1. Structural Bioinformatics
Elodie Laine
Master BIM-BMC Semestre 3,
Laboratoire de Biologie Computationnelle et Quantitative (LCQB)
e-documents:

2. Introduction
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3. What is a protein? 1-Dimensional text
WPLSSSVPSQKTYQGSYGFRLGFLH
2-Dimensional series of strand and helices
3-Dimensional set of points/shape
Proteins play essential and very diverse roles in all processes governing life. They are made of essential building blocks, namely amino acids.
Amino acid: common [central C-alpha with H attached + amino group (NH2) + carboxyl group (COOH)] + radical.
During proteins synthesis they are joined end-to-end by the formation of peptide bond (condensation -> release of water) => residues
The common scaffold constitues the backbone of the protein and the radicals represent the side chains.
There exist 20 different types of aa encoded in protein genes displaying different radicals and thus different physico chemical properties. z y x
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4. What is a protein? tumor-supressor P53 DNA binding domain
Proteins play essential and very diverse roles in all processes governing life. They are made of essential building blocks, namely amino acids.
Amino acid: common [central C-alpha with H attached + amino group (NH2) + carboxyl group (COOH)] + radical.
During proteins synthesis they are joined end-to-end by the formation of peptide bond (condensation -> release of water) => residues
The common scaffold constitues the backbone of the protein and the radicals represent the side chains.
There exist 20 different types of aa encoded in protein genes displaying different radicals and thus different physico chemical properties.
Elodie Laine –

5. What is a protein? tumor-supressor P53 DNA binding domain
Proteins play essential and very diverse roles in all processes governing life. They are made of essential building blocks, namely amino acids.
Amino acid: common [central C-alpha with H attached + amino group (NH2) + carboxyl group (COOH)] + radical.
During proteins synthesis they are joined end-to-end by the formation of peptide bond (condensation -> release of water) => residues
The common scaffold constitues the backbone of the protein and the radicals represent the side chains.
There exist 20 different types of aa encoded in protein genes displaying different radicals and thus different physico chemical properties.
Elodie Laine –

6. What is a protein made of?
one amino-acid
aRginine
lysine (K)
aspartate (D)
glutamate (E)
asparagiNe
glutamine (Q)
Cysteine
Methionine
Histidine
Serine
Threonine
Valine
Leucine
Isoleucine
phenylalanine (F)
tYrosine
tryptophan (W)
Glycine
Alanine
Proline
Peptidic bond
20 amino acids
Proteins play essential and very diverse roles in all processes governing life. They are made of essential building blocks, namely amino acids.
Amino acid: common [central C-alpha with H attached + amino group (NH2) + carboxyl group (COOH)] + radical.
During proteins synthesis they are joined end-to-end by the formation of peptide bond (condensation -> release of water) => residues
The common scaffold constitues the backbone of the protein and the radicals represent the side chains.
There exist 20 different types of aa encoded in protein genes displaying different radicals and thus different physico chemical properties.
Elodie Laine –

7. ~10’s to ~1000’s of amino acid residues
Protein structure
1st level of organisation : primary structure
…QNCQLRPSGWQCRPTRGDCDLPEFCPGDSSQCPDVSLGDG…
~10’s to ~1000’s of amino acid residues
Covalent bonds
1 protein = 1 polypeptidic chain
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8. Protein structure 2nd level of organisation : secondary structure
β-sheet
α-helix
Backbone-backbone
weak chemical bonds
Other elements: 310 helix > turns > loops > random coil
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9. Protein structure 3rd level of organisation : tertiary structure
A protein sequence adopts a particular fold in solution, which corresponds to a free energy minimum
Types of non-covalent interactions:
salt bridges
hydrogen bonds
hydrophobic contacts
pi-pi stacking…
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10. 4th level of organisation : quaternary structure
Protein structure
4th level of organisation : quaternary structure
Arrangements of domains within a protein or of proteins within a macro-molecular assembly
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11. Protein structure representations
sticks
spheres
All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves.
surface
cartoon
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12. Protein structure representations
protein kinase
~ 300 amino acid residues
~ 5000 atoms ( dof)
sticks
Each atom is colored according to its element (N: blue, O: red, C: grey).
The sticks represent the covalent bonds (~1.5 Angstroms) between atoms.
The atoms are at the extremities or intersection of the sticks.
All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves.
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13. Protein structure representations
spheres
The sphere represents the volume taken by the atom.
The radius of the sphere depends on the type of atom. It is called the van der Waals radius.
All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves.
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14. Protein structure representations
The molecular surface delimits the volume that is not penetrated by water molecules in solution.
It is obtained by rolling a probe (sphere of 1.4 Angstroms) on the protein.
surface
All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves.
1 Angstrom = m = 0.1 nm
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15. Biochemical units
Hydrophobic side chain
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16. Biochemical units Charged side chain Polar side chain
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17. Biochemical units Special Chirality
disulfide bridge
oxidation
reduction
Cys
bond
Chirality
The translation machinery of protein has evolved to utilize only one of the chiral forms of amino acids : the L-form
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18. Backbone torsion angles
Structural units
Planar peptide units
Backbone torsion angles
The conformation of the whole main chain of the polypeptide is completely determined when the rotation angles φ (N-Cα) and ψ = (Cα-C’) are defined with high accuracy.
Peptide unit: from one C-alpha to the next one ; all the atoms in such a unit are fixed in a plane with the bond lengths and bon angles very nearly the same in all units in all proteins.
The only DOF of a peptide unit are rotations around its bonds : Calpha-C’ (psi) and N-Calpha (phi)
The conformation of the whole main chain is completely determined when these two angles are defined with high accuracy
ω = angle between Cα-N-C & N-C-Cα planes - The ω angle is normally 0° (cis) or 180° (trans).
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19. Structural units Ramachandran diagram +180
Most combinations of φ and ψ for an amino acid are not allowed because of steric collisions between the side chain and main chain
310 = 310-helix
α = α-helix
β = extended β-stand
Lα = left-handed α-helix
polyP = extended polyproline
Ramachandran et al. (1963) J. Mol. Biol.
Ramachandran et al. (1968) Adv. Protein. Chem.
-180
-180
+180
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20. Structural units Ramachandran diagram
Glycine can adopt a much wider range of conformations than the other residues and thus plays a structurally very important role
310 = 310-helix
α = α-helix
β = extended β-stand
Lα = left-handed α-helix
polyP = extended polyproline
Ramachandran et al. (1963) J. Mol. Biol.
Ramachandran et al. (1968) Adv. Protein. Chem.
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21. Sequence-structure-function paradigm
Dynamics
- Tumour-supressor protein p53’s disordered segments help it interact with hundreds of partners.
Tumour-supressor protein p53’s disordered segments help it interact with hundreds of partners.
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22. Structured & disordered protein building blocks
Structured domains and intrinsically disordered regions (IDRs) are two fundamental classes of functional building blocks of proteins. The synergy between disordered regions and structured domains increases the functional versatility of proteins.
Because IDRs generally lack bulky hydrophobic amino acids,
they are unable to form the well-organized hydrophobic core that
makes up a structured domain31,44 and hence their functionality
arises in a different manner as compared to the classical
structure−function view of globular, structured proteins. In this
framework, protein sequences in a genome can be viewed as
modular because they are made up of combinations of structured
and disordered regions
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23. Multiple isoforms from a single gene
Does one sequence code for one protein?
- Tumour-supressor protein p53’s disordered segments help it interact with hundreds of partners.
Alternative splicing produces several isoforms from the same gene, by combining subsets of exons in different ways
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24. Protein functions pumps drugs and poisons out of cells
stores iron ions inside cells
recognizes foreign objects
hormones
supports organs and tissues
copies the information held in a DNA strand
sensor of light
breaks down food in the stomach
rotary motor powered by electrochemical energy
forms structural girders
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25. Protein functions
The enzyme aconitase is a key player in the central pathway of energy production. It converts citrate into isocitrate.
Moonlighting proteins lead double lives, performing two entirely different functions
The iron regulatory protein 1 interacts with messenger RNA to control the levels of iron inside cells.
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26. Hydrophobic-polar (HP) 2D-lattice model
Protein folding prediction problem
The geometric configuration of a protein’s native state determines its macroscopic properties, behaviour and function.
The number of possible conformations for a given protein is astronomical.
ex: 100aa, 3 conf/aa => conf
1 fold/10-13 sec => 1027 years (age of Universe: 1010 years)
And yet protein do fold spontaneously in a matter of milliseconds.
How can it be ?
Comparison with DNA: the structure of DNA, made up of only 4 different nucleotide building blocks that occur in two pairs, is relatively simple, regular and predictable.
How can we solve the problem?
The space of biologically accessible conformations is much smaller than that of all possible conformations ?
rapid fomation of local interactions = folding of modules / nucleation points
presence of intermediate/transition states (molten globules)
funnel-like energy landscape where the native state corresponds to a deep free energy minimum
HP model : square where each bead is an amino acid, 2 types of amino acids and non-zero interaction energies only for HH contacts
Hydrophobic-polar (HP) 2D-lattice model
Levinthal’s paradox
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27. Protein dynamics spatio-temporal scales
Native state formation
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28. Protein structures are about...
Chemistry
atoms, bonds, chirality, pH...
Physics
forces, molecular mechanics...
Biology
functions, processes, cellular environment...
Mathematics
combinatorics (of interactions, of domains)...
Informatics
automated algorithms, data analysis...
Proteins play essential and very diverse roles in all processes governing life. They are made of essential building blocks, namely amino acids.
Amino acid: common [central C-alpha with H attached + amino group (NH2) + carboxyl group (COOH)] + radical.
During proteins synthesis they are joined end-to-end by the formation of peptide bond (condensation -> release of water) => residues
The common scaffold constitues the backbone of the protein and the radicals represent the side chains.
There exist 20 different types of aa encoded in protein genes displaying different radicals and thus different physico chemical properties.
Elodie Laine –

29. Algorithms in structural bioinformatics: what for ?
To predict protein structures
experimental data analysis and 3-dimensional model building
secondary or tertiary structure prediction based on the sequence
known protein sequences
protein sequences with function
known protein structures
increasing gap
A l’heure actuelle, les grands programmes de séquençage de génomes génèrent un très grand nombre de séquences protéiques dont la fonction et la structure est inconnue.
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30. Algorithms in structural bioinformatics: what for ?
To predict protein structures
To compare protein structures
classification of proteins (divergent/convergent evolution)
identification of active sites, functional motifs or binding sites
Phylogenetic tree of 38 CATH Architecture domain structures
Optimal (P<0.01) most parsimonious A (26,323 steps; CI = , RI = ; g1 = −0.427) tree was reconstructed from a protein domain census in 492 completely sequenced genomes. The phylogeny was plotted into circular tree diagram and cartoon representations of the core structures labeled with each CATH id were mapped onto the leaves of the tree. The Venn diagram shows the diversity of A in the three superkingdoms, Archaea, Bacteria and Eukarya.
doi: /journal.pcbi g003
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31. Algorithms in structural bioinformatics: what for ?
To predict protein structures
To compare protein structures
To simulate protein motions
atomic-level description of the mechanisms underlying protein activity
characterization of intermediate conformations that can be targeted by drugs
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32. Algorithms in structural bioinformatics: what for ?
To predict protein structures
To compare protein structures
To simulate protein motions
To characterize protein interactions
protein interaction sites identification and complex structures prediction
discimination between true partners in the cell and non-interactors
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33. Algorithms in structural bioinformatics: what for ?
To predict protein structures
To compare protein structures
To simulate protein motions
To characterize protein interactions
To discover and design drugs
putative druggable pockets identification
binding mode and relative affinity prediction
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34. Conclusion
Proteins are composed of amino acid residues linked by a peptidic bond. There exist 20 types of amino acids with different physico- chemical properties.
A protein is a polypeptidic chain. Four levels of organization determine the 3D atomic coordinates of a protein structure.
Proteins fulfill various biological functions: structural, enzymatic, of transport… Some proteins can have multiple functions.
Proteins are dynamic and flexible objects which adapt their shape in response to environmental conditions.
Algorithm in structural bioinformatics can help predict and classify protein structures, describe their motions and interactions, design new drugs.
Bon ensemble de leurres:
๏ Contient des conformations qui sont proches de la structure native.
๏ Contient des structures issues de différentes protéines, qui
appartiennent à des classes structurales différentes.
๏ Contient un grand nombre de structures.
๏ Contient des structures représentatives de différentes régions de
l’espace conformationnel.
Structure proche de la native: comment l’évaluer ?
๏ pourcentage de contacts natifs;
๏ rmsd
Elodie Laine –