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II. Patterns and forms in protein structure
2. Patterns and forms in protein structure
•Helices and sheets
•The hierarchical nature of protein architecture
•Structure based classification of proteins
•protein folding: Intra-cellular pathogens and the
survival of the flattest
•Protein folding and disease: Amyloidoes, Parkinson,
Huntington, Prion disease
Protein Secondary Structure
-helix
-sheet
These secondary structures are highly
present in proteins due to:
-They keep the main strain in an
unstrained conformation
- Satisfy the hydrogen-bonding potential
of the main-chain N-H and C=O groups
These secondary structures link in a specific way in different combinations to perform the
final protein structure
-helices are formed from a single consecutive set of residues in the amino acid sequence
The H-bond links the C=O group of residue i with the H-N group of residue i + 4
There are alternatives to the helix configuration giving more constrained or less
constrained structures:
-310 helices, in which hydrogen bonds form between residues i and i + 3
- -helices, in which hydrogen bonds form between residues i and i + 5
This configurations are much rarer due to the constraints and effects they have on the
protein stability.
-sheets are formed by lateral interactions of several
independent sets of residues.
They can bring together sections of the chain widely
separated in the amino acid sequence
In this figures, all the strands are anti-parallel
Tertiary and quaternary structure
Tertiary structures are the result of the different combinations
of helices and sheets
The different combinations lead to different spatial
arrangements and different patterns of interactions between
amino acids of helices and sheets. This will be the basis for the
so called FOLDING PATTERN
Many proteins contain more than one subunit, or monomer.
They may be multiple copies of the same polypeptide chain, or
combinations of different polypeptide chains which assembly
form the QUATERNARY STRUCTURE
Protein stability and denaturation
The native structure of proteins can be broken up, by heating or by high concentrations
of certain chemicals such as urea (DENATURATION)
Denaturation destroys the secondary, tertiary and quaternary structures but leaves the
polypeptide chain intact.
The stability of the the main chain will ensure that, ones natural conditions restored, the
protein will acquire the normal productive folding conformation and thus its function.
Proteins are only stable under very narrow conditions of solvent and temperatures.
Breaking these conditions will break the intimate intramolecuar interactions, will change
the main configurations of the backbone and will lead to non-productive conformations
Giving the changeability of these conditions, the cell has developed many mechanisms to
buffer these effects (Moran et al. 1996; Fares et al. 2002 a, Fares et al. 2002 b, Fares et
al. 2004).
Productive protein conformation
The protein conformation ensures the intra-molecular interactions that are essential for
forming the active sites and therefore for enabling the protein to have a biological
activity.
Active sites in enzymes only require 10% of the total number of amino acids in the
protein. The different molecular interactions between different local secondary protein
structures have the role of:
- Scafolding to enable the appropriate conformation for the formation of the active site
- enable conformational changes as part of the mechanism activity (Steroid Hormone
receptors)
- Some residues are in strained conformation playing an important role in catalysis
Due to the crowded cell environment, slow-folding proteins tend to aggregate nonspecifically leading to several known diseases:
Alzheimer, Prion disease
The role of chaperones is essential in ensuring correct protein folding
Protein structure and conformation
5. Proteins are polymers containing a
backbone or a main chain of repeating
units (peptides) with the main chain
attached to it
O
O
-N-C-C-N-C-C-........
Si-1
Si
Amino Acids
Amino acids vary in
size
Asymmetric carbon
Hydrogen-bonding potential
charge
Amino acids are
chemical building blocks
aliphatic
beta-branched
CS-S A
L
M
aromatic
P
G
S
CH
V
D
E
T
I
F
Y
N
W
H
K
Q
negative
R
positive
hydrophobic
charged
polar
What amino acids look like
side chain
R
H N
amino
group
H
C
H
C
OH
O
carboxyl group
Sidechain nomenclature
C
beta;
first sidechain position
X
delta position
Xg
Xd
Xe
zeta position
Xz
Xh
carbon alpha, central chiral
carbon of the amino acid
gamma position
epsilon position
eta position
Small amino acids
Gly: G
Pro: P
Ala:A
Asp: D
Cys:C
Ser:S
Aliphatic amino acids
Val: V
Leu: L
Ala:A
Ile: I
-branched amino acids
Thr: T
Ile: I
Val: V
Aromatic amino acids
Phe: F
Tyr: Y
Trp: W
His: H
Polar amino acids
Ser:S
Asn: N
Gln: Q
Tyr: Y
Thr: T
Positively charged amino acids
Lys: K
His: H
Arg: R
Negatively charged amino acids
Asp: D
Glu: E
Chirality
• Amino acids are not flat and two dimensional!
• Groups are arranged around the central carbon atom in a
tetrahedral fashion (why?)
• There are two possible ways for the groups to be arranged:
Amino acid chirality
L-form
CO
R
R
C
C
H
amino acids in
proteins are almost
always in the L-form
N
N
D-form
CO
H
D-form occurs rarely -peptide antibiotics, some
peptide toxins
Peptide chemistry
amino acids dissociate in aqueous solution
to form a zwitterion (ionic species with two
independent charged groups)
O
R
H
H
H
H
O-
C
N+
H
C
C
C
N+
H
H
O
R
O-
Peptide chemistry
the amino acid polymer forms
when the carboxyl group of
one amino acid condenses with
the amino group of the next
H20
R
H
O
H
H
N
C
C
N
C
H
H
O
peptide bond
R
C
OH
Protein folding
The energy of protein conformation depends on:
Interaction of sidechains and main chains
Native state
Interaction with solvents and ligands
The environmental conditions of the cell
Proteins follow the shortest temporal and energetical pathway to
acquire the most stable conformation
Denatured
Spontaneous
aggregation
Non-specific
aggregates
Chaperones
Functional
conformations
Protein Folds: sequential, spatial and topological arrangement of
secondary structures
The Globin fold
A
mRNA
protein
DnaK
DnaJ
a
c
b
GroEL
B
ATP and
GroES
binding
GroES
GroEL
ADP + Pi and
GroES
release
Vertical transmission of E. coli as a simulating system
of endosymbiosis
t=1
t=2
t=3
12 lines REL4548 (MAF)
12 lines REL7550 (MXR)
t = 135
Comptenece experiments
ara
ara+
Day –2: grow on LB every competitor
Day –1: adapt to DM25 ( 3-5 replicaqtes)
Day 0: mix both competitors 1:1, determine
their proportions
Day +1: determine proportionsof
competitors, estimate W
BamHI
HindIII
yjeH
HindIII SalI
tetA
P
tetR
normal
mutator
1.0
W
0.8
0.6
0.4
Ancestral
evolved
groE
Pbla S
P
c
groE
XhoI
L
GroEL as a compensatory mechanism
groES
137 Å
groEL
57 KDa
146 Å
Intermediate domain
Apical domain
Y199, S201, Y203, F204, L234, 237, 259
V263, 264
Equatorial domain
A. pisum PS
99
S. Avenae PS
97
95
M. Persicae PS
R. padi PS
96
100
100
S. graminum PS
P. populeum PS
T. caerulescens PS
C. leucomelas PS
99
T. salignus PS
T. suberi PS
E. carotovora
100
100
100
95
0,05
E. aerogenes
E. coli
S. typhimurium
B. germanica PS
93
E. libidus PS
100
P. americana PS
99
99
B. orientalis PS
L. dicipiens PS
100
B. gingivalis
P. gingivalis
E. coli
0.05
Positive selection in the endosymbiont GroEL
R.maidis PS
R.padi PS
S.graminum PS
M. persicae PS
S. avenae PS
P.populeum PS
C. Leucomelas PS
T. caerulescens PS
B. pistaciae PS
T. suberi PS
T. salignus PS
W. glossinidia PS
B. tabaci PS
A. proteus PS
100
100
94
100
99
42
100
B
77
94
100
A
100
E
D
99
C
97
100
E. carotovora
K. pneumoniae
64
100
E. aerogenes
99
S. enterica
61
100 S. typhimurium
J
S. glossinidia SS
100
S. oryzae PS
P. putida
100
P. aeruginosa
100 P. gingivalis
B. gingivalis
L. dicipiens PS
100
I
G
E. libidus PS
93 F
100
B. germanica PS
B. orientalis PS
99 H
100
P. americana PS
0.1
gproteobacteria
Flavobacteria
Branch
Average 
A
21.98
B
13.45
C
1.57
D
1.37
E
2.58
F
1.42
G
3.93
H
3.98
I
3.68
J
4.035
Convergent adaptive evolution in GroEL from
endosymbiotic bacteria
A
B
Protein structure stability and its ability and specificity to bind
ligands depend on different chemical forces:
Covalent bonds
Hydrogen bonding
Hydrophobic effect
Conformation of polypeptide chain
Condensation of amino acids produces a polypeptide chain, with
the backbone atoms linked through the peptide bond
The angles of internal rotation around the bonds determine the
pattern of protein folding
Simple bonds not restricted by the electronic structure
but by esteric collisions
The double bond character of the peptide restricts
internal rotation
The peptide group occurs in cis and trans forms, being
trans more stable for all amino acids except for
Proline
All the cis forms in a polypeptide are restricted to
Proline and the amino acid preceding it due to the
small difference in energy between cis and trans
The dominance of the trans peptide bonds determines
two angles for the main chain conformation of each
residue  and , being some of their combinations
disallowed from the energetic point of view
 = -125º, and  = +125º
The Sasisekaran-Ramakrishnan-Ramachandran diagram