Structural Bioinformatics

dasypygalstockingsBiotechnology

Oct 2, 2013 (4 years and 1 month ago)

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1

Levels of Protein
Structure

Primary to Quaternary Structure

2

Learning Objectives


After today you should be able to:



Define the structural levels of proteins.


Identify the structural units of the protein backbone.


Explain why some backbone conformations are
“forbidden”, i.e. not found in natural proteins.


Name properties on which the amino acids can be
grouped.


Name more amino acids than you could before


One and three letter codes


3

Amino Acids


Proteins are built from
amino acids



Amino group and acid
group



Side chain at C
a



Chiral, only one
enantiomer found in
proteins (L
-
amino acids)



20
natural amino acids

N

O

C

C
a

C
g

C
b

C
e

S
d

Methionine

4

L
-
amino acids in Living organisms

N:
14

C:
12

O:
16

5

How to Group Them?


Many features


Charge +/
-


Acidic vs. basic (pK
a
)


Polarity (polar/non
-
polar)


Type, distribution


Size


Length, weight, volume, surface area


Type (Aromatic/aliphatic)

6

The Amino Acids

Asn
(N)

Asp (D)

Gln
(Q)

Glu (E)

His (H)

Lys (K)

Arg (R)

Tyr (Y)

Trp (W)

Phe (F)

Gly (G)

Pro (P)

Ile (I)

Met (M)

Leu (L)

Ala (A)

Val (V)

Ser (S)

Cys (C)

Thr (T)

7

Amino Acids

Livingstone & Barton,
CABIOS
,
9
,
745
-
756
,
1993

A


Ala

C


Cys

D


Asp

E


Glu

F


Phe

G


Gly

H


His

I


Ile

K


Lys

L


Leu

M


Met

N


Asn

P


Pro

Q


Gln

R


Arg

S


Ser

T


Thr

V


Val

W


Trp

Y
-

Tyr

8

Blosum
62
substitution matrix

9

The Evolution Way



Based on
Blosum
62
matrix


Measure of
evolutionary
substitution
probability

10

The Simple Aliphatic

Ile (I)

Met (M)

Leu (L)

Val (V)

Ala (A)

11

The Small Polar

Thr (T)

Cys (C)

Ser (S)

Cystin

12

The Unusual


P, G


Also aliphatic


Structural impact



Strictly speaking,
proline is an
imino
acid

Gly (G)

Pro (P)

13

The Acidic and Their Derivatives

Asn (N)

Asp (D)

Gln (Q)

Glu (E)

14

The Basic

His (H)

Lys (K)

Arg (R)

15

The Aromatic

Tyr (Y)

Trp (W)

Phe (F)

His (H)

16

Proteins Are Polypeptides


The peptide bond


A polypeptide chain

18

Ramachandran Plot


Allowed backbone torsion angles in proteins

N

H

19

Small Exercise (
5
minutes)


For the polypeptide on the
left discuss the following
with your neighbour:


Why is the lower right
quadrant a ”forbidden”
region in the
Ramachandran plot?


What makes Gly a special
amino acid when it comes
to Ramachandran plots?


What about Pro?

20

Structure Levels


Primary structure = Sequence
(of amino acids)



Secondary Structure = Helix,
sheets/strands, bends, loops &
turns (all defined by H
-
bond
pattern in backbone)



Structural Motif = Small,
recurrent arrangement of
secondary structure, e.g.


Helix
-
loop
-
helix


Beta hairpins


EF hand (calcium binding motif)


Many others…



Tertiary structure = Arrangement
of Secondary structure elements
within one protein chain

MSSVLLGHIKKLEMGHS…

21


Myoglobin








Haemoglobin

Quaternary Structure


Assembly of
monomers/subunits
into protein complex


Backbone
-
backbone,
backbone
-
side
-
chain &
side
-
chain
-
side
-
chain
interactions:


Intramolecular vs.
intermolecular contacts.


For ligand binding side
chains may or may not
contribute. For the latter,
mutations have little
effect.

a

a

a

b

b

22

Hydrophobic Core


Hydrophobic side chains go into the core of
the molecule


but the main chain is highly
polar.


The polar groups (C=O and NH) are
neutralized through formation of H
-
bonds.

Myoglobin

Surface

Interior

23

Hydrophobic vs. Hydrophilic


Globular protein (in
solution)


Membrane protein (in
membrane)

Myoglobin

Aquaporin

24

Hydrophobic vs. Hydrophilic


Globular protein (in
solution)


Membrane protein (in
membrane)

Myoglobin

Aquaporin

Cross
-
section

Cross
-
section

25

Characteristics of Helices


Aligned peptide
units


Dipolar
moment


Ion/ligand binding


Secondary and
quaternary
structure packing


Capping residues


The
a

helix
(i→
i+4)


Other helix types!
(3
10
,
p
)

N

C

26

Helix Types

28

b
-
Sheets


Multiple strands


sheet


Parallel vs. antiparallel


Twist





Coil regions between
the secondary structure
elements


Thioredoxin

29

b
-
Sheets


Multiple strands


sheet


Parallel vs.
antiparallel


Twist



30

b
-
Sheets


Multiple strands


sheet


Parallel vs.
antiparallel


Twist

31

b
-
Sheets


Multiple strands


sheet


Parallel vs.
antiparallel


Twist


32

b
-
Sheets


Multiple strands


sheet


Parallel vs. antiparallel


Twist



Strand interactions are
non
-
local



Flexibility


Vs. helices


Folding

Antiparallel

Parallel

33

Summary



Amino acids in Living organisms have L
-
configuration


One & three letter codes


Groups of amino acids: hydrophobic ...


The backbone of polypeptides form regular
secondary structures.


Helices, sheets & loops.


34

Building Blocks

NH
2
/NH
3
+

S/SH

Guanidine

Im
idazole

Phenyl

Indole

C
a

H
-
bond

Amide

C/CH/CH
2
/CH
3

COOH

OH

Peptide unit (amide)

N

C

O

N

C

O

35

Building Blocks

N

O

C

C
a

C
g

C
b

C
e

S
d

Methionine

Single amino
acid

Residue

N

O

C

C
a

O

N

O

C

C
a

O
n
-
1

N
n+
1

C
n
-
1

c
1

c
2

c
3

f

y

O

36

Procedure

1.
Build backbone in
extended
conformation (strand).

2.
Twist to align all
peptide units (look at
the C=O groups).

3.
Add H
-
bonds (i+
4
) to
construct an ideal
a
-
helix.

4.
Add side chains along
the way (pointing
“down”).

N

C