A new approach towards deciphering the protein code: The protein assembly model

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A new approach towards deciphering the protein
code The protein assembly model

• Claire Lesieur
• lesieur_at_lapp.in2p3.fr

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Elements of the living world
Protein
Nucleus
Lipids
DNA
CHON
Chromosome
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Protein Biological activities

• Cutting
• Recognition
• Enzyme
• Signaling
• Carrier
• Shape generator
• Road networks

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Structure-function relationshipin proteins

• Function
• Shape
• How the shape provides a particular function
• How the shape is acquired

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The protein folding problem

• How it folds Mechanisms of protein folding
• How the information is encrypted in the
  sequences CODING problem

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Mechanism
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Code still unknown

• X-ray crystallography NMR PDB
• 3D modeling PDB
• 70 Sequence similarity 3D modeling

70 similarity different shape Low sequence
similarity similar shape Amino acids on the
surface of proteins changeable
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Transmembrane domains of Membrane proteins
b-strands transmembrane domain 1010101 a-helice
transmembrane domain 11111111111111111
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Biologically active amino acids
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Sequence-Shape predictions

• Geometrical constrain
• Chemical constrain

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To read sequences you need to determined
comparable sequences

• Domains
• Shape and role

Sequence Pattern
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Protein assembly
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Aerolysine
Trends in Microbiology (2000). Vol 8 (4)169-172
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Cholera toxin
CtxA
CtxB5

• AB5 toxin
• A catalytic subunit
• B receptor binding subunit
• GM1 cell receptor
• Endocytosed and traffic to the ER
• ADP ribosylation of Ga subunit
• Increase of cAMP leading to water loss

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Experimental approach
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Assembly in vitro
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2D structural level short range interaction
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3D structural level long range interaction

• Trp-fluorescence

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Functional test
HISTIDINE
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LTB
CtxB
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N-terminal
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• Kinetics differences
• On pathway intermediates differences
• It is particular amino acids that are responsible
  for each individual step of assembly and folding

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Fundamental question

• Alzheimer, Parkinson, Prion diseases

Protein X FOLD state healthy
Information for interfaces
(Protein X)n Assembly state Lethal
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Theoritical approach

• Protein Interface formation
• Rules?
• Mechanism?
• Preferential geometries related to preferential
  sequences of amino acids?

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INTERFACES Zone de contact entre monomeres
voisins
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Analyses des interfaces
Interface Trimer pentamer heptamer
Brin 1 Brin 2
0101 0101 Ch111Ch
n.a. Ch111Ch 1111/1
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Trimeric Domain
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Fibritin like domain
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Oligomeric proteins
Nombre de monomer 2 3 4 5
6 7 8 9 10 11 12 Nombre
de cas 5722 1035 2340 168 721 46 512 45
87 8 205
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Programme detection Protein Interfaces
Monomer M
513 -524 LMITTECMVTDL aaa-bbbbbbb-
Monomer M 1
35-49 GRNVVLDKSFGAPTI --bbbb-------bb
Distances
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PUTATIVE LIPOPROTEIN from E. CAROTOVORA
3BDU 20-29, 38-53
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Common protein interfaces of unrelated proteins
3BDU 1--111011-110110--10 1G31
0--1-1001-100100--00 1JBM 11001000101100101101 1
LNX 1--0100010110000---1 1N9R
0--0100011110010--11 1J2P ----1000101100101--1 1
HX5 ------0011110010--11 1LEP
0---10001000--00--11 Con2 ----1-001-1100-0-
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1LEP 1-8, 88-94, 40-57
1WNR 1-8, 88-94, 44-57, 62-77
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1N9R
yeast
Methanobacterium Thermautriophicum extremophile
1JBM
P. aerophilum bacterium
1LNX
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yeast
1 1
Methanobacterium Thermautriophicum extremophile
1JBM 12-18, 42-50, 64-83
1 1 1
P. Aerophilum Hyperthermophilic bacterium
1LNX 10-15, 25-32, 40-48, 63-77
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2CBY
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Conclusion

• Geometry and function related
• Family of protein interfaces
• Assembly keys

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Future

• Classification of protein interfaces Database
• Systematic analysis of protein interfaces-subjecti
  ve classification
• Mathematical approach Laurent Vuillon (LAMA)
• Functional analysis of protein interfaces
• Protein Assembly mechanism from block Giovanni
  Feverati
• Stoechiometry/Symmetry Paul Sorba
• Experimental tests Claire Lesieur

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Acknowledgment

• Alicia Ng Ling
• Mun Keat Chong
• Boon Leng Chua
• Danyang Kong
• Giovanni Feverati
• Paul Sorba