Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems
Journal article, 2018

Entropy calculations represent one of the most challenging steps in obtaining the binding free energy in biomolecular systems. A novel computationally effective approach (IE) was recently proposed to calculate the entropy based on the computation of protein ligand interaction energy directly from molecular dynamics (MD) simulations. We present a study focused on the application of this method to flexible molecular systems and compare its performance with well-established normal mode (NM) and quasiharmonic (QH) entropy calculation approaches. Our results demonstrated that the IE method is intended for calculating entropy change for binding partners in fixed conformations, as by the original definition of IE, and is not applicable to the molecular complexes in which the interacting partners undergo significant conformational changes during the binding process.

Author

Gergely Kohut

Hungarian Academy of Sciences

Adam Liwo

Gdansk University of Technology

Szilvia Bosze

Eötvös Loránd University (ELTE)

Tamas Beke-Somfai

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry, Physical Chemistry

Sergey A. Samsonov

Gdansk University of Technology

Journal of Physical Chemistry B

1520-6106 (ISSN) 1520-5207 (eISSN)

Vol. 122 32 7821-7827

Subject Categories

Physical Chemistry

Biophysics

Theoretical Chemistry

DOI

10.1021/acs.jpcb.8b03658

PubMed

30049211

More information

Latest update

10/8/2018