Computational Study on the Function of Water within a Helix Antifreeze Protein Dimer and in the Proc

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Computational Study on the Function of Water
within a ß-Helix Antifreeze Protein Dimer and in
the Process of Ice-Protein Binding

• Zuoyin Yang, Yanxia Zhou, Kai Liu, Yuhua Cheng,
  Ruozhuang Liu, Guangju Chen and Zongchao Jia
  Biophysical Journal 85 2003

Xiuquan Sun 11 13 2003
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Outline

• Introduction
• Computational Methods
• Results and Discussion
• Conclusion
• Critique

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TmAFP

• Antifreeze protein (AFP) is a kind of protein
  that can lower the freezing point of a solution
  to help many organisms protect themselves from
  freezing in subzero temperatures. AFPs could
  improve the storage of blood, tissues and organs,
  and protect crops from frost and preserve the
  textures of frozen foods.
• Tenebrio molitor AFP (TmAFP) is from insects.

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The structure of TmAFP
Cited from Nature 406, 322 - 324 (2000)
YIH-CHERNG LIOU
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Computational Methods

• Molecular Mechanics
• Based on classical-mechanical model of
  molecular structures
• Quantum Mechanics
• Based on the Schrodinger's equation

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The Bridge-linked Interaction of Water with the
TmAFPs
Interaction energies (kcal/mol) calculated with
various methods
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Regular Water in the Aqueous TmAFP-water System

• After the simulations, the RMSD of the resulting
  TmAFP from the starting structure is only 1.10 Å.
• the standard derivations of the total energy,
  potential energy, kinetic energy, and temperature
  were only 12.90, 31.23, 25.17 kcal/mol, and 2.14
  K.

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Movements of the Oxygen Atoms
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Modeling the Complex of TmAFP-water and Ice in
Solution
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OO Distance Variation of the Hydroxyl
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Interaction Energy between TmAFP and Ice
Interaction energies (Einter) in models A and B
(kcal/mol),
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Adsorption Models for TmAFP on Ice
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Conclusion

• It is likely that by increasing the number of
  "lattice" points or "density" on the ice-binding
  site, TmAFP would have a better chance to
  initiate the recognition and binding process.
  TmAFP appears to force the water molecules out of
  the protein.

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Critique

• They got a very important result to help us
  further understand TmAFP-ice binding at molecular
  level.
• We need do more experiments and simulations to
  confirm the result.
• Different methods give us very different results,
  hope they can figure out what will affect the
  simulation results and improve the methods.