Modelling the Physical Properties of Biomolecules with Computer Simulation

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Modelling the Physical Properties of Biomolecules
with Computer Simulation
Jon Mitchell and Sarah Harris Polymer IRC School
of Physics and Astronomy Leeds University
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Computational Biophysics Group
i) DNA mechanics, topology and packaging Sarah
Harris/Jon Mitchell Tannie Liverpool/Neil
Thomson ii) MD Simulations of Amyloid-like
aggregates Josh Berryman Sheena
Radford iii) Multiscale models of charge
transfer through DNA David Reha William Barford
iv) Melting kinetics of RNA aptamers
Jonathan Westwood Peter Stockley/Alistair
Smith v) Calculation of protein dielectric
constants George Patargias John Harding vi)
Thermodynamics of peptide aggregation
Postdoc Amalia Aggeli/Tom McLeish
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The Structure of Duplex DNA
Helical repeat 10 base pairs / 34Å
Helix diameter 20Å
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Classical (MD) with AMBER
MD represents all of the atoms as classical
balls possessing atom types which mimic the
chemistry of the biomolecule.
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Contents of the Simulation Cell
Biomolecules are very sensitive to their
environment. The most accurate MD calculations
include water and counterions explicitly These
calculations are extremely computationally
expensive and require parallel resources such
as the NGS
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Contents of the Simulation Cell
Biomolecules are very sensitive to their
environment. The most accurate MD calculations
include water and counterions explicitly These
calculations are extremely computationally
expensive and require parallel resources such
as the NGS
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The Limitations of MD

• MD cannot be used to investigate biological
  processes which
• i) Occur over very long timescales (gt100ns)
• ii) Involve very large complexes (gt1,000,000
  atoms)
• iii) Require bond breaking/formation or charge
  transfer

We need to continuously develop new simulation
methods to investigate the more difficult
questions in biology
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Biomechanical Properties of DNA
Topoisomerases change the twist of DNA by cutting
and resealing the strands
Reading the genetic code involves separating the
two DNA strands
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Nanomanipulation of DNA
The action of molecular motors can be mimicked in
the laboratory using nanomanipulation techniques.
DNA Unzipping Unzipping DNA measures the force
required to rupture individual base pairs.
DNA Pulling DNA can be pulled apart by an
external force.
DNA Twisting DNA can be denatured by
twisting/untwising
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Simulating DNA Stretching
In silico the DNA must be stretched far faster
than in the experiment which can introduce
artefacts into the results
Denaturation bubbles form when the DNA is held
under tension for some time the DNA becomes
entropically unstable.
Slow unbinding requires a smaller force, but
melting must occur fast enough for transcription.
Force, thermodynamics and kinetics are intimately
connected in biology
Harris S. A. et al (2005) Biophys J. 88,
1684-1691.
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Melting of d(AT)30
d(AT)30 melts irreversibly from the ends of the
helix
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DNA Supercoiling and Packing
In chromosomes, 1-20cm of DNA is densely packaged
into only 1-10µm
Topoisomerase
Relaxed DNA
DNA gyrase
Supercoiled DNA
Bacterial DNA is compacted by supercoiling the
circular plasmids into higher order helical
structures. Cellular DNA is generally
under-wound only thermophiles contain enzymes
which can over-wind DNA
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Simulations of 90bp DNA Circles
A circle containing 90bp solvent consists of
150,000 atoms 1ns takes 48hrs on 32
processors of the Oxford NGS node.
10nm
8 helical turns Alternating AT
90bp of DNA possesses 8.5 helical turns when
torsionally relaxed
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Undertwisted DNA Circles
When the DNA is under-wound by 2.5 turns the DNA
locally melts to relieve torsional stress
6 helical turns Alternating AT
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Overtwisted DNA Circles
DNA overtwisted by 1.5 turns undergoes a buckle
instability to form a supercoiled structure which
relaxes when one strand is nicked.
Supercoiling occurs spontaneously as it is
thermodynamically favourable
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The Importance of the Environment
Under-winding lead to negative supercoiling only
for larger circles in high salt conditions
Reducing the salt to 0.01M leads to rapid
unwinding due to electrostatic repulsion between
crossed DNA strands
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Frustrated DNA Circles
Supercoiling relieves torsional stress but
requires sharp bends at the apices
These terms almost balance for circles of 118
base pairs.
This system undergoes large thermal fluctuations
between circular and supercoiled structures
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Some Concluding Remarks
These simulations are unavoidably computationally
expensive
MD is capable of exploring the mechanics of
single molecules in atomic detail
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Thanks

• Sarah Harris
• EPSRC
• NGS (Shiv Kaushal Joanna Schmidt)
• Leeds Supercomputer (Alan Real)

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Twisting, Supercoiling and Transcription
Bacteria placed under environmental stress
respond using dramatic changes in the levels of
supercoiling to alter gene expression.
Under-winding is thought to promote cellular
processes which require strand separation (eg
transcription, translation, replication) by
destablising the duplex.
Untwisting critically weakens the van der Waals
interactions between stacked bases and lead to
strand separation