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Related Experiment Videos

Interatomic potentials and solvation parameters from protein engineering data for buried residues.

Andrei L Lomize1, Mikhail Y Reibarkh, Irina D Pogozheva

  • 1College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA. almz@umich.edu

Protein Science : a Publication of the Protein Society
|July 27, 2002
PubMed
Summary

This study quantifies Van der Waals (vdW) interaction energies, hydrogen bond (H-bond) energies, and atomic solvation parameters (ASPs) for protein mutants. These derived parameters follow the "like dissolves like" rule in condensed media.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Engineering

Background:

  • Understanding interatomic forces and solvation is crucial for predicting protein stability and function.
  • Accurate thermodynamic data from protein mutants provides a basis for deriving fundamental energetic parameters.

Purpose of the Study:

  • To derive Van der Waals (vdW) interaction energies, hydrogen bond (H-bond) energies, and atomic solvation parameters (ASPs).
  • To develop a model for calculating free-energy differences in protein mutants.
  • To analyze these parameters in the context of condensed media and protein interiors.

Main Methods:

  • Utilized thermodynamic stabilities of 106 protein mutants with available crystal structures.
  • Employed an originally designed model for calculating free-energy differences.

Related Experiment Videos

  • Analyzed substitutions in alpha-helices and beta-sheets of T4, human, and hen lysozymes and HI ribonuclease.

    • Main Results:

    • Determined vdW and H-bond energies smaller than in molecular mechanics, adhering to the "like dissolves like" rule in condensed media.
    • Quantified Lennard-Jones potential depths for various atom type interactions and H-bond potentials (-1.5 to -1.8 kcal/mole).
    • Derived atomic solvation parameters (ASPs) for protein interiors, showing distinct values for different atom types (e.g., O: -66 cal/moleA(2), N: -21 cal/moleA(2)).

    Conclusions:

    • The derived parameters provide insights into interatomic interactions and solvation within protein structures.
    • vdW interactions between protein atoms are reduced across water interfaces.
    • The findings contribute to more accurate computational modeling of protein thermodynamics.