Molecular Dynamic Studies

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Molecular Dynamic Studies of
Electrostatic Effects on the Vibration
of Heme-bound Ligands in Myoglobin
Jakub Kostal Steve Sontum Thesis Presentation
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Courtesy of www.mcsrr.org
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O2/CO
Binding of CO/O2 to Fe in Heme
CO ligand
N
N
N
Fe
N
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Process of Ligand binding in Heme
www.chemistry.wustl.edu
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Bound vs. free HemeThe Ultimate Puzzle

• Myoglobins ability to bind oxygen is readily
  poisoned by its stronger affinity for carbon
  monoxide
• The affinity for CO is greatly reduced compared
  to free heme

How does ligand surroundings in myoglobins Heme
pocket influence ligand binding?
1. Sterics
2. Electrostatic interactions
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Heme Pocket for Dummies
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Studying Electrostatic Effects Vibration of CO
bond

• Triple bond character causes high vibration
  stretching frequencies
• ?(CO) used to characterize different conformers
  of the bound state

• Equilibrium IR absorbance spectrum of bound CO
  shows the major sub states A0, A1 and A 3 are
  associated with CO stretching bands at 1966,
  1945, and 1927cm-1
• Dispersion of A sub states thought to be caused
  by electrostatic interactions between the CO
  dipole and the imidazole chain of the distal
  His64, which assumes different dynamic
  conformations

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Studying Electrostatic Effects Vibration of CO
bond

• Triple bond character causes high vibration
  stretching frequencies
• ?(CO) used to characterize different conformers
  of the bound state

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Models for electrostatic interactions in the CO
complexes - amino acid mutations
A (A3) Asn68 Mb (?CO 1938cm-1 ?Fe-C
527cm-1) B (A1, A2) Wild-Type Mb (?CO
1945cm-1 ?Fe-C 507cm-1) C (A0) Val64/Thr68
Mb (?CO 1984cm-1 ?Fe-C 477cm-1)

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Preliminary studies on our projectBuilding a
simple Theoretical Model

• Generation of a vibrational force field using
  RESP method for various heme analogs with bound
  CO ligand
• Classical MD model built
• Dynamic Simulation of an out-of-plane electric
  field using Li ions to predict changes in CO
  vibrations based on experimental observations
• Hypothesis

Li (/-)
Li (-/)
?(CO) lt ?(CO)
Molecular Dynamics Trajectory
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Observed Vibrational Shifts

• Expected trends somewhat preserved only at high
  e. field intensities

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Torquing motion of the CO ligand

• Fe-C-O bond locked in one torquing mode
  throughout the dynamic trajectory at higher E.
  field intensities
• Dominant mode at higher E. field
• Torquing motion accounts for additional
  centripetal stretching of the CO bond

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Analysis of the torquing mode
Normal direction Reversed direction

• Fe-O angle to the normal (?) is greater than Fe-C
  angle to the normal of the heme plane (?). This
  differences increases with reversed e. field
• Direction of the electric field changes ? and ?
• As the intensity of e. field increases, ? and ?
  increase as well
• As the temperature increases, both angles
  increase

X-axis time (0.01ps) Y-axis angle (degree)
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MD Trajectory of Full Myoglobin
Inside heme pocket
N?
N?
Out of heme pocket
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Conclusions and Future Work

• We have successfully generated RESP force field
  for CO heme model to study the effect of
  electrostatic fields on the vibration of CO.
• We have observed a toquing motion of the CO
  ligand induced by electrostatic fields of high
  intensities.
• We have analyzed 2ns MD trajectory of full
  myoglobin and observed that distal His64 spends
  88 of the time inside and 12 outside of the
  heme pocket.
• Generate force fields for similar O-O and NO
  bound heme models (in progress)

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Acknowledgments

• Steve
• Meghan
• Judy

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References

• Spiro T. G., Kozlowski P. M. 1998. Discordant
  results on FeCO deformability in heme proteins
  reconciled by density functional theory. J. Am.
  Chem. Soc. 120 4524-4525
• Phillips G. N., Teodoro M. L., Tiansheng L.,
  Smith B., Olson J. S.. 1999. Bound CO Is a
  Molecular Probe of Electrostatic Potential in the
  Distal Pocket of Myoglobin. J. Phys. Chem. B.
  103 8817-8829
• Nienhaus K., Pengchi D., Kriegl J. M., Nienhaus
  G. U. 2003. Structural Dynamics of Myoglobin
  Effect of Internal Cavities on Ligand Migration
  and Binding. Biochemistry. 42 9647-9658

• Ray, G. B., X.-Y. Li, J. A. Ibers, J. L. Sessler,
  and T. G. Spiro. 1994. How far proteins bend the
  FeCO unit? Distal polar and steric effects in
  heme proteins and models. J. Am. Chem. Soc. 116
  162-176.
• Rovira, C., K. Kunc, J. Hutter, P. Ballone, and
  M. Parrinello. 1997. Equilibrium geometries and
  electronic structure of iron-porphyrin complexes
  a density functional study. J. Phys. Chem. A.
  1018914-8925.

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Solvated WT Trajectory