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Temperature Dependence of Peptide Conformational Equilibria from Simulations at a Single Temperature
Ankita Katiyar1, Ward H Thompson1
1Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States.
The Journal of Physical Chemistry. A
|March 15, 2021
Summary
This study introduces a new method to calculate protein internal energy and entropy from single-temperature simulations. This approach simplifies conformational free energy calculations and aids in understanding protein structure-function relationships.
Area of Science:
- Computational chemistry
- Biophysics
- Protein dynamics
Background:
- Protein structure is crucial for biological function.
- Calculating conformational free energies is essential for understanding protein behavior.
- Current methods often require multi-temperature simulations.
Purpose of the Study:
- To develop a method for calculating temperature derivatives of conformational free energy from single-temperature simulations.
- To enable the decomposition of internal energy into contributions from specific interactions.
- To apply this method to alanine dipeptide in aqueous solution.
Main Methods:
- Extension of fluctuation theory.
- Calculation of temperature derivative of conformational free energy.
- Decomposition of internal energy contributions.
- Implementation within metadynamics for accelerated sampling.
Main Results:
- Successfully calculated internal energy and entropy from single-temperature simulations.
- Demonstrated the decomposition of internal energy contributions.
- Validated the method on alanine dipeptide using metadynamics.
Conclusions:
- The developed method simplifies the calculation of thermodynamic properties related to protein conformation.
- This approach is compatible with advanced sampling techniques like metadynamics.
- Facilitates a deeper understanding of protein structure-function relationships.
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