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Tenenbaum A. Energy condensation and dipole alignment in protein dynamics. Phys Rev E 2024; 109:044401. [PMID: 38755822 DOI: 10.1103/physreve.109.044401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The possibility that distant biomolecules in a cell interact via electromagnetic (e.m.) radiation was proposed many years ago to explain the high rate of encounters of partners in some enzymatic reactions. The results of two recent experiments designed to test the propensity of protein bovine serum albumin (BSA) to interact via e.m. radiation with other proteins were interpreted in a theoretical framework based on three main assumptions: (i) in order to experience this kind of interaction the protein must be in an out-of-equilibrium state; (ii) in this state there is a condensation of energy in low-frequency vibrational modes; and (iii) the hydration layers of water around the protein sustain the energy condensation. In the present paper we present the results of molecular dynamics simulations of BSA in four states: at equilibrium and out-of-equilibrium in water, and at room and high temperature in vacuum. By comparing physical properties of the system in the four states, our simulations provide a qualitative and quantitative assessment of the three assumptions on which the theoretical framework is based. Our results confirm the assumptions of the theoretical model showing energy condensation at low frequency and electretlike alignment between the protein's and the water's dipoles; they also allow a quantitative estimate of the contribution of the out-of-equilibrium state and of the water to the observed behavior of the protein. In particular, it has been found that in the out-of-equilibrium state the amplitude of the oscillation of the protein's dipole moment greatly increases, thereby enhancing a possible absorption or emission of e.m. radiation. The analysis of BSA's dynamics outlined in the present paper provides a procedure for checking the propensity of a biomolecule to interact via e.m. radiation with its biochemical partners.
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Affiliation(s)
- Alexander Tenenbaum
- Physics Department, Sapienza University, Piazzale Aldo Moro 5, 00185 Roma, Italy
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Azizi K, Gori M, Morzan U, Hassanali A, Kurian P. Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution. PNAS NEXUS 2023; 2:pgad257. [PMID: 37575674 PMCID: PMC10416812 DOI: 10.1093/pnasnexus/pgad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023]
Abstract
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Matteo Gori
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Uriel Morzan
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Philip Kurian
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
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Lechelon M, Meriguet Y, Gori M, Ruffenach S, Nardecchia I, Floriani E, Coquillat D, Teppe F, Mailfert S, Marguet D, Ferrier P, Varani L, Sturgis J, Torres J, Pettini M. Experimental evidence for long-distance electrodynamic intermolecular forces. SCIENCE ADVANCES 2022; 8:eabl5855. [PMID: 35171677 PMCID: PMC8849397 DOI: 10.1126/sciadv.abl5855] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/22/2021] [Indexed: 05/31/2023]
Abstract
Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent experiments, on the basis of different physical effects detected by fluorescence correlation spectroscopy and terahertz spectroscopy, respectively, we demonstrate experimentally the activation of resonant electrodynamic intermolecular forces. This is an unprecedented experimental proof of principle of a physical phenomenon that, having been observed for biomacromolecules and with long-range action (up to 1000 Å), could be of importance for biology. In addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space.
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Affiliation(s)
- Mathias Lechelon
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Yoann Meriguet
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Matteo Gori
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Quantum Biology Lab, Howard University, 2400 6th St NW, Washington, DC 20059, USA
| | - Sandra Ruffenach
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Ilaria Nardecchia
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Elena Floriani
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
| | - Dominique Coquillat
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Teppe
- Laboratoire Charles Coulomb, University of Montpellier, CNRS, Montpellier, France
| | - Sébastien Mailfert
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Didier Marguet
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Pierre Ferrier
- Centre d’Immunologie de Marseille-Luminy, Aix-Marseille Univ., CNRS, Inserm, Marseille, France
| | - Luca Varani
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
| | - James Sturgis
- Laboratoire d’Ingenierie des Systèmes Macromoleculaires, Aix-Marseille Univ., CNRS, Marseille, France
| | - Jeremie Torres
- Institut d’Electronique et des Systèmes, University of Montpellier, CNRS, Montpellier, France
| | - Marco Pettini
- Aix-Marseille Univ., Université de Toulon, CNRS, Marseille, France
- Centre de Physique Théorique, CNRS, Marseille, France
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Optical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model. Nat Commun 2022; 13:813. [PMID: 35145091 PMCID: PMC8831584 DOI: 10.1038/s41467-022-28461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/25/2022] [Indexed: 12/01/2022] Open
Abstract
Molecular forces induced by optical excitations are connected to a wide range of phenomena, from chemical bond dissociation to intricate biological processes that underpin vision. Commonly, the description of optical excitations requires the solution of computationally demanding electronic Bethe-Salpeter equation (BSE). However, when studying non-covalent interactions in large-scale systems, more efficient methods are desirable. Here we introduce an effective approach based on coupled quantum Drude oscillators (cQDO) as represented by the many-body dispersion model. We find that the cQDO Hamiltonian yields semi-quantitative agreement with BSE calculations and that both attractive and repulsive optical van der Waals (vdW) forces can be induced by light. These optical-vdW interactions dominate over vdW dispersion in the long-distance regime, showing a complexity that grows with system size. Evidence of highly non-local forces in the human formaldehyde dehydrogenase 1MC5 protein suggests the ability to selectively activate collective molecular vibrations by photoabsorption, in agreement with recent experiments. The authors devise an efficient quantum approach to address the van der Waals interactions due to photoexcitations by approximating the Bethe-Salpeter equation. Both attractive/repulsive forces can arise, that could couple to collective protein dynamics.
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Transition between Random and Periodic Electron Currents on a DNA Chain. Int J Mol Sci 2021; 22:ijms22147361. [PMID: 34298980 PMCID: PMC8303785 DOI: 10.3390/ijms22147361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.
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