Thermodynamic calculations in biological systems

L. Mario Amzel, Xavier Siebert, Anthony Armstrong, German Pabon

Research output: Contribution to journalReview articlepeer-review


The ability to compute intra- and inter-molecular interactions provides the opportunity to gain a deeper understanding of previously intractable problems in biochemistry and biophysics. This review presents three examples in which molecular dynamics calculations were used to gain insight into the atomic detail underlying important experimental observations. The three examples are the following: (1) Entropic contribution to rate acceleration that results from conformational constraints imposed on the reactants; (2) Mechanism of force unfolding of a small protein molecule by the application of a force that separates its N- and C-terminals; and (3) Loss of translational entropy experienced by small molecules when they bind to proteins.

Original languageEnglish (US)
Pages (from-to)239-254
Number of pages16
JournalBiophysical Chemistry
Issue number3
StatePublished - Oct 3 2005


  • Extension by force
  • Molecular dynamics
  • Rate acceleration
  • Translational entropy

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry


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