of atoms B-C-D

31
Ethane Rotation
32
Protein Conformation Framework
  • Bond rotation determines protein folding, 3D
    structure
  • Torsion angle (dihedral angle) t
  • Measures orientation of four linked atoms in a
    molecule A, B, C, D
  • tABCD defined as the angle between the normal to
    the plane of atoms A-B-C and normal to the plane
    of atoms B-C-D
  • Three repeating torsion angles along protein
    backbone ?, f, ?

33
Backbone Torsion Angles
34
Backbone Torsion Angles
  • Dihedral angle ? rotation about the peptide
    bond, namely Ca1-C-N- Ca2

35
Backbone Torsion Angles
36
Backbone Torsion Angles
  • Dihedral angle ? rotation about the peptide
    bond, namely Ca1-C-N- Ca2
  • Dihedral angle f rotation about the bond
    between N and Ca

37
Backbone Torsion Angles
38
Backbone Torsion Angles
  • Dihedral angle ? rotation about the peptide
    bond, namely Ca1-C-N- Ca2
  • Dihedral angle f rotation about the bond
    between N and Ca
  • Dihedral angle ? rotation about the bond
    between Ca and the carbonyl carbon

39
Backbone Torsion Angles
40
Backbone Torsion Angles
  • ? angle tends to be planar (0º - cis, or 180 º -
    trans) due to delocalization of carbonyl pi
    electrons and nitrogen lone pair

41
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42
Backbone Torsion Angles
  • ? angle tends to be planar (0º - cis, or 180 º -
    trans) due to delocalization of carbonyl pi
    electrons and nitrogen lone pair
  • f and ? are flexible, therefore rotation occurs
    here

43
Backbone Torsion Angles
44
Backbone Torsion Angles
  • ? angle tends to be planar (0º - cis, or 180 º -
    trans) due to delocalization of carbonyl pi
    electrons and nitrogen lone pair
  • f and ? are flexible, therefore rotation occurs
    here
  • However, f and ? of a given amino acid residue
    are limited due to steric hindrance
  • Only 10 of the area of the f, ? space is
    generally observed for proteins
  • First noticed by G.N. Ramachandran

45
G.N. Ramachandran
  • Used computer models of small polypeptides to
    systematically vary f 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, f and ? angles which cause spheres to
    collide correspond to sterically disallowed
    conformations of the polypeptide backbone

46
Ramachandran Plot
  • Plot of f vs. ?
  • Repeating values of f and ? along the chain
    result in regular structure
  • For example, repeating values of f -57 and ?
    -47 give a right-handed helical fold (the
    alpha-helix)
  • The structure of cytochrome C-256 shows many
    segments of helix and the Ramachandran plot shows
    a tight grouping of f, ? angles near -50, -50

47
The structure of cytochrome C-256 shows many
segments of helix and the Ramachandran plot shows
a tight grouping of f, ? angles near -50,-50
cytochrome C-256 Ramachandran plot
alpha-helix
48
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49
Ramachandran Plot
  • White sterically disallowed conformations
    (atoms in the polypeptide come closer than the
    sum of their van der Waals radii)
  • Red sterically allowed regions (namely
    right-handed alpha helix and beta sheet)
  • Yellow sterically allowed if shorter radii are
    used (i.e. atoms allowed closer together brings
    out left-handed helix)

50
Alanine Ramachandran Plot
51
Arginine Ramachandran Plot
52
Glutamine Ramachandran Plot
53
Glycine Ramachandran Plot
Note more allowed regions due to less steric
hindrance
54
Proline Ramachandran Plot
Note less allowed regions due to structure
55
Sequence Similarity
  • Sequence similarity implies structural,
    functional, and evolutionary commonality
  • Small mutations generally well-tolerated by
    native structure

56
Sequence Similarity Exception
  • Sickle-cell anemia resulting from one residue
    change
  • Replace highly polar (hydrophilic) glutamate in
    hemoglobin with nonpolar (hydrophobic) valine

57
Sickle-cell mutation in hemoglobin sequence
58
Sequence Similarity Exception
  • Sickle-cell anemia resulting from one residue
    change
  • Replace highly polar (hydrophilic) glutamate in
    hemoglobin with nonpolar (hydrophobic) valine
  • Causes hemoglobin molecules to repel water and be
    attracted to one another
  • Leads to the formation of long protein filaments
    that distort the shape of red blood cells giving
    them their sickled shape
  • Rigid structure of sickle cells blocks
    capillaries and prevents red blood cells from
    delivering oxygen

59
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