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A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
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Why are Vibrational Lines Narrow in Proteins?

Daniel R Martin1, Dmitry V Matyushov2

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Protein internal electric fields are strong, but vibrational lines are narrow. This occurs because proteins do not sample enough configurations during the vibrational probe

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Area of Science:

  • Biophysics
  • Computational Biology
  • Spectroscopy

Background:

  • Vibrational Stark effect reveals strong internal electric fields in proteins (few V/Å).
  • Numerical simulations support these high field values.
  • Simulations also predict significant electric field fluctuations, suggesting line broadening.

Purpose of the Study:

  • Reconcile the discrepancy between predicted broad vibrational lines and experimentally observed narrow lines in proteins.
  • Investigate the role of protein dynamics and configuration sampling in vibrational line shapes.

Main Methods:

  • Analysis of vibrational Stark effect data in proteins.
  • Utilizing numerical simulations of protein electric fields.
  • Applying fluctuation-dissipation arguments to interpret line broadening.

Main Results:

  • Protein internal electric fields are strong, reaching several volts per angstrom.
  • Simulations indicate substantial fluctuations in these electric fields.
  • Experimentally observed vibrational lines in proteins are unexpectedly narrow.

Conclusions:

  • The narrowness of vibrational lines is attributed to insufficient sampling of protein configurations within the vibrational probe's lifetime.
  • Slow electric field fluctuations (tens of nanoseconds) are dynamically frozen on the vibrational timescale.
  • This nonergodic sampling explains the narrow lines despite strong internal fields.