From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

Mondal, Sayantan; Bagchi, Biman

doi:10.1016/j.sbi.2022.102462

Cited by 23 publications

(29 citation statements)

References 42 publications

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“…1,2 The structure and dynamics of these biological waters are substantially different from neat bulk water. 3,4 It has been widely recognized that water molecules present in biological systems act as active components in a multitude of processes such as bond breaking events, electron transfer reactions, and also in conformational changes. 2,4−6 Moreover, water has been shown to modulate internal fluctuations within biomolecules.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Although water is recognized as the matrix or elixir of life , the precise microscopic mechanism of its role remains poorly understood. Because of the small size and low molecular weight, water molecules are continuously in a state of rapid motion, even within biological cells. , The structure and dynamics of these biological waters are substantially different from neat bulk water. , It has been widely recognized that water molecules present in biological systems act as active components in a multitude of processes such as bond breaking events, electron transfer reactions, and also in conformational changes. ,− Moreover, water has been shown to modulate internal fluctuations within biomolecules. , Although the precise origin of this controlling effect of water remains largely unknown, the conformational and energy fluctuations in water are believed to be major drivers that help modulate the coupling with proteins …”

Section: Introductionmentioning

confidence: 99%

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Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

2023

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The coupling between the conformational fluctuations of DNA and its surrounding environment, consisting of water and ions in solution, remains poorly understood and relatively less investigated as compared to proteins. Here, with the help of molecular dynamics simulations and statistical mechanical analyses, we explore the dynamical coupling among DNA, water, and counterions through correlations among respective energy fluctuations in both double- (ds-) and single-stranded (ss-) DNA solutions. Fluctuations in the collective DNA-water and DNA-ion interaction energies are found to be strongly anticorrelated across all the systems. The fluctuations of DNA self-energy, however, are weakly coupled to DNA-water and DNA-ion interactions in ds-DNA. An enhancement of the DNA-water coupling is observed in ss-DNA, where the system is less rigid. All the interaction energies exhibit 1/f noise in their energy power spectra with surprisingly prominent bimodality in the DNA-water and DNA-ion fluctuations. The nature of the energy spectra appears to be indifferent to the relative rigidity of the DNA. We discuss the role of the observed correlations in ion-water motions on a DNA duplex in the experimentally observed anomalous slow dielectric relaxation and solvation dynamics and in furthering our understanding of the DNA energy landscape.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

2023

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“…1,2 The structure and dynamics of these biological waters are substantially different from neat bulk water. 3,4 It has been widely recognized that water molecules present in biological systems act as active components in a multitude of processes such as bond-breaking events, electron transfer reactions, and also in conformational changes. [2][3][4][5][6] Moreover, water has been shown to modulate internal fluctuations within biomolecules.…”

Section: Introductionmentioning

confidence: 99%

“…3,4 It has been widely recognized that water molecules present in biological systems act as active components in a multitude of processes such as bond-breaking events, electron transfer reactions, and also in conformational changes. [2][3][4][5][6] Moreover, water has been shown to modulate internal fluctuations within biomolecules. 7,8 Although the precise origin of this controlling effect of water remains largely unknown, the conformational and energy fluctuations in water are believed to be major drivers that help modulate the coupling with proteins.…”

Section: Introductionmentioning

confidence: 99%

Bimodal 1/fnoise and anticorrelation between DNA-Water and DNA-Ion energy fluctuations

Mukherjee

Mondal

Bagchi

2022

Preprint

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Coupling between the fluctuations of DNA and its surroundings consisting of water and ions in solution remains poorly understood and relatively less investigated as compared to proteins. Here, with the help of molecular dynamics simulations and statistical mechanical analyses, we explore the dynamical coupling between DNA, water, and counterions through correlations among respective energy fluctuations in both double (ds-) and single-stranded (ss-) DNA solutions. Fluctuations in the collective DNA-Water and DNA-Ion interaction energies are found to be strongly anti-correlated across all the systems. The fluctuations of DNA self-energy, however, are weakly coupled to DNA-water and DNA-ion interactions in ds-DNA. An enhancement of the DNA-water coupling is observed in ss-DNA, where the system is less rigid. All the interaction energies exhibit 1/f noise in their energy power spectra with surprisingly prominent bimodality in the DNA-water and DNA-ion fluctuations. The nature of the energy spectra appears to be indifferent to the relative rigidity of the DNA. We discuss the role of the observed correlations in ion-water motions on a DNA duplex in the experimentally observed anomalous slow dielectric relaxation and solvation dynamics, and in furthering our understanding of the DNA energy landscape.

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“…In ET reactions, quantum tunneling of an electron between the redox sites within a macromolecule is largely controlled by the environment that creates the necessary preconditions for an electron jump. Both fast fluctuations of solvent polarization and relatively slow and large-scale reorganization of the environment around the redox sites are important in these processes [ 7 , 8 , 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Semiclassical Theory of Multistage Nonequilibrium Electron Transfer in Macromolecular Compounds in Polar Media with Several Relaxation Timescales

Feskov

2022

IJMS

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Many specific features of ultrafast electron transfer (ET) reactions in macromolecular compounds can be attributed to nonequilibrium configurations of intramolecular vibrational degrees of freedom and the environment. In photoinduced ET, nonequilibrium nuclear configurations are often produced at the stage of optical excitation, but they can also be the result of electron tunneling itself, i.e., fast redistribution of charges within the macromolecule. A consistent theoretical description of ultrafast ET requires an explicit consideration of the nuclear subsystem, including its evolution between electron jumps. In this paper, the effect of the multi-timescale nuclear reorganization on ET transitions in macromolecular compounds is studied, and a general theory of ultrafast ET in non-Debye polar environments with a multi-component relaxation function is developed. Particular attention is paid to designing the multidimensional space of nonequilibrium nuclear configurations, as well as constructing the diabatic free energy surfaces for the ET states. The reorganization energies of individual ET transitions, the equilibrium energies of ET states, and the relaxation properties of the environment are used as input data for the theory. The effect of the system-environment interaction on the ET kinetics is discussed, and mechanisms for enhancing the efficiency of charge separation in macromolecular compounds are analyzed.

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From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

Cited by 23 publications

References 42 publications

Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

Bimodal 1/fnoise and anticorrelation between DNA-Water and DNA-Ion energy fluctuations

Semiclassical Theory of Multistage Nonequilibrium Electron Transfer in Macromolecular Compounds in Polar Media with Several Relaxation Timescales

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