Topic 3

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4 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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A brief
refresher on protein
structure

Topic 3

Perhaps the most important structural bioinformatics
result ever published…

Chothia
, C. &
Lesk
, A.

M. (1986).
The relation
between the divergence of sequence and structure
in proteins.

E
MBO
J.
, 5(4):823
-
826.

Starting now, the relationships
identified by this simple graph will
impact everything we do throughout
the remainder of the class.

Levels of Protein Structures



primary structure


(set of covalent bonds within the structure)



secondary
structure (helices, strands, coils/loops)




tertiary
structure
(
3D packing of secondary structures)






quaternary
structure



(
spatial arrangements of multiple chains)


LIRLFKSHPETLEKFDRFKHL…

Levels of Protein Structures

Globular protein

Fibrous protein

Membrane protein

The three most common classes of proteins

Formation of a Peptide Bond by Condensation

Amino Acid
1

Amino Acid
2

Peptide bond

Note: this
chemistry will not
work as drawn!

Peptide bond is the amide linkage that is formed between two amino
acids, which results in (net) release of a molecule of water (H
2
O).

The four atoms in the yellow box form a rigid planar unit and, as we will
see next, there is no rotation around the C
-
N bond.

The primary structure is the set of all covalent bonds within the protein, which is approximated
by the sequence (
-
CSS). Note:
Primary structure
or
sequence
, but not
primary sequence
.


Peptides

Q: why is the pentapeptide
SGYAL

different than
LAYGS
?


A Closer Look at the Peptide Bond



The
carbonyl
group has a partial negative charge and the amide nitrogen
has a partial positive charge, which set up a small electric dipole.




The peptide C
-
N bond has a partial double
-
bond character (partial
sharing of two pairs of electrons between O and N.




The peptide bond is planar and rigid, cannot rotate freely (see next slide).




Resonance: delocalization of bonding electrons over more than one
chemical bond.

Lehninger

Principles of Biochemistry


A Closer Look at the Peptide Bond

But, bonds N
-
C


and
C


-
C can rotate, which can be described by two torsion
angles:


(phi) and

(psi).



(phi): C
-
N
-
C

-
C


(psi):
N
-
C

-
C
-
N



(omega):
C

-
C
-
N
-

C




In principle,


and


can have any value between
-
180
O

and +180
O
. But due
to
steric

interference……


A Closer Look at the Peptide Bond

Bond lengths : C


-
C


C
-
N


N
-
C



The peptide bond is normally in the trans configuration (~99.6% of the time)







=

180
O



One exception is for proline. T
he fraction of X
-
Pro peptide bonds in the
cis

isomer
under unstrained conditions ranges from 10
-
40%. The fraction depends slightly on the
preceding amino acid X.


Note the differences between C
-
N and N
-
C


An (a.) unstable vs. (b.) the most stable Ala
-
Ala dipeptide conformation

(a.)

(b.)

Rotation of phi

Rotation of psi

The rotatable backbone torsion angles

The Ramachandran plot


With a molecular modeling kit, prove to yourself that (0,0) is an unallowable due to a steric
clash.

Liu et al. Nature Chemical Biology.
3
, 619
-

629 (2007)


Prolyl

cis
-
trans

isomerization

as a molecular switch


The local environment of proline within
a protein can influence the relative free
energies of the
cis

and
trans

isomeric
states, leading to wide variations in the
ratio of
cis
:
trans

populations in different
proteins. Although most structures
require proline to adopt one or the other
isomer in the context of native protein
folds, several recent structures show the
presence of both populations for specific
proline

residues
.


--

The primary structure is a complete description of the covalent
bond network within a protein.


--

This is almost(!) completely described by the sequence of amino
acids.


--

If you know that the protein is AVG…, you can look up the
structures of A, V and G, plus what you know about peptide
bonding allows you to complete the covalent bond structure.


--

So, when does the primary structure not fully describe the
covalent bond network?




Final thoughts on primary structure

Secondary structure = local regions of proteins characterized by (
i.
) similar
/
癡汵敳v慮搠a
楩i

b慣abo湥⁨祤牯来 bo湤n湧


Proteins are composed of repeating structural elements


Hydrogen Bond

H
-
bond donor


H
-
bond acceptor



A weak bond involving the sharing of an electron with a hydrogen atom

Directionality of the H
-
bond

Common hydrogen bonds in
biological systems


Secondary Structure:

-
helix

5.4 Å

3.6 residue

Image from “Protein Structure and Function” by Gregory A
Petsko

and Dagmar
Ringe




=
-
57
O
,


=
-
47
O

Hydrogen bond pattern: C=
O

(
i
) and
N
-
H (
i+4
)

The

-
he汩l


Protein Secondary Structure:

helices


=
-
49
O
,

=
-
26
O

Hydrogen bond pattern: C=
O

(
i
) and
N
-
H (
i+3
)

Residues per turn: 3


=
-
57
O
,

=
-
70
O

Hydrogen bond pattern: C=
O

(
i
) and
N
-
H (
i+5
)

Residue per turn: 4.4



Other
helical conformations




3
10

helix,














helix


Image from “Protein Structure and Function” by Gregory A
Petsko

and Dagmar
Ringe



Amphipathic

helix

hydrophobic

Hydrophilic

protein packing and function



-
sheet (Pleated Sheet)

7
Å

6.5Å



=
-
139
O
,


= +ㄳ1
O



=
-
119
O
,


= +1ㄳ
O

Anti
-
parallel

-
sheet

Parallel

-
sheet

Lehninger

Principles of Biochemistry

The

-
p汥慴a搠獨eet

Amino acid propensity

Used in the first generation of secondary structure prediction methods, e.g. Chou
-
Fasman



-
turns



the distance between the C


atom of residue
i

and the C


atom of residue i+3


is less than 7Å




the central two residues are not helical




on the basis of the phi, psi angles of residues i+1 and i+2



-
turns

Lehninger

Principles of Biochemistry

Turn propensities (Ft/
Fb
)


Ramachandran

Plot

Red: allowed regions

Yellow: additionally allowed regions

White: disallowed regions

Relating the Ramachandran plot to secondary structures

PROLINE

GLYCINE

THE 18 STANDARD
AMINO ACIDS

Not all Ramachandran plots are created equal.

Tertiary structure = the 3D shape of a single protein chain, which is stabilized by a large
number of noncovalent interactions.

Ruminations on protein stability...



Protein stability is a small difference of
large

numbers.



Proteins are stable (

G < 0) only over a narrow environmental range.



In fact, there are forces pushing the equilibrium between folded and unfolded in
both directions.



Stabilizing forces:

Intraprotein salt bridges, hydrogen bonds, dipole
-
dipole interactions and VDW
interactions (all of which are electrostatic in nature).



Destabilizing forces:

Primarily electrostatic interactions with solvent and conformational entropy
reduction
.


SCOP = structure classification of proteins

SCOP = structure classification of proteins

SCOP = structure classification of proteins

SCOP = structure classification of proteins

Motif vs. Domain vs. Tertiary structure

There are many different ways to represent a protein structure

It is
common, and sometimes useful, to
think of protein structures as scaffolding upon which

慣瑩癥a獩瑥s


慲a
慴瑡ahe搮

Conformational changes within the tetramer structure underlie the differences in oxygen affinity
between oxy
-

and
deoxy
-
hemoglobin.

Monoclonal antibodies.