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Related Experiment Video

Updated: Jun 6, 2026

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
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Energy landscapes associated with macromolecular conformational changes from endpoint structures.

Arianna Fornili1, Barbara Giabbai, Gianpiero Garau

  • 1Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy. arianna.fornili@kcl.ac.uk

Journal of the American Chemical Society
|November 19, 2010
PubMed
Summary

We developed a new computational method to quantify the energy of protein shape changes. This approach accurately predicts enzyme binding and reveals how a single residue

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Area of Science:

  • Biochemistry and structural biology
  • Computational biophysics

Background:

  • Macromolecular function is modulated by conformational changes, impacting ligand binding and enzymatic activity.
  • Quantitative characterization of the energetics of these dynamic structural interconversions remains a challenge due to a lack of unified methods.

Purpose of the Study:

  • To introduce a novel in silico approach for quantitative characterization of conformational energy landscapes.
  • To enable unbiased investigation of complex molecular rearrangements without user-defined collective variables.

Main Methods:

  • Combined essential dynamics sampling and nonequilibrium free-energy calculations.
  • Applied the method to analyze conformational changes in a bacterial nucleoside hydrolase.

Main Results:

  • Quantitative free-energy profiles accurately predicted the experimental binding constant for the enzyme.
  • Demonstrated the rate-limiting nature of the conformational transition.
  • Identified an unexpected regulatory role of a single residue's protonation state in substrate binding and product release.

Conclusions:

  • The novel computational approach provides a unified method for studying macromolecular conformational energetics.
  • This technique offers insights into enzyme mechanisms, including substrate binding and product release regulation.