Macromolecular structure

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Macromolecular structure

• Bioinformatics

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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

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Determination of protein structure

• Structure

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Crystallisation
Hanging drop method / vapour diffusion method
Microscope
1-Dilute protein solution
Microscope slide
many different conditions of 12 must be tried
2-Concentrated salt solution
Crystal
Slide courtesy from Shoshana Wodak
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Determination of protein structure
Diffraction pattern
Atomic model
Slide courtesy from Shoshana Wodak
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The resolution problem
q
q
q
A high resolution protein structure 1.5 - 2.0 Å
resolution
Slide courtesy from Shoshana Wodak
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Nuclear Magnetic Resonance (NMR)
Source Branden Tooze (1991)
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Interatomic forces

• Covalent interactions
• Hydrogen bonds
• Hydrophobic/hydrophilic interactions
• Ionic interactions
• van der Waals force
• Repulsive forces

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Structure databases

• Structure

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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)

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PDB entry header
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CATH - A protein domain classification

• In CATH, protein domains are classified according
  to a tree with 4 levels of hierarchically
• Class
• Architecture
• Topology
• Homology

Figure from Shoshana Wodak
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Classifications of protein structures (domains)
CATH structural classification of proteins,
http//www.biochem.ucl.ac.uk/bsm/cath/
SCOP Structural classification of
proteins http//scop.mrc-lmb.cam.ac.uk/s
cop/ FSSPFold classification based on
structure alignments http//www.sander.e
bi.ac.uk/fssp/ HSSP Homology derived
secondary structure assignments
http//www.sander.ebi.ac.uk/hssp/
DALIClassification of protein domains
http//www.ebi.ac.uk/dali/domain/ VAST
structural neighbours by direct 3D structure
comparison http//www.ncbi.nlm.nih.gov
80/Structure/VAST/vast.shtml CE Structure
comparisons by Combinatorial Extension
http//cl.sdsc.edu/ce.html
Slide courtesy from Shoshana Wodak
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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.
  2002. 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.

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Secondary structure elements

• Structure

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Secondary structure - ?-helix
3.6 residues
hydrogen bond
Source Branden Tooze (1991)
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Hydrophobicity of side-chain residues in helices
Blue polar Red basic or acidic
Source Branden Tooze (1999)
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Secondary structure - ? sheets
Antiparallel
Parallel
Source Branden Tooze (1991)
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Secondary structure - twist of ? sheets
Mixed ? sheet
Source Branden Tooze (1991)
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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)
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The Ramachandran map
Dipeptide unit
Dipeptide unit
Slide courtesy from Shoshana Wodak
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Tertiary structure

• Structure

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Combinations of secondary structures
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Analysis of structure

• Bioinformatics

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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
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Analyzing conformational changes
Open form
Closed form
Citrate synthase, ligand induced conformational
changes Domain motion and small structural
distortions
Slide courtesy from Shoshana Wodak
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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
Cathepsin D
DNA Methyltransferase
Slide courtesy from Shoshana Wodak
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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
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Lactate dehydrogenase
Domains From Contact Map
Slide courtesy from Shoshana Wodak
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Structure prediction

• Structure

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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.

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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

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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
  gt70 similarity with the query, a good model can
  be expected.
• When the similarity is lt40, homology modeling
  gives poor results.
• The lack of available structures constitutes one
  of the main limitations to homology modeling
• In 2004, PDB contains

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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)

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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.

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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.