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Bioinformatics. Macromolecular structure. Contents. Determination of protein structure Structure databases Secondary structure elements (SSE) Tertiary structure Structure analysis Structure alignment Domain recognition Structure prediction Homology modelling

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Macromolecular structure


  • 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



Determination of protein structure

Jacques van [email protected]


Hanging drop method / vapour diffusion method


1-Dilute protein solution

Microscope slide

many different

conditions of 1&2

must be tried

2-Concentrated salt solution


Slide courtesy from Shoshana Wodak

Determination of protein structure
Determination of protein structure

Diffraction pattern

Atomic model

Slide courtesy from Shoshana Wodak

The resolution problem
The resolution problem




A high resolution protein structure : 1.5 - 2.0 Å resolution

Slide courtesy from Shoshana Wodak

Nuclear magnetic resonance nmr
Nuclear Magnetic Resonance (NMR)

Source: Branden & Tooze (1991)

Interatomic forces
Interatomic forces

  • Covalent interactions

  • Hydrogen bonds

  • Hydrophobic/hydrophilic interactions

  • Ionic interactions

  • van der Waals force

  • Repulsive forces



Structure databases

Jacques van [email protected]

Structure databases
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)

Cath a protein domain classification




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

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


  • 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.



Secondary structure elements

Jacques van [email protected]

Secondary structure helix
Secondary structure - -helix




3.6 residues

hydrogen bond

Source: Branden & Tooze (1991)

Hydrophobicity of side chain residues in helices
Hydrophobicity of side-chain residues in helices

Blue: polar

Red: basic or acidic

Source: Branden & Tooze (1999)

Secondary structure sheets
Secondary structure -  sheets



Source: Branden & Tooze (1991)

Secondary structure twist of sheets
Secondary structure - twist of  sheets

Mixed  sheet

Source: Branden & Tooze (1991)

Angles of rotation
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)

The ramachandran map
The Ramachandran map

Dipeptide unit

Dipeptide unit

Slide courtesy from Shoshana Wodak



Tertiary structure

Jacques van [email protected]

Combinations of secondary structures

Retinol binding protein (PDB:1rpb)




Combinations of secondary structures



Analysis of structure

Jacques van [email protected]

Structure structure alignment and comparison
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

Analyzing conformational changes
Analyzing conformational changes

Open form

Closed form

Citrate synthase, ligand induced conformational changes

Domain motion and small structural distortions

Slide courtesy from Shoshana Wodak

Defining domains what for
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

Methods for identifying domains
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.










Slide courtesy from Shoshana Wodak

Lactate dehydrogenase

Domains From Contact Map

Slide courtesy from Shoshana Wodak



Structure prediction

Jacques van [email protected]

Methods for structure prediction
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.

Homology modelling steps
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

Homology modelling similarity search
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

Homology modelling backbone modelling
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)

Homology modelling side chain modelling
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.

Homology modelling refinement
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.