Energy fluctuations shape free energy of nonspecific biomolecular interactions

DOI10.1007/S10955-012-0421-1MaRDI QIDQ411519zbMATH OpenOpenAlexFDO

Authors Michael Elkin, Ingemar Andre, David B. Lukatsky

Publication date 4 April 2012

Published in Journal of Statistical Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1101.4529

zbMATH Keywords

fluctuationsfree energy of biomolecular interactions

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Statistical mechanics of polymers (82D60)

Abstract: Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of protein-protein, protein-DNA, and protein-RNA binding. Here, using a variant of the Derrida model, we predict that for a large class of biomolecular interactions, it is possible to accurately estimate the relative free energy of binding based on the fluctuation properties of their energy spectra, even if a finite number of the energy levels is known. We show that the free energy of the system possessing a wider binding energy spectrum is almost surely lower compared with the system possessing a narrower energy spectrum. Our predictions imply that low-affinity binding scores, usually wasted in protein-protein and protein-DNA docking algorithms, can be efficiently utilized to compute the free energy. Using the results of Rosetta docking simulations of protein-protein interactions from Andre et al., Proc. Natl. Acad. Sci. U.S.A. 105, 16148 (2008), we demonstrate the power of our predictions.

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Cites work

• scientific article; zbMATH DE number 3133146 (Why is no real title available?)
• Emergence of symmetry in homooligomeric biological assemblies
• The probabilistic method. With an appendix on the life and work of Paul Erdős.

Cited in

(4)

• Free Energy Calculations in Biological Systems. How Useful Are They in Practice?
• Energy landscapes of protein self-assembly: lessons from native topology-based models
• Towards an understanding of the temperature/pressure configurational and free-energy landscape of biomolecules
• Entropy and Free Energy in Structural Biology

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