Protein modelling

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Protein modelling

• Protein structure is the key to understanding
  protein function
• Protein structure
• Topics in modelling and computational methods
• Comparative/homology modelling
• Fold recognition
• Fold prediction
• Dynamics of proteins

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Motivation

• Protein structure determines protein function
• For the majority of proteins the structure is not
  known

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Steps in comparative modelling

• Find suitable template(s)
• Build alignment between target and template(s)
• Build model(s)
• Replace sidechains
• Resolve conflicts in the structure
• Model loops (regions without an alignment)
• Evaluate and select model(s)

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State of the art in homology modelling

• Template search
• (iterative) sequence database searches (PSIBLAST)
• Alignment step
• multiple alignment of close to fairly distant
  homologues
• Modelling step
• rigid body assembly
• segment matching
• satisfaction of spatial constraints

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Modelling by spatial restraints

• Generate many constraints
• Homology derived constraints
• Distances and angles between aligned positions
  should be similar
• Stereochemical constraints
• Bond lengths, bond angles, dihedral angles,
  nonbonded atom-atom contacts
• Model derived by minimizing restraints

Modeller Sali Blundell (1993)
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Loop modelling

• Exposed loop regions usually more variable than
  protein core
• Often very important for protein function
• Loops longer than 5 residues difficult to built
• Mini-protein folding problem

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Model evaluation

• Check of stereochemistry
• bond lengths angles, peptide bond planarity,
  side-chain ring planarity, chirality, torsion
  angles, clashes
• Check of spatial features
• hydrophobic core, solvent accessibility,
  distribution of charged groups,
  atom-atom-distances, atomic volumes, main-chain
  hydrogen bonding
• 3D profiles/mean force potentials
• residue environment

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Knowledge-based mean force potentials

• Compute typical atomic/residue environments based
  on known protein structures

Melo Feytmanns (1997)
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Modelling a transcription factor

• Sequence from different species
• Is binding to ligand conserved?

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Ligand binding domain
hydrogen bonds to ligand
homo-serine lactone moiety binding
acyl moiety binding
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DNA binding domain
DNA binding domain
Linker
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New Loop
Template
Target
Variable loops
MODELLER output
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Ligand binding pocket
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Errors in comparative modelling

1. Side chain packing
2. Distortions and shifts
3. Loops
4. Misalignments
5. Incorrect template

True structure
Template
Model
Marti-Renom et al. (2000)
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Modelling accuracy
Marti-Renom et al. (2000)
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Applications of homology modelling
Marti-Renom et al. (2000)
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Structural genomics

• Post-genomics
• many new sequences, no function
• Aim a structure for every protein
• High-throughput structure determination
• robotics
• standard protocols for cloning/expression/crystall
  ization

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Structural coverage
high quality models
Complete models
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Vitkup et al. (2001)
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Target selection
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Protein modelling

• Protein structure is the key to understanding
  protein function
• Protein structure
• Topics in modelling and computational methods
• Comparative/homology modelling
• Fold recognition
• Fold prediction
• Dynamics of proteins

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Fold recognition

• Structure is more conserved than sequence

Limit of sequence similarity searches
Structural similarity
Target
Protein structures
Fold space
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Fold recognition / Threading

• Is a sequence compatible with a structure?
• The idea evolutionary related proteins share
  common folding motifs
• Contact matrix motif
• Mean-force potentials to score every contact
• Optimize alignment to minimize pseudo-energy

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Protein modelling

• Protein structure is the key to understanding
  protein function
• Protein structure
• Topics in modelling and computational methods
• Comparative/homology modelling
• Fold recognition
• Fold prediction
• Dynamics of proteins

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Results

• Small molecules ok
• Proteins with mostly a-helices ok
• Proteins with mostly ß-sheets not so ok

Simons et al. (1997)
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Dynamics of proteins

• Protein structure is the key to understanding
  protein function
• Protein structure
• Topics in modelling and computational methods
• Comparative/homology modelling
• Fold recognition
• Fold prediction
• Dynamics of proteins

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Dynamics of proteins

• Local Motions (0.01 to 5 Å, 10-15 to 10-1 s)
• Atomic fluctuations
• Sidechain Motions
• Loop Motions
• Rigid Body Motions (1 to 10Å, 10-9 to 1s)
• Helix Motions
• Domain Motions (hinge bending)
• Subunit motions
• Large-Scale Motions (gt 5Å, 10-7 to 104 s)
• Helix coil transitions
• Dissociation/Association
• Folding and Unfolding

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Molecular dynamics/molecular modelling

• Molecular mechanics
• Normal mode analysis
• Quantum mechanical simulations
• ...

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Molecular mechanics

• Atom representation
• sphere
• charge
• topology
• Forces
• Bonded interactions
• Non-bonded interactions
• Electrostatic interactions
• Van-der-Waals interactions
• Forcefields AMBER, GROMOS, ...
• Newton's law of mechanics

http//cmm.info.nih.gov/modeling/guide_documents/m
olecular_mechanics_document.html
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Molecular mechanics

• Molecular mechanics simulations take long!
• because of the size of the system
• Proteins are large
• Water molecules to consider solvent effects
• 10.000 to millions of atoms
• because of the number of iterations
• update atom positions according to time-scale of
  fastest fluctuations bond vibrations ca. 1 fs
• movements of interest frequently have long
  time-scale,e.g. folding
• 1s gt 1015 iterations!

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Benefit of simulations

• Result is an ensemble of structures
• Time-averaged statistical quantities
• e.g., relative free energies of different
  conformations
• Protein engineering
• e.g., relative free energies of different mutants
• Physical accuracy of models?
• chemical reactions?
• cutoff and long-range interactions?
• dielectric constant?

movie from C. Letner, G. Alter Journal of
Molecular Structure (Theochem) 368 (1996) 205212
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The end

• Proteins are beautiful!

www.holmgroup.org