Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions
Elkin, Michael ; André, Ingemar LU
and Lukatsky, David B.
(2012)
In Journal of Statistical Physics
146(4).
p.870-877
- 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... (More)
- 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. USA 105: 16148, 2008), we demonstrate the power of our predictions. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/2515245
- author
- Elkin, Michael
; André, Ingemar
LU
and Lukatsky, David B.
- organization
- publishing date
- 2012
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Free energy of biomolecular interactions, Fluctuations
- in
- Journal of Statistical Physics
- volume
- 146
- issue
- 4
- pages
- 870 - 877
- publisher
- Springer
- external identifiers
-
- wos:000301730400012
- scopus:84858333449
- ISSN
- 1572-9613
- DOI
- 10.1007/s10955-012-0421-1
- language
- English
- LU publication?
- yes
- id
- 10328500-9961-4adf-b28d-0a48868e011a (old id 2515245)
- date added to LUP
- 2016-04-01 14:29:23
- date last changed
- 2022-03-29 21:13:47
@article{10328500-9961-4adf-b28d-0a48868e011a,
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. USA 105: 16148, 2008), we demonstrate the power of our predictions.}},
author = {{Elkin, Michael and André, Ingemar and Lukatsky, David B.}},
issn = {{1572-9613}},
keywords = {{Free energy of biomolecular interactions; Fluctuations}},
language = {{eng}},
number = {{4}},
pages = {{870--877}},
publisher = {{Springer}},
series = {{Journal of Statistical Physics}},
title = {{Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions}},
url = {{http://dx.doi.org/10.1007/s10955-012-0421-1}},
doi = {{10.1007/s10955-012-0421-1}},
volume = {{146}},
year = {{2012}},
}