Methods for Calculating the Entropy and Free Energy and their Application to Problems Involving Protein Flexibility and Ligand Binding

Author(s): Hagai Meirovitch, Srinath Cheluvaraja, Ronald P. White.

Journal Name: Current Protein & Peptide Science

Volume 10 , Issue 3 , 2009

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Abstract:

The Helmholtz free energy, F and the entropy, S are related thermodynamic quantities with a special importance in structural biology. We describe the difficulties in calculating these quantities and review recent methodological developments. Because protein flexibility is essential for function and ligand binding, we discuss the related problems involved in the definition, simulation, and free energy calculation of microstates (such as the α-helical region of a peptide). While the review is broad, a special emphasize is given to methods for calculating the absolute F (S), where our HSMC(D) method is described in some detail.

Keywords: Helmholtz free energy, F, entropy, S, thermodynamic quantities, protein flexibility, ligand binding

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Article Details

VOLUME: 10
ISSUE: 3
Year: 2009
Page: [229 - 243]
Pages: 15
DOI: 10.2174/138920309788452209
Price: $58

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