ii. patterns and forms in protein structure 2. patterns and forms in protein structure helices and...
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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 non-specifically 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
-N-C-C-N-C-C-........
O O
Si-1 Si
Amino acids are chemical building blocks
HK
R
E
D
F YW
IL
V
M
A
Q
S N
T
CH
G PC
S-S
polar
positive
negative
charged
beta-branched
aliphatic
aromatic
hydrophobic
Sidechain nomenclature
C
X
X
X
carbon alpha, central chiralcarbon of the amino acid
beta;first sidechain position
gamma position
delta position
epsilon position
zeta position X
X
Xeta position
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
C
R
HN CO
C
R
HNCO
L-form D-form
amino acids inproteins are almostalways in the L-form
D-form occurs rarely --peptide antibiotics, somepeptide toxins
Peptide chemistry
C
R
HN+ C
O
O-
H
HC
R
H
N+ C
O
O-H H
H
amino acids dissociate in aqueous solutionto form a zwitterion (ionic species with twoindependent charged groups)
Peptide chemistry
C
R
HN C
O
H20
H
H C
R
H
N C
O
OH
H
peptide bond
the amino acid polymer formswhen the carboxyl group of one amino acid condenses withthe amino group of the next
Protein folding
The energy of protein conformation depends on:
Interaction of sidechains and main chains
Interaction with solvents and ligands
The environmental conditions of the cell
Native state
Proteins follow the shortest temporal and energetical pathway to acquire the most stable conformation
DenaturedSpontaneous aggregation
Non-specific aggregates
Chaperones
Functional conformations
Protein Folds: sequential, spatial and topological arrangement of secondary structures
The Globin foldThe Globin fold
t = 1
t = 2
t = 3
t = 13512 lines REL4548 (MAF)12 lines REL7550 (MXR)
Vertical transmission of E. coli as a simulating system of endosymbiosis
Comptenece experiments
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
Day –2: grow on LB every competitor
ara ara+
BamHI
PP
HindIII HindIII
Pbla
tetA tetRyjeH
groE
SalI XhoI
S L
0.4
0.6
0.8
1.0normalmutator
Ancestral evolved groEc
W
groES groEL
137 Å
57 KDa146 Å
Apical domain
Y199, S201, Y203, F204, L234, 237, 259
V263, 264
Intermediate domain
Equatorial domain
GroEL as a compensatory mechanism
95100
100
100
99
100100
96
99
97
95
0,05
A. pisum PS
S. Avenae PS
M. Persicae PSR. padi PS
S. graminum PS
P. populeum PS
T. caerulescens PS
C. leucomelas PS
T. salignus PS
T. suberi PSE. carotovora
E. coli
S. typhimurium
E. aerogenes
0.05
100
9999
93
100
B. germanica PS
E. libidus PS
P. americana PS
B. orientalis PS
L. dicipiens PS
B. gingivalis
P. gingivalis
E. coli
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
E. carotovora
K. pneumoniae
E. aerogenes
S. enterica
S. typhimurium
S. glossinidia SS
S. oryzae PS
P. putida
P. aeruginosa
P. gingivalis B. gingivalis
L. dicipiens PS
100
99
100
100
100
100
10061
9910064
97
99
100
100
100
100
94
100
99
94
100
77100
42
0.1
A
B
Flavobacteria E. libidus PS
B. germanica PS B. orientalis PS
P. americana PS100
93
CD
E
FH
GI
J
-proteobacteria
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
Positive selection in the endosymbiont GroEL
Protein structure stability and its ability and specificity to bind ligands depend on different chemical forces:
Hydrogen bonding
Covalent bonds
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