Bioinformatics. Macromolecular structure

Transcription

1 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 Structure Determination of protein structure Jacques van Helden

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

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

6 The resolution problem q 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 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 HEADER TRANSCRIPTION REGULATION 06-MAR-92 1D66 1D66 2 COMPND GAL4 (RESIDUES 1-65) COMPLEX WITH 19MER DNA 1D66 3 SOURCE (SACCHAROMYCES $CEREVISIAE) OVEREXPRESSED IN (ESCHERICHIA 1D66 4 SOURCE 2 $COLI) 1D66 5 AUTHOR R.MARMORSTEIN,S.HARRISON 1D66 6 REVDAT 1 15-APR-93 1D66 0 1D66 7 JRNL AUTH R.MARMORSTEIN,M.CAREY,M.PTASHNE,S.C.HARRISON 1D66 8 JRNL TITL /DNA$ RECOGNITION BY /GAL4$: STRUCTURE OF A 1D66 9 JRNL TITL 2 PROTEIN(SLASH)/DNA$ COMPLEX 1D66 10 JRNL REF NATURE V D66 11 JRNL REFN ASTM NATUAS UK ISSN D66 12 REMARK 1 1D66 13 REMARK 2 1D66 14 REMARK 2 RESOLUTION. 2.7 ANGSTROMS. 1D66 15 REMARK 3 1D66 16 REMARK 3 REFINEMENT. 1D66 17 REMARK 3 PROGRAM CORELS;TNT;XPLOR 1D66 18 REMARK 3 AUTHORS J.SUSSMAN;D.TRONRUD;A.BRUNGER 1D66 19 REMARK 3 R VALUE D66 20 REMARK 3 RMSD BOND DISTANCES ANGSTROMS 1D66 21 REMARK 3 RMSD BOND ANGLES 2.9 DEGREES 1D66 22 REMARK 4 1D66 23 REMARK 4 THERE ARE TWO DNA CHAINS WHICH HAVE BEEN ASSIGNED CHAIN 1D66 24 REMARK 4 INDICATORS *D* AND *E*. THERE ARE TWO PROTEIN CHAINS 1D66 25 REMARK 4 WHICH HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. 1D66 26 REMARK 4 EACH PROTEIN - DNA COMPLEX CONTAINS FOUR BOUND CD IONS. 1D

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 Structure Secondary structure elements Jacques van Helden

16 Secondary structure - α-helix Carbon Nitrogen Oxygen hydrogen bond 3.6 residues 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 - β sheets Antiparallel Parallel Source: Branden & Tooze (1991)

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

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

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

22 Structure Tertiary structure Jacques van Helden

23 Combinations of secondary structures Retinol binding protein (PDB:1rpb) β-sheet α-helix loop

24 Bioinformatics Analysis of structure Jacques van Helden

25 Structure-structure alignment and comparison Structure A Structure B 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 1-cut 4-cuts N C 2-cuts Slide courtesy from Shoshana Wodak

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

30 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.