Protein folding as a nonlinear nonequilibrium thermodynamic process

Popov, E. M.

doi:10.1080/15216549900201473

Cited by 9 publications

(11 citation statements)

References 26 publications

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“…This is consistent with the statement of the second law, which states that a finite amount of organization may be purchased at the expense of a greater amount of disorganization in a series of coupled processes . Some of the coupled processes in living systems include enzymatic reactions, thermal diffusivity in tissues, drug delivery, protein folding, biological oscillations, membrane transport, and the Turing instabilites with appropriate kinetics and large differences in diffusion rates of metabolites. ,− …”

Section: Introductionsupporting

confidence: 85%

“…Some biological pathways occur at near global equilibrium conditions. By the conservation of mass, some flow-force relations of the enzyme catalyzed and other chemical reactions can be described by a simple hyperbolic-tangent function. ,,− , Therefore, a plot of reaction velocity versus affinity has three regions; at regions with very high positive and negative affinity values with the reaction velocity is almost independent of affinity. In between these regions, the reaction velocity varies smoothly, leading to a quasi-linear region around the inflection point.…”

Section: Reaction-transport Processes With Thermodynamic Couplingmentioning

confidence: 99%

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Influence of Subenvironmental Conditions and Thermodynamic Coupling on a Simple Reaction-Transport Process in Biochemical Systems

Tevatia

Demi̇rel

Blum

2014

Ind. Eng. Chem. Res.

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Living systems must continuously receive substrates from subenvironment, and the population metabolic rate model is affected on this flow of substrates to be metabolized, its relevant variables, and the rate at which operates. This study focuses on the influences of resistances and bulk phase factors with in the subenvironment and by thermodynamic coupling on reaction-transport processes representing a simple enzymatic conversion of a substrate to a product. Thermodynamic coupling refers to mass flow, or a reaction velocity that occurs without or opposite to the direction imposed by its primary thermodynamic driving force. We considered the effects of (i) subenvironment resistances for the heat and mass flows of reacting substrate in the form of the ratios of Sherwood to Nusselt numbers, (ii) the subenvironment bulk phase temperatures and concentration of substrate, and (iii) the cross-coefficients responsible for the induced effects due to the thermodynamic coupling. In order to study these effects, the thermodynamically coupled balance equations using the first order simple elementary reaction are derived and solved numerically. In the balance equations, the linear phenomenological equations are used by assuming that the system is in the vicinity of global equilibrium. The overall results show that the subenvironment factors and cross-coefficients due to thermodynamic coupling may have considerable effects on reaction-transport processes.

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Section: Introductionsupporting

confidence: 85%

Section: Reaction-transport Processes With Thermodynamic Couplingmentioning

confidence: 99%

Influence of Subenvironmental Conditions and Thermodynamic Coupling on a Simple Reaction-Transport Process in Biochemical Systems

Tevatia

Demi̇rel

Blum

2014

Ind. Eng. Chem. Res.

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“…The way molecules are organized, e.g. the protein folding, and biological order [21][22][23][24], biological oscillation [25], membrane transport in biological systems [26] can be studied by the nonequilibrium thermodynamics analysis. Structured stationary states of living systems need a constant supply of energy to maintain their states.…”

Section: Introductionmentioning

confidence: 99%

Linear-nonequilibrium thermodynamics theory for coupled heat and mass transport

Demi̇rel

Sandler

2001

International Journal of Heat and Mass Transfer

100

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Linear-nonequilibrium thermodynamics (LNET) has been used to express the entropy generation and dissipation functions representing the true forces and flows for heat and mass transport in a multicomponent fluid. These forces and flows are introduced into the phenomenological equations to formulate the coupling phenomenon between heat and mass flows. The degree of the coupling is also discussed. In the literature such coupling has been formulated incompletely and sometimes in a confusing manner. The reason for this is the lack of a proper combination of LNET theory with the phenomenological theory. The LNET theory involves identifying the conjugated flows and forces that are related to each other with the phenomenological coefficients that obey the Onsager relations. In doing so, the theory utilizes the dissipation function or the entropy generation equation derived from the Gibbs relation. This derivation assumes that local thermodynamic equilibrium holds for processes not far away from the equilibrium. With this assumption we have used the phenomenological equations relating the conjugated flows and forces defined by the dissipation function of the irreversible transport and rate process. We have expressed the phenomenological equations with the resistance coefficients that are capable of reflecting the extent of the interactions between heat and mass flows. We call this the dissipation-phenomenological equation (DPE) approach, which leads to correct expression for coupled processes, and for the second law analysis.

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“…NE thermodynamic of living systems is closely associated with the concepts of biochirality, entropy, biological information processing, and aging [ 12 ]. NE thermodynamic theories, in particular, Classical Irreversible Thermodynamics (CIT) [ 13 ], complemented by the concept of fluctuating entropy [ 14 , 15 ], provide a valuable formalism for understanding the dynamics of living systems, including the origin of life, cell differentiation, as well as the synthesis of the homochiral population of proteins and the spontaneous loss of conformational entropy during folding [ 16 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Dyakin

Dyakina-Fagnano

McIntire

et al. 2021

IJMS

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In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.

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Protein folding as a nonlinear nonequilibrium thermodynamic process

Cited by 9 publications

References 26 publications

Influence of Subenvironmental Conditions and Thermodynamic Coupling on a Simple Reaction-Transport Process in Biochemical Systems

Influence of Subenvironmental Conditions and Thermodynamic Coupling on a Simple Reaction-Transport Process in Biochemical Systems

Linear-nonequilibrium thermodynamics theory for coupled heat and mass transport

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

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