1. Macromolecular structure
Bioinformatics
Macromolecular structure

2. Contents Determination of protein structure Structure databases
Secondary structure elements (SSE)
Tertiary structure
Structure analysis
Structure alignment
Domain recognition
Structure prediction
Homology modelling
Threading/folder recognition
Secondary structure prediction
ab initio prediction

3. Determination of protein structure
Jacques van Helden

4. Crystallisation Hanging drop method / vapour diffusion method
Microscope
1-Dilute protein solution
Microscope slide
many different
conditions of 1&2
must be tried
2-Concentrated salt solution
Crystal
Slide courtesy from Shoshana Wodak

5. Determination of protein structure
Diffraction pattern
Atomic model
Slide courtesy from Shoshana Wodak

6. The resolution problemq q q
A high resolution protein structure : Å resolution
Slide courtesy from Shoshana Wodak

7. Nuclear Magnetic Resonance (NMR)
Source: Branden & Tooze (1991)

8. Interatomic forces Covalent interactions Hydrogen bonds
Hydrophobic/hydrophilic interactions
Ionic interactions
van der Waals force
Repulsive forces

9. Jacques van Helden jvanheld@ucmb.ulb.ac.be
Structure
Structure databases
Jacques van Helden

10. Structure databases PDB (Protein database)
Official structure repository
SCOP (Stuctural Classification Of Proteins)
Structure classification. Top level reflect structural classes.The second level, called Fold, includes topological and similarity criteria.
CATH (Class, Architecture, Topology and Homologous superfamily)

11. PDB entry header

12. CATH - A protein domain classification
In CATH, protein domains are classified according to a tree with 4 levels of hierarchically
Class
Architecture
Topology
Homology
Class
Architecture
Topology
Figure from Shoshana Wodak

13. Classifications of protein structures (domains)
CATH: structural classification of proteins, [
SCOP: Structural classification of proteins [
FSSP:Fold classification based on structure alignments [
HSSP: Homology derived secondary structure assignments [
DALI:Classification of protein domains [
VAST: structural neighbours by direct 3D structure comparison [
CE: Structure comparisons by Combinatorial Extension [
Slide courtesy from Shoshana Wodak

14. Books
Branden, C. & Tooze, J. (1991). Introduction to protein structure. 1 edit, Garland Publishing Inc., New York and London.
Westhead, D.R., J.H. Parish, and R.M. Twyman Bioinformatics. BIOS Scientific Publishers, Oxford.
Mount, M. (2001). Bioinformatics: Sequence and Genome Analysis. 1 edit. 1 vols, Cold Spring Harbor Laboratory Press, New York.
Gibas, C. & Jambeck, P. (2001). Developing Bioinformatics Computer Skills, O'Reilly.

15. Secondary structure elements
Jacques van Helden

16. Secondary structure - -helix
Carbon
Nitrogen
Oxygen
3.6 residues
hydrogen bond
Source: Branden & Tooze (1991)

17. Hydrophobicity of side-chain residues in helices
Blue: polar
Red: basic or acidic
Source: Branden & Tooze (1999)

18. Secondary structure -  sheets
Antiparallel
Parallel
Source: Branden & Tooze (1991)

19. Secondary structure - twist of  sheets
Mixed  sheet
Source: Branden & Tooze (1991)

20. Angles of rotation
Each dipeptide unit is characterized by two angles of rotation
Phi around the N-Calpha bond
Psi around the Calpha-C bond
Image from Branden & Tooze (1999)

21. The Ramachandran map Slide courtesy from Shoshana Wodak Dipeptide unit

22. Jacques van Helden jvanheld@ucmb.ulb.ac.be
Structure
Tertiary structure
Jacques van Helden

23. Combinations of secondary structures
loop
-helix
-sheet
Retinol binding protein (PDB:1rpb)

24. Jacques van Helden jvanheld@ucmb.ulb.ac.be
Bioinformatics
Analysis of structure
Jacques van Helden

25. Structure-structure alignment and comparison
Structure B
Structure A
Question: Is structure A similar to structure B ?
Approach: structure alignments
Slide courtesy from Shoshana Wodak

26. Analyzing conformational changes
Open form
Closed form
Citrate synthase, ligand induced conformational changes
Domain motion and small structural distortions
Slide courtesy from Shoshana Wodak

27. Defining Domains: What for?
Link between domain structure and function
Different structural domains
can be associated with
different functions
Enzyme active sites are
often at domain interfaces;
domain movements play
a functional role
DNA Methyltransferase
Cathepsin D
Slide courtesy from Shoshana Wodak

28. Methods for Identifying Domains
Underlying principle
Domain limits are defined by identifying groups of residues such that the number of contacts between groups is minimized. N N C C
4-cuts
1-cut N C
2-cuts
Slide courtesy from Shoshana Wodak

29. Lactate dehydrogenase
Domains From Contact Map
Slide courtesy from Shoshana Wodak

30. Jacques van Helden jvanheld@ucmb.ulb.ac.be
Structure
Structure prediction
Jacques van Helden

31. Methods for structure prediction
Homology modelling
Building a 3D model on the basis of similar sequences
Threading
Threading the sequence on all known protein structures, and testing the consistency
Secondary structure prediction
ab initio prediction of tertiary structure
For proteins of normal size, it is almost impossible to predict structures ab initio.
Some results have been obtained in the prediction of oligopeptide structures.

32. Homology modelling - steps
Similarity search
Modelling of backbone
Secondary structure elements
Loops
Modelling of side chains
Refinement of the model
Verification
Steric compatibility of the residues

33. Homology modelling - similarity search
Starting from a query sequence, search for similar sequences with known structure.
Search for similar sequences in a database of protein structures.
Multiple alignment.
A weight can be assigned to each matching protein (higher score to more similar proteins)
The higher is the sequence similarity, the more accurate will be the predicted structure.
When one disposes of structure for proteins with >70% similarity with the query, a good model can be expected.
When the similarity is <40%, homology modeling gives poor results.
The lack of available structures constitutes one of the main limitations to homology modeling
In 2004, PDB contains

34. Homology modelling - Backbone modelling
Modelling of secondary structure elements
a-helices
b-sheets
For each secondary structure element of the template, align the backbone of query and template.
Loop modelling
Databases of loop regions
Loop main chain depends on number of aa and neighbour elements (a-a, a-b, b-a, b-b)

35. Homology modelling - Side chain modelling
Side-chain conformation (model building and energy refinement)
Conserved side chains take same coordinates as in the template.
For non-conserved side chains, use rotamer libraries to determine the most favourable conformation.

36. Homology modelling - refinement
After the steps above have been completed, the model can be refined by modifying the positions of some atoms in order to reduce the energy.