Protein conformational entropy is not slaved to water

Marques, Bryan S.; Stetz, Matthew A.; Jorge, Christine; Valentine, Kathleen G.; Wand, A. Joshua; Nucci, Nathaniel V.

doi:10.1038/s41598-020-74382-5

Cited by 16 publications

(15 citation statements)

References 58 publications

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“…However, these dynamics show similar dielectric responses, making it difficult to derive a simplified description of biomolecular functions based on microscopic hydration properties (10,11). Indeed, such a direct link between the fast dynamics and biological functions is not supported by a recent study of NMR relaxation (12).…”

Section: Introductionmentioning

confidence: 99%

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Tokunaga

Tanaka

Iida

et al. 2021

Biophysical Journal

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Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at $0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 3 10 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.

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Section: Introductionmentioning

confidence: 99%

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Tokunaga

Tanaka

Iida

et al. 2021

Biophysical Journal

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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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“…5 In contrast, fast librational motions of side-chains (picoseconds to nanoseconds) require little to no rearrangement of surrounding molecules and are therefore largely uncoupled from the bath. 5,9 Less is known about internal motions that are not directly exposed to the bath. Furthermore, for diffusive processes occurring on rough reaction coordinates, such as that expected for a protein, 1,10 it is unclear how protein−bath coupling manifests on intermediate time scales.…”

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confidence: 99%

“…However, in the high-viscosity regime, the system spends increasing amounts of time relaxing in local free-energy basins corresponding to tier 2 motions, which have been shown to be independent of solvent viscosity. 5,9 Deviations from Kramers' theory are therefore expected in the high viscosity regime, as the reaction time becomes more strongly governed by local fluctuations. A central assumption in Kramers' theory is that the bath fluctuations are Markovian, i.e., uncorrelated in time.…”

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confidence: 99%

“…Early work by Frauenfelder and colleagues , on the binding kinetics of carbon monoxide to myoglobin revealed that large-scale conformational dynamics of the protein were strongly coupled to the fluctuations of the bath. From this work emerged a framework for understanding protein motions based on a rugged free energy landscape and a hierarchy of dynamic time scales. − Slow global conformational motions (milliseconds to seconds) require a significant rearrangement of solvent molecules surrounding the protein and are therefore coupled to the viscosity of the bath . In contrast, fast librational motions of side-chains (picoseconds to nanoseconds) require little to no rearrangement of surrounding molecules and are therefore largely uncoupled from the bath. , Less is known about internal motions that are not directly exposed to the bath.…”

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confidence: 99%

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Protein–Bath Coupling of an Internal Reaction Coordinate at Intermediate Time Scales

Lee

Talele

King

2021

J. Phys. Chem. Lett.

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Thermally activated barrier-crossing processes are central to protein reaction kinetics. A determining factor for such kinetics is the extent to which the protein's motions are coupled to the surrounding bath. It is understood that slow large-scale conformational motions are strongly coupled to the environment, while fast librational motions are uncoupled. However, less is known about protein−bath coupling of reaction coordinates located on the interior of a protein and with dynamics on intermediate time scales. In this work, we use single molecule 2D fluorescence lifetime correlation spectroscopy to study the microsecond chemical reaction occurring in the chromophore pocket of eGFP. The equilibrium reaction involves a dihedral rotation of a glutamic acid residue and a rearrangement of the local hydrogen-bonding network surrounding the endogenous chromophore, with no accompanying large-scale conformational changes. We observe that the internal chemical reaction is coupled to the solvent viscosity, though the scaling deviates from Kramers' behavior. We attribute this deviation to the internal friction of the protein, which weakens the protein−solvent coupling at high viscosity and intermediate time scales.

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Protein conformational entropy is not slaved to water

Cited by 16 publications

References 58 publications

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

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

Protein–Bath Coupling of an Internal Reaction Coordinate at Intermediate Time Scales

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