Cooperativity, absolute interaction, and algebraic optimization

DOI10.1007/S00285-020-01540-8MaRDI QIDQ2204875zbMATH OpenOpenAlexWikidataFDO

Authors Yanyan Li

Publication date 16 October 2020

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

Copyright license Creative Commons Attribution 4.0 International

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

Mathematics Subject Classification ID

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

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.

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Cited in

(4)

• Analysing protein energy data by a stochastic model for cooperative interactions: comparison and characterization of cooperativity
• A measure to quantify the degree of cooperativity in overall titration curves
• Cooperation and competition in multidisciplinary optimization
• Variational approach for a class of cooperative systems

Describes a project that uses

Uses Software

• SCIP

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