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Emergent Collective Dynamics in Bioenergetic Molecular Systems

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Entropy and Biology".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 8789

Special Issue Editors


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Guest Editor
Biocybernetics Systems and Technologies Division, Russian Technological University (MIREA), 119454 Moscow, Russia
Interests: collective dynamics in biosystems; bioenergetics; computational systems biology; biophotonics

E-Mail Website
Guest Editor
Biocybernetics Systems and Technologies Division, Russian Technological University (MIREA), 119454 Moscow, Russia
Interests: collective dynamics in biosystems; bioenergetics; computational systems biology; biophotonics

Special Issue Information

Dear Colleagues,

One of the key concepts in life science is the structure–function relationship in biomolecules participating in enzymatic reactions and signal/energy/charge transfer. The development of this concept revealed that protein function critically depends on flexible and changeable molecular structures rather than rigid and fixed ones. This finding essentially enriched this concept through consideration of collective vibration dynamics of protein structures, which has been shown to play a crucial role in the molecular mechanisms of an impressive efficacy of biosystem function, especially of bioenergetic systems. Sidechains in proteins retaining considerable entropy have been reported to participate in collective vibration and wave-like excitations in biomolecules. A present intensive investigation in this area is associated with the extended concept of the dynamical structure–protein function relationship as a fundamental paradigm in molecular biosystem theories.

This topic focuses on an exploration of the one of the most central challenges in bioenergetics—an understanding of molecular mechanisms underlying highly efficient energy generation, transfer and transformation in cellular processes such as photosynthesis, mitochondrial bioenergetics, and enzymatic energy metabolism. The rapid advances in this area are fostered by the application of experimental and theoretical approaches developed in solid, soft matter, nonlinear and active-matter physics which are being explored to understand the extremely effective function of living matter. The topic covers different aspects of emergent dynamics in molecular structures driven by energy pumping, such as soliton dynamics describing highly effective long-distance transport of energy/charge within macromolecules, Frohlich’s coherent vibrational dynamics in biosystems, resonance energy transfer in enzyme active centers, wave-like energy transfer in proteins and membranes, quantum coherence in biomolecules, long-lived collective vibrational protein excitations, and others. The topic is not limited to these phenomena and seeks to encompass a wide spectrum of emergent collective dynamics in biosystems, which makes them extremely effective functioning active matter.

Prof. Dr. Alexey Goltsov
Prof. Dr. Vasiliy N. Kadantsev
Guest Editors

Manuscript Submission Information

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Keywords

  • collective dynamics in proteins
  • quantum coherent states in bioenergitic systems
  • soliton in molecular chains
  • Frohlich’s coherent vibrational dynamics
  • long-lived collective vibrational protein excitations
  • nonlinear physics
  • active matter physics

Published Papers (4 papers)

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Research

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17 pages, 2905 KiB  
Article
Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System
by Semen V. Nesterov, Lev S. Yaguzhinsky, Raif G. Vasilov, Vasiliy N. Kadantsev and Alexey N. Goltsov
Entropy 2022, 24(12), 1813; https://doi.org/10.3390/e24121813 - 13 Dec 2022
Cited by 3 | Viewed by 1369
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Emergent Collective Dynamics in Bioenergetic Molecular Systems)
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15 pages, 2344 KiB  
Article
Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines
by Danfeng Shi, Ke An, Honghui Zhang, Peiyi Xu and Chen Bai
Entropy 2022, 24(5), 620; https://doi.org/10.3390/e24050620 - 29 Apr 2022
Cited by 3 | Viewed by 1925
Abstract
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the [...] Read more.
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines. Full article
(This article belongs to the Special Issue Emergent Collective Dynamics in Bioenergetic Molecular Systems)
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9 pages, 279 KiB  
Article
From Micro to Macro: A Relativistic Treatment of the Chiral Energy Shifts Caused by Static Electromagnetic Effects on Free Electrons
by Philip Kurian
Entropy 2022, 24(3), 358; https://doi.org/10.3390/e24030358 - 01 Mar 2022
Viewed by 1926
Abstract
Free electron systems are ubiquitous in nature and have demonstrated intriguing effects in their collective interactions with weak electric and magnetic fields, especially in aqueous environments. Starting from the Dirac Hamiltonian, a fully relativistic expression is derived for the electron energy shift in [...] Read more.
Free electron systems are ubiquitous in nature and have demonstrated intriguing effects in their collective interactions with weak electric and magnetic fields, especially in aqueous environments. Starting from the Dirac Hamiltonian, a fully relativistic expression is derived for the electron energy shift in the presence of a spatiotemporally constant, weak electromagnetic field. The expectation value of this energy shift is then computed explicitly using the Fourier transforms of the fermionic fields. To first order in the electromagnetic fields, the average relativistic energy shift is found to be completely independent of the electron spin-polarization coefficients. This effect is also considerably larger than that predicted in quantum mechanics by the analogous Zeeman shift. Finally, in the non-relativistic limit, it is shown how to discriminate between achiral and completely polarized states, which leads to a concluding discussion of possible mesoscopic and macroscopic manifestations of electron spin states across many orders of magnitude in the physical world, with stark implications for biological and other complex systems. Full article
(This article belongs to the Special Issue Emergent Collective Dynamics in Bioenergetic Molecular Systems)
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Review

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21 pages, 2346 KiB  
Review
T-cell Receptor Is a Threshold Detector: Sub- and Supra-Threshold Stochastic Resonance in TCR-MHC Clusters on the Cell Surface
by László Bene, Miklós Bagdány and László Damjanovich
Entropy 2022, 24(3), 389; https://doi.org/10.3390/e24030389 - 10 Mar 2022
Cited by 2 | Viewed by 2647
Abstract
Stochastic resonance in clusters of major histocompatibility molecules is extended by a more detailed description of adaptive thresholding and by applying the notion of suprathreshold stochastic resonance as a stochastically quantizing encoder of transmembrane signaling downstream of major histocompatibility molecules and T-cell receptors [...] Read more.
Stochastic resonance in clusters of major histocompatibility molecules is extended by a more detailed description of adaptive thresholding and by applying the notion of suprathreshold stochastic resonance as a stochastically quantizing encoder of transmembrane signaling downstream of major histocompatibility molecules and T-cell receptors on the side of presenting and recognizing cells, respectively. The adaptive nature of thresholding is partly explained by a mirroring of the noncognate–cognate dichotomy shown by the T-cell receptor structure and the kinetic-segregation model of the onset of T-cell receptor triggering. Membrane clusters of major histocompatibility molecules and T-cell receptors on their host cells are envisioned as places of the temporal encoding of downstream signals via the suprathreshold stochastic resonance process. The ways of optimization of molecular prostheses, such as chimeric antigen receptors against cancer in transmembrane signaling, are suggested in the framework of suprathreshold stochastic resonance. The analogy between Förster resonance energy transfer and suprathreshold stochastic resonance for information transfer is also discussed. The overlap integral for energy transfer parallels the mutual information transferred by suprathreshold stochastic resonance. Full article
(This article belongs to the Special Issue Emergent Collective Dynamics in Bioenergetic Molecular Systems)
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