Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations

Wakai, Nobuhiko; Takemura, Kazuhiro; Morita, Takami; Kitao, Akio

doi:10.1371/journal.pone.0085852

Cited by 21 publications

(20 citation statements)

References 63 publications

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“…Currently, the influence of external conditions, such as temperature, pressure, electric field, and solvation on the structure during processing has been the focus of MD studies to access changes of proteins during processing (Russo et al., ; Stănciuc, Banu, Bolea, Patraşcu, & Aprodu, ; Stănciuc, Crețu, Banu, & Aprodu, ; Vagadia, Vanga, Singh, & Raghavan, ). For instance, studies to evaluate external electric field and pressure on proteins can be cited (Singh, Orsat, & Raghavan, ; Wakai, Takemura, Morita, & Kitao, ). It is important to note that most of molecular changes are associated with the functional properties of proteins such as gelation (Bello, Fragosovázquez, & Basurto, ; Sang et al., ).…”

Section: Simulation As An Aid For Food Researchmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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Section: Simulation As An Aid For Food Researchmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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“…Using molecular dynamics simulations at 0.1 and 60 MPa Wakai et al (2014) modeled the pressure responses of C. armatus and C. yaquinae α-actin monomers in comparison to those of C. acrolepis and the shallow-living carp, as well as rabbit, human and chicken actins. These species have similar primary sequences; the two deeper species have a lysine as residue 137 near the active site; the other species have a glutamine.…”

Section: Actinmentioning

confidence: 99%

Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms

Yancey

Siebenaller

2015

Journal of Experimental Biology

128

116

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Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic 'piezolyte' or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.

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“…Biochemical properties of these proteins practically have not been studied. At the same time, great amounts of information about these species habits (Dayton, P.K and Hessler, R.R., 1972) and feeding patterns (Drazen, J.C et al, 2001), along with their biological and biochemical mechanisms of adaptation to low temperatures and high pressures (Wakai, N et al, 2014;Morita, T., 2010) have been accumulated in scientific literature at the present time.…”

Section: Introductionmentioning

confidence: 99%

The Comparative Study of Myofibrillar Proteins of Skeletal Muscles of Some Deep-Sea Fish Species

Ep¹,

Ev²

2017

FisheriesSciences.com

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Abstract:Comparative characteristics, common and distinctive features of qualitative and quantitative composition of myofibril proteins of skeletal muscles of some deep-sea fish species (Podonema longipes, Coryphaenoides cinereus, Coryphaenoides pectoralis) have been determined. Myofibrillar proteins were extracted from the skeletal muscle of three species deep-sea fish and their relative molecular mass was estimated by SDS/polyacrylamide gel electrophoresis. Subunit and quantitative compositions of deep-sea fish proteins were determined. The molecular weight of predominant contractile proteins, myosin (with heavy chains and two light chains), actin, troponin and tropomyosin was about 492, 47, 38 and 35 kDa, respectively for all fish species. The myosin/actin ratios were determined to be 2.85, 2.76 and 2.56 respectively for C. cinereus, P. longipes, and C. pectoralis. The Ca 2+ -ATPase activity of C. cinereus and P. longipes actomyosins was significantly higher at low ionic strengths (0.317 and 0.324 µМ P i mg -1 min -1 accordingly) than at high ionic strengths (0.257 and 0.221 µМ P i mg -1 min -1 accordingly). At the same time the Mg 2+ -ATPase activity value remained almost constant at both high and low ionic strengths (0.169-0.178 µМ P i mg -1 min -1 ). The Ca 2+-ATPase activity of C. cinereus, P. longipes and C. pectoralis myosins was 0.534, 0.641 and 0.376 µМ P i mg -1 min -1 respectively.

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Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations

Cited by 21 publications

References 63 publications

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms

The Comparative Study of Myofibrillar Proteins of Skeletal Muscles of Some Deep-Sea Fish Species

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