Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

Kavitha, L.; Priya, R.; Ayyappan, N.; Gopi, D.; Jayanthi, S.

doi:10.1007/s10867-015-9389-9

Cited by 5 publications

(5 citation statements)

References 46 publications

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“…Strong coupling condition (E b ) h À v 0 ) provides soliton stability. Under the above circumstances, system dynamics may be described within simple time-dependent extension of the Pekar's variation theory [99][100][101][102][103][104][105][106][107][108][109][110][111]. Because of that, the trial state was chosen in the form…”

Section: The Modelmentioning

confidence: 99%

“…The soliton model can also be applied to the study of dynamics of electrons in macromolecular chains, in the presence of an external electric field [102]. Similarly, in their study of proton dynamics in the molecular chains, Kavitha et al assumed the soliton mechanism of motion of the formed quasi-particle [103]. However, in the case of excitations of a different nature (such as vibronic excitations), it may be necessary to apply an approach in which the semi-classical approximation is not applicable because the vibron and the accompanying deformation form nonadiabatic polaron [90,92,104,105].…”

Section: Long-distance Electron Transport Along Dna Macromolecular Chainsmentioning

confidence: 99%

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A review on nonlinear DNA physics

et al. 2020

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The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

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Section: The Modelmentioning

confidence: 99%

Section: Long-distance Electron Transport Along Dna Macromolecular Chainsmentioning

confidence: 99%

A review on nonlinear DNA physics

et al. 2020

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“…Theoretical consideration of the proton transport as a collective phenomenon emerging in molecular systems has been first carried out in the framework of Davydov soliton theory [ 26 ]. Davydov soliton [ 27 ] or other similar self-localized states [ 28 , 29 ] and collective excitations [ 30 , 31 ] have long been and still are considered as promising candidates for the role of charge and energy carriers within proteins [ 32 ], along the lipid membrane surface [ 33 , 34 ], and on interfaces of biopolymers and artificial membranes [ 35 ]. The concept of solitary waves was developed to described the mechanism underlying highly effective transport of charge and energy in molecular systems in the form of collective excitations which are described by autolocalized solutions (solitons) of nonlinear wave equations [ 36 ].…”

Section: Introductionmentioning

confidence: 99%

Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System

Nesterov

Yaguzhinsky²,

Василов³

et al. 2022

Entropy

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The results of many experimental and theoretical works indicate that after transport of protons across the mitochondrial inner membrane (MIM) in the oxidative phosphorylation (OXPHOS) system, they are retained on the membrane–water interface in nonequilibrium state with free energy excess due to low proton surface-to-bulk release. This well-established phenomenon suggests that proton trapping on the membrane interface ensures vectorial lateral transport of protons from proton pumps to ATP synthases (proton acceptors). Despite the key role of the proton transport in bioenergetics, the molecular mechanism of proton transfer in the OXPHOS system is not yet completely established. Here, we developed a dynamics model of long-range transport of energized protons along the MIM accompanied by collective excitation of localized waves propagating on the membrane surface. Our model is based on the new data on the macromolecular organization of the OXPHOS system showing the well-ordered structure of respirasomes and ATP synthases on the cristae membrane folds. We developed a two-component dynamics model of the proton transport considering two coupled subsystems: the ordered hydrogen bond (HB) chain of water molecules and lipid headgroups of MIM. We analytically obtained a two-component soliton solution in this model, which describes the motion of the proton kink, corresponding to successive proton hops in the HB chain, and coherent motion of a compression soliton in the chain of lipid headgroups. The local deformation in a soliton range facilitates proton jumps due to water molecules approaching each other in the HB chain. We suggested that the proton-conducting structures formed along the cristae membrane surface promote direct lateral proton transfer in the OXPHOS system. Collective excitations at the water–membrane interface in a form of two-component soliton ensure the coupled non-dissipative transport of charge carriers and elastic energy of MIM deformation to ATP synthases that may be utilized in ATP synthesis providing maximal efficiency in mitochondrial bioenergetics.

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“…Theoretical consideration of the proton transport as a collective phenomenon emerging in molecular systems has been first carried out in the framework of Davydov soliton theory (Antonchenko et al 1983). Davydov soliton (Davydov 1982) or other similar self-localized states (Austin et al 2003; Pang 2012) and collective excitations (Bolterauer et al 1991; Kadantsev and Goltsov 2020) have long been and still are considered as promising candidates for the role of charge and energy carriers within proteins (Kavitha et al 2016), along the lipid membrane surface (Manousakis 2005; Kadantsev and Goltsov 2022), and on interfaces of biopolymers and artificial membranes (Matsui and Matsuo 2020). The concept of solitary waves was developed to described the mechanism underlying highly effective transport of charge and energy in molecular systems in the form of collective excitations which are described by autolocalized solutions (solitons) of nonlinear wave equations (Davydov 1985).…”

Section: Introductionmentioning

confidence: 99%

Contribution of the collective excitations to the coupled proton and energy transport along mitochondrial crista membrane in oxidative phosphorylation system

Nesterov

Yaguzhinskiy

Василов

et al. 2022

Preprint

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The results of many experimental and theoretical works indicate that after transport of protons across the mitochondrial inner membrane (MIM) in oxidative phosphorylation system (OXPHOS), they are retained on the membrane-water interface in non-equilibrium state with free energy excess due to low proton surface-to-bulk release. This well-established phenomenon suggests that proton trapping on the membrane interface ensures vectorial lateral transport of protons from proton pumps to ATP synthases (proton acceptors). Despite the key role of the proton transport in bioenergetics, the molecular mechanism of proton transfer in OXPHOS is not yet completely established. Here, we developed a dynamic model of long-range transport of energized protons along the MIM accompanied by collective excitation of localized wave prorogating on the membrane surface. Our model is based on the new data on the macromolecular organization of OXPHOS showing the well-ordered structure of respirasomes and ATP synthases on the cristae membrane folds. We developed a two-component dynamic model of the proton transport considering two coupled subsystems: the ordered hydrogen bond chain of water molecules and lipid headgroups of MIM. We analytically obtained two-component soliton solution in this model, which describe the motion of the proton kink, corresponding to successive proton hops in the HB chain, and coherent motion of a compression soliton in the chain of lipid headpolar groups. The local deformation in a soliton range facilitates proton jumps due to water molecules approaching each other in the HB chain. We suggested that the proton-conducting structures formed along the cristae membrane surface promotes direct lateral proton transfer in OXPHOS. Collective excitations at the water-membrane interface in a form of two-component soliton ensure the coupled non-dissipative transport of charge carriers and elastic energy of MIM deformation to ATP synthases that may be utilized in ATP synthesis providing maximal efficiency in mitochondrial bioenergetics.

show abstract

Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

Cited by 5 publications

References 46 publications

A review on nonlinear DNA physics

A review on nonlinear DNA physics

Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System

Contribution of the collective excitations to the coupled proton and energy transport along mitochondrial crista membrane in oxidative phosphorylation system

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