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Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior
Summary
Molecular dynamics simulations reveal that low-frequency atomic fluctuations in decaglycine alpha-helices are significant above 100 K. These findings challenge the harmonic approximation and offer insights into protein dynamics.
Area of Science:
- Biophysics
- Computational Chemistry
- Structural Biology
Background:
- Understanding atomic fluctuations is crucial for protein dynamics and function.
- The harmonic approximation is a common model for atomic displacements, but its validity at different temperatures is debated.
Purpose of the Study:
- To compare mean square amplitudes of atomic fluctuations in decaglycine alpha-helices using molecular dynamics (MD) simulations with analytic harmonic results and experimental data.
- To investigate the temperature dependence and frequency contributions to atomic fluctuations.
Main Methods:
- Molecular dynamics simulations of decaglycine alpha-helix at seven temperatures (5-300 K).
- Comparison of simulation results with analytic harmonic approximation.
- Analysis of fluctuation time dependence and relaxation times.
- Comparison with experimental X-ray diffraction data (Debye-Waller factors) for metmyoglobin and ferrocytochrome c.
Main Results:
- The harmonic approximation significantly underestimates atomic displacement amplitudes above 100 K.
- Low-frequency modes (<75 cm(-1)) dominate atomic fluctuations.
- A contribution with a very long relaxation time (>10 ps) was observed.
- Quantum corrections to fluctuation amplitudes are small above 50 K.
Conclusions:
- Molecular dynamics simulations provide a more accurate representation of atomic fluctuations in polypeptides than the harmonic approximation at higher temperatures.
- Low-frequency, long-timescale motions play a critical role in protein dynamics.
- MD simulations align with experimental observations of atomic fluctuations in proteins.
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