Cooperativity, absolute interaction, and algebraic optimization

DOI10.1007/S00285-020-01540-8zbMATH Open1451.92129arXiv1906.10006OpenAlexW3088967323WikidataQ99618164 ScholiaQ99618164MaRDI QIDQ2204875FDOQ2204875

Authors: Yanyan Li 

Publication date: 16 October 2020

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: We consider a measure of cooperativity based on the minimal absolute interaction required to generate an observed titration behavior. We describe the corresponding algebraic optimization problem and show how it can be solved using the nonlinear algebra tool exttt{SCIP}. Moreover, we compute the minimal absolute interactions for various binding polynomials that describe the oxygen binding of various hemoglobins under different conditions. While calculated minimal absolute interactions are consistent with the expected outcome of the chemical modifications, it ranks the cooperativity of the molecules differently than the maximal Hill slope.

Full work available at URL: https://arxiv.org/abs/1906.10006

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Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Polynomial optimization (90C23)

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Cited In (3)

• Analysing protein energy data by a stochastic model for cooperative interactions: comparison and characterization of cooperativity
• Cooperation and competition in multidisciplinary optimization
• Variational approach for a class of cooperative systems

Uses Software

• SCIP

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