Simulation of Conformational Transitions and Free Energy Calculations of PcrA DNA Helicase Hao Wang Molecular Recognition Group School of Pharmacy University of Nottingham

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Simulation of Conformational Transitions and Free
Energy Calculations of PcrA DNA HelicaseHao
WangMolecular Recognition GroupSchool of
PharmacyUniversity of Nottingham
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Introduction

• DNA helicases are important enzymes involved in
  DNA replication, repair, and recombination.
• DNA helicases are molecular motors to separate
  the ds-DNA through the conformational changes
  coursed by the ATP hydrolysis.
• PcrA DNA helicase from Bacillus
  Stearothermophilus was crystallized by Dale
  Wigley and Panos Soultanas

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Substrate Complex Product Complex
Substrate Complex
Cell, Vol. 97, 75-84, April 2, 1999
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Research Aim

• Find the Reaction Pathway of the process from the
  substrate complex to the product complex.
• Calculate the free energy profile along the
  pathway.

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Simulation System

• 637 residues in the protein
• 15 bases on the short chain of DNA, and 20 bases
  on the long chain
• 11439 atoms in protein and DNA
• The ATP hydrolysis wasnt included
• Explicit solvent (TIP3P)
• 52 Na ions were added
• 25419 water molecules were added
• 87619 atoms in the system
• Amber force field
• 300K
• 8 CPU years simulation on this project

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• The computational methods to simulate the
  conformational changes of known ended system
• 1. Optimize the first guessed pathway between two
  conformations.
• 2. Use extra constraints to drive the molecule in
  the direction of the target structure.

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End
Start
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Chain Minimization Path
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End
Start
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Targeted Molecular Dynamics
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WHAM

• Weighted Histogram Analysis Method ( WHAM ) is a
  method using umbrella sampling to provide a free
  energy profile along a given reaction coordinate.
• Umbrella sampling is a well-established free
  energy technique using an artificial biasing
  window potential to sample unfavourable areas of
  conformational space.
• Usually this biasing is a standard harmonic
  potential applied to a bond length, angle or
  dihedral.
• In this research, the RMSD is used as the
  biasing.
• Using the TMD to search a certain RMSD region
  along the reaction path.
• Using WHAM program written by Alan Grossfield.
• Computer Physics Communications 91 (1995) 275-282

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• RMSD to the product complex along the TMD path

• RMSD to the product complex along the Chain
  Minimization path

If the two reaction pathway are similar, the RMSD
values along the diagonal line should be very
small. This picture shows the two methods find a
similar path.
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Free Energy Profile

• Chain Minimisation

• Targeted MD

The RMSD to the product complex reduces from 3 to
1.7 The free energy of the product complex is
higher than that of the substrate complex The
height of free energy barriers are different The
scale of the free energy profiles are
different The ATP hydrolysis only can offer
7.3kcal/mol energy
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Future Work

• Calculating the Free Energy changes from the
  product complex to the substrate complex.
• Investigating the barriers involved.
• Coupling between the ATP hydrolysis and the
  dynamics.

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Acknowledgments

• Dr Charlie Laughton and Dr Stephen Doughty
• Dr Panos Soultanas
• Professor Mark Searle
• Everyone in the Molecular Recognition Group
• Dr. Ian Withers
  Ms. Verity Hudson
• Mr. Daniel Warner
  Ms. Michele Burke
• Dr. Mark Beardsell
  Mr. Angelo Pugliese
• Mr. Supat Jiranusornkul
• University of Nottingham and Spirogen Ltd for
  funding