Download Lecture 2 Protein conformation Recap Recap… Proteins

10/21/10
Recap
Proteins…..
Lecture 2
Protein conformation
–  > 50% dry weight of a cell
–  Cell’s building blocks and molecular tools.
–  More important than genes
–  A large variety of functions
http://www.tcd.ie/Biochemistry/courses/jf_lectures.php
Recap…
Proteins are the key functional molecules of life
8 types of protein function
1.  Enzymatic
2.  Structural
3.  Storage
4.  Transport
5.  Hormonal
6.  Receptor
7.  Contractile and Motor
8.  Defensive
–  A large variety of shapes and sizes.
Proteins
1.  Proteins - What are they? And why are they
important?
2.  The building blocks (aa’s) and how they are
connected
3.  The hierarchy of protein structure
4.  Three-dimensional protein structure
5.  How are protein structures determined?
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Recap…
Amino Acid Polymers
•  Amino acids - Are linked by peptide bonds
Peptide
bond
•  Proteins are polymers of amino acids
(polypeptides)
OH
SH
CH2
•  Amino acids divide into 4 subgroups
CH2
H
Petide bond is formed by a
dehydration reactionCatalytic reaction
H
N
•  20 R groups = 20 aa’s
OH
CH2
H
C
C
H
O
N
H
C
C
H
O
OH H
(a)
N
C
C
H
O
OH
H 2O
OH
OH
CH2
Petide bond - covalent bond
(b)
• 
Protein Conformation and
Function
Polypeptides
C
C
H
O
Amino end
(N-terminus)
N
H
C
C
H
O
N
C
C
H
O
•  Sequence of the aa polymer determines the 3D shape of the
polypeptide
OH
Backbone
Carboxyl end
(C-terminus)
•  Two models of protein conformation
- formed one at a time starting from N-terminus
- range from a few monomers to 1000 or more
•  Specific polypeptides- unique sequence of aa’s
Side chains
SH
Peptide
bond CH2
H
H
H N
CH2
Groove
Eg. Lysozyme- an enzyme that
Breaks down bacterial cell walls
by recognizing and binding to
specific molecules on the bacteria
(a) A ribbon model
•  Proteins are not just chains of aa’s, they are defined by their
shape – interactions between backbone residues and R-groups
Groove
•  A protein’s specific conformation - determines how it functions
•  eg. Enzyme binds substrate
(b) A space-filling model
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Protein structure
Four Levels of Protein Structure
•  Primary structure
–  Is the unique sequence of amino acids in
a polypeptide
HN
Amino acid
+
Gly Pro Thr Gly
Thr
Gly
3
Amino
end
subunits
Glu
CysLysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala
aa sequence determined by
inherited genetic information
Glu Lle
Asp
Thr
Lys
Ser
Lys Trp Tyr
Leu Ala
Gly
lle
Ser
ProPhe
His Glu
Ala Thr PheVal
Asn
His
Ala
Glu
Val
Asp
Tyr
Arg
Ser
Arg
Gly Pro
Thr Ser
Tyr
Thr
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Thr
Ala
Val
Val
LysGlu
Thr
AsnPro
o
c –
o
Carboxyl end
•  Secondary structure
–  Is the folding or coiling of the polypeptide into a repeating
configuration
–  Includes the α helix and the β pleated sheet
–  Result of Hydrogen bonding between the repeating
backbone of a polypeptide
Amino acid
subunits
O H H
C C N
C N
H
R
R
O H H
C C N
C C N
O H H
R
R
R
H
H
C
C
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
O C
N H
N H
C
C
R
R
N
Alpha-helix
Beta pleated sheet
N
O H H
O H H
R
R
C C N
C C N
N
C C N
R C C
R C C
OH H
OH H
O
R
R
O
O
C
H
C
H
H
H C N HC
C
C N HC N
N
H
H
C
O
C
C
O
R
R
O
O
R
O
C
H
H
NH C N
C
H
O C
R
R
H
C
N HC N
H
O C
β pleated sheet
H
α helix
-Repeated coils or folds in patterns contribute to the overall
conformation of a protein
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Hydrogen bonds
Hydrogen bonds
•  Hydrogen bonds are formed by the attraction between a partial
positive charge on the H atom of the amino group and the partial
negative charge on the O atom of the peptide bond
•  Alpha helix - the bonds are formed
between repeating atoms on the
same polypeptide chain
•  Hydrogen bonds are formed by the attraction between a partial
positive charge on the H atom of the amino group and the partial
negative charge on the O atom of the peptide bond
R
aa
C
C
N
O
H
H
•  Beta sheets – the bonds are formed
between polypeptide chains
lying side by side
aa
H
H O
N
C
C
aa
•  Alpha helix - the bonds are formed
between repeating atoms on the
same polypeptide chain
R
aa
C
C
ΔN
Δ-O
H
H
•  Beta sheets – the bonds are formed
between polypeptide chains
lying side by side
H
aa
aa
N
Δ-
R
aa
C
aa
•  Hydrogen bonds are formed by the attraction between a partial
positive charge on the H atom of the amino group and the partial
negative charge on the O atom of the peptide bond
R
•  Beta sheets – the bonds are formed
between polypeptide chains
lying side by side
C
Hydrogen bonds
•  Hydrogen bonds are formed by the attraction between a partial
positive charge on the H atom of the amino group and the partial
negative charge on the O atom of the peptide bond
aa
ΔH O
R
Hydrogen bonds
•  Alpha helix - the bonds are formed
between repeating atoms on the
same polypeptide chain
aa
Δ+
C
C
ΔN
Δ-O
H
Δ+
ΔH O
H
N
Δ-
C
R
aa
HΔ+
C
Δ+
aa
•  Alpha helix - the bonds are formed
between repeating atoms on the
same polypeptide chain
eg keratin
•  Beta sheets – the bonds are formed
between polypeptide chains
lying side by side
eg. Silk fibrion
Individually weak, but strong when repeated
R
aa
aa
Δ+
C
C
ΔN
Δ-O
H
HΔ+
Δ+
ΔH O
H
N
Δ-
C
C
Δ+
aa
aa
R
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O
Alpha-helix
Secondary structure
Beta pleated sheet
N
Up to 60% of a
polypeptide chain
contains a
secondary
structure
Beta sheet
Alpha helix
Results from interactions between atoms in the polypeptide backbone
β-Sheet
α-Helix
•  C
N
O of amino acid 1 binds to the
H of amino acid 4
•  C
N
O of amino acid on chain 1 binds to the
H on chain 2
•  3.6 residues per helical turn
•  Consists of β-strands - short (5-8 residues)
•  Right-handed coil
•  Two types
•  All H bonds have same orientation
–  Parallel
–  Anti-parallel
•  Most prevalent structure in
polypeptide
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Turns
β-Sheet
N-Terminus
C-Terminus
R
R
R
R
R
R
C-Terminus
N-Terminus
R
R
•  Bends
•  Usually contain glycine (small R grp=tight U
shape) or proline
R
N-Terminus
•  3-4 residues
C-Terminus
R
R
R
C-Terminus
N-Terminus
http://www.youtube.com/watch?v=wM2LWCTWlrE
Protein structure
•  Allow proteins to fold into highly compact
structures
•  Larger turns are called loops or bends
Tertiary structure
–  Is the overall three-dimensional shape of a
polypeptide ; final shape of a polypeptide
–  Results from interactions between the side
chains of the amino acids
Hydrogen
bond
CH2
CH
2
O
H
O
H 3C
H 3C
CH
CH3
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
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Tertiary structure
•  Bonds involved in 3D structure
 Hydrophobic
 Van der Waals
 Hydrogen Bonds
 Ionic bonds/salt bridges
 Disulphide bridges
Tertiary structure
Hydrophobic interactions
•  Non-polar “R” groups
repelled by water
•  Tend to cluster
together
•  Force themselves into
the core of a protein
•  Stabilise the overall
structure
water
Hydrophobic
amino acid
Tertiary structure
•  Van der Waals interactions:
occur between hydrophobic non-polar side
chains in close contact
Tertiary Structure
•  Hydrogen bonds – between polar side
chains
•  Examples of amino acid side chains
that may hydrogen bond to each other:
Two alcohols: ser, thr, and tyr.
Valine
H 3C
CH
CH3
H 3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Alcohol (OH) and an acid : asp and tyr
Two acids (COO-): asp and glu
Alcohol and amine (NH3+): ser and lys
Alcohol and amide (NH2): ser and asn
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Tertiary structure
Tertiary structure
•  Ionic bonds /Salt bridges
form between positively and
negatively charged side groups
•  Disulphide bridges form
between 2 cysteine residues
•  result from the neutralization of
an acid and amine on side
chains.
•  Disulfide bonds are formed by
oxidation of the sulfhydryl
groups (-SH) on cysteine.
•  The final interaction is ionic
between the positive
ammonium group and the
negative acid group.
•  Different protein chains or
loops within a single chain are
held together by the strong
covalent disulfide bonds.
•  Any combination of the various
acidic or amine amino acid
side chains will have this
effect.
•  Eg. Insulin contains important
disulphide bridges.
Quaternary Structure
–  Is the overall protein structure that results from the
aggregation of two or more polypeptide subunits
Quaternary structure
Fibrous
Trimer of alpha-helical
Polypeptide chains
Globular
Globular protein4 Polypeptide chains/ subunits
Primarily alpha-helical
β Chains
–  A variety of bonding interactions including hydrogen
bonding, salt bridges, and disulfide bonds hold the
various chains into a particular geometry.
Iron
Heme
α Chains
–  There are two major categories of proteins with
quaternary structure - fibrous and globular.
Collagen
Structure allows for great strength
Rigid resistant to stretch
Function = connective tissue in
skin, bone, tendons, ligaments.
40% of all human protein
Hemoglobin
4 polypeptides bind together to
form a round globular shape
Functions = carries oxygen
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Hemoglobin
Quaternary structure
Fibrous
Globular
insulin
Globular proteins are usually
round in shape and tend to be
a mix of alpha-helical and Beta
sheet
Beta sheet structure of silk fibroin
allows for strength and flexibility
Protein structure summary…
Protein structure summary…
•  The conformation of a protein determines its function
•  Proteins are made of polypeptides which are polymers
of amino acids
•  Amino acid polymers are linked by peptide bonds
•  The amino acid sequence determines the 3-D shape
of the Protein
•  There are four levels of protein structure
http://www.youtube.com/watch?v=iaHHgEoa2c8&feature=related
Primary Secondary
Ter/ary Quaternary 9