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All chemical processes exhibit two main universal features. They are stochastic because chemical reactions might happen only after random successful collisions of reacting species, and they are dynamic because the amount of reactants and products change with time. Since biological processes rely heavily on specific chemical reactions, stochasticity and dynamics are also crucial features for all living systems. To understand the molecular mechanisms of chemical and biological processes, it is important to develop and apply theoretical methods that fully incorporate the randomness and dynamic nature of these systems. In recent years, there have been significant advances in formulating and exploring such theoretical methods. As an illustration of such developments, in this review, the recent applications of stochastic kinetic models for various biological processes are discussed. Specifically, we focus on applying these theoretical approaches to investigate the biological signaling, clearance of bacteria under antibiotics, T cells activation in the immune system, and cancer initiation dynamics. The main advantage of the presented stochastic kinetic models is that they generally can be solved analytically, allowing to clarify the underlying microscopic picture, as well as explain the existing experimental observations and make new testable predictions. This theoretical approach becomes a powerful tool in uncovering the molecular mechanisms of complex natural phenomena.
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Kinetic Proofreading
Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution—an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment—is shown to be widely employed by biological processes that transmit genetic and regulatory information.
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- Award ID(s):
- 2111763
- PAR ID:
- 10414676
- Date Published:
- Journal Name:
- Annual Review of Biochemistry
- Volume:
- 91
- Issue:
- 1
- ISSN:
- 0066-4154
- Page Range / eLocation ID:
- 423 to 447
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1146/annurev-biochem-040320-103630
