Dynamic Model for Enzyme Action

Zhao, Qinyi

doi:10.2174/092986611794328618

Cited by 8 publications

(14 citation statements)

References 51 publications

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“…In view of protein thermodynamic structure theory, enzyme activity corresponds to one thermal system (con formation in terms of biochemistry) within a protein, and this relation could be guaranteed theoretically [13,15]. One method to judge correctness of this opinion comes from enzyme kinetics.…”

Section: Enzyme Regulation Via Influence On Abundance Of Active Confomentioning

confidence: 99%

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A thermodynamic and theoretical view for enzyme regulation

Zhao¹

2015

Biochemistry Moscow

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Precise regulation is fundamental to the proper functioning of enzymes in a cell. Current opinions about this, such as allosteric regulation and dynamic contribution to enzyme regulation, are experimental models and substantially empirical. Here we proposed a theoretical and thermodynamic model of enzyme regulation. The main idea is that enzyme regulation is processed via the regulation of abundance of active conformation in the reaction buffer. The theoretical foundation, experimental evidence, and experimental criteria to test our model are discussed and reviewed. We conclude that basic principles of enzyme regulation are laws of protein thermodynamics and it can be analyzed using the concept of distribution curve of active conformations of enzymes.

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Section: Enzyme Regulation Via Influence On Abundance Of Active Confomentioning

confidence: 99%

“…This enables us to formulate a dynamic model for enzyme action and an allodynamic regulation model for protein regulation [15,16]. This is a purely theoretical and ther modynamic model for protein regulation, and many the oretical questions have been resolved.…”

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confidence: 99%

A thermodynamic and theoretical view for enzyme regulation

Zhao¹

2015

Biochemistry Moscow

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“…Allodynamic and allosteric regulation of the receptor and enzyme may also feature in this mechanism. 6 …”

Section: Agonist Efficiency and Conformational Distribution Of A Recementioning

confidence: 99%

“…[1][2][3] The protein dynamics, as well as protein conformation, is relevant to the biological functions of a protein. [4][5][6] Therefore, a method to quantitatively analyze the conformational change of a protein is of great importance in protein science and is applicable to various fields, such biochemistry and molecular biology on.…”

Section: Introductionmentioning

confidence: 99%

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Partition Function of the Protein Conformational State

Zhao¹

2012

Jnl of Comp & Theo Nano

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The partition function is a fundamental concept of equilibrium thermodynamics. It encodes the particle distribution at different energy levels within a thermal system. By modifying the partition function of a particle, the partition function of a protein conformational state has been obtained. According to the protein thermodynamic structure theory, a protein conformational state represents one thermal system within a protein. The partition function of it encodes the thermodynamic relation among the different conformational states of a protein. Many experimental observations and models in enzymology, biochemistry, and molecular biology have been summarized and reexamined by applying this concept. This paper discusses the following: (1) the partition function of a protein conformational state; (2) the conformation distribution between the two states; (3) the protein conformation distribution along the temperature gradient and the protein conformation stability curve; (4) the agonist efficiency and conformational distribution of a receptor along voltage; (5) the enzyme active conformation distribution along the temperature gradient; (6) the enzyme active conformation distribution with respect to protein flexibility; (7) a revision of the Arrhenius equation for enzymatic reactions; and (8) the biophysical nature of conformational equilibrium and deformation.

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Revised equation of enzymatic kinetics and thermodynamic mechanisms for directed evolution of enzymes

Zhao

2022

Int J of Chemical Kinetics

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The equation of enzymatic kinetics is revised, and thermodynamic mechanisms of directed evolution of enzymes are proposed based on both that and the thermodynamic model of enzyme action. In theory, there are two mechanisms of enzymes to improve its catalysis efficiency in directed evolution. The first refers to the change of activation energy of enzymatic reactions. The modulation of structural compatibility between enzyme and substrate serves as the second mechanism and the major motivation for enzymes to enhance their catalysis in situations of directed evolution.

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Dynamic Model for Enzyme Action

Abstract: Our analysis shows that a comprehensive understanding of enzymology can be established on the basis of protein thermodynamic structure theory.

Cited by 8 publications

References 51 publications

A thermodynamic and theoretical view for enzyme regulation

A thermodynamic and theoretical view for enzyme regulation

Partition Function of the Protein Conformational State

Revised equation of enzymatic kinetics and thermodynamic mechanisms for directed evolution of enzymes

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