Distribution function implied dynamics versus residence times and correlations

Solvation shells of myoglobin

V. Lounnas, Bernard Pettitt

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

The dynamics of water at the protein-solvent interface is investigated through the analysis of a molecular dynamics simulation of metmyoglobin in explicit aqueous environment. Distribution implied dynamics, harmonic and quasiharmonic, are compared with the simulated macroscopic dynamics. The distinction between distinguishable solvent molecules and hydration sites developed in the previous paper is used. The simulated hydration region within 7 Å from the protein surface is analyzed using a set of 551 hydration sites characterized by occupancy weights and temperature B-factors determined from the simulation trajectory. The precision of the isotropic harmonic and anisotropic harmonic models for the description of proximal solvent fluctuations is examined. Residence times and dipole reorientation times of water around the protein surface are compared with NMR and ESR results. A correlation between diffraction experiment quantities such as the occupancy weights and temperature factors and the residence and correlation times resulting from magnetic resonance experiments is found via comparison with simulation.

Original languageEnglish (US)
Pages (from-to)148-160
Number of pages13
JournalProteins: Structure, Function and Genetics
Volume18
Issue number2
StatePublished - 1994
Externally publishedYes

Fingerprint

Myoglobin
Solvation
Hydration
Distribution functions
Membrane Proteins
Metmyoglobin
Weights and Measures
Temperature
Water
Magnetic resonance
Molecular Dynamics Simulation
Paramagnetic resonance
Molecular dynamics
Magnetic Resonance Spectroscopy
Diffraction
Experiments
Trajectories
Nuclear magnetic resonance
Molecules
Computer simulation

Keywords

  • dynamics
  • myoglobin
  • solvation

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Structural Biology

Cite this

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AB - The dynamics of water at the protein-solvent interface is investigated through the analysis of a molecular dynamics simulation of metmyoglobin in explicit aqueous environment. Distribution implied dynamics, harmonic and quasiharmonic, are compared with the simulated macroscopic dynamics. The distinction between distinguishable solvent molecules and hydration sites developed in the previous paper is used. The simulated hydration region within 7 Å from the protein surface is analyzed using a set of 551 hydration sites characterized by occupancy weights and temperature B-factors determined from the simulation trajectory. The precision of the isotropic harmonic and anisotropic harmonic models for the description of proximal solvent fluctuations is examined. Residence times and dipole reorientation times of water around the protein surface are compared with NMR and ESR results. A correlation between diffraction experiment quantities such as the occupancy weights and temperature factors and the residence and correlation times resulting from magnetic resonance experiments is found via comparison with simulation.

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