Numerical Recipes--The Art of Scientific Computing.

Fritsch, Frederick N.; Press, William H.; Flannery, Brian P.; Teukolsky, Saul A.; Vetterling, William T.

doi:10.2307/2007938

Cited by 992 publications

(87 citation statements)

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“…Initially, each system is energy minimized using the steepest descent method ( 1 ) for 10,000 steps, followed by heating it to 300 K in 200 ps using Berendsen thermostat and barostat ( 72 ) with a coupling constant of 0.5 ps each. Restraints of 25 kcal/mol/Å 2 are applied on heavy atoms during the heating process.…”

Section: Methodsmentioning

confidence: 99%

“…THPTA not only helps in maintaining the Cu(I) oxidation state during the experimental tenure against aerial oxidation, it also enables the protection of biomolecules from oxidative damage by ROS species that might be generated during the reaction (61,62). 1 H NMR and 13 C NMR is used to confirm the preparation of THPTA that is subsequently used in our experiments (Fig. S6A and S6B).…”

Section: Cu(i) and Not Cu(ii) Triggers Hctr1 Endocytosismentioning

confidence: 99%

“…Copper is a micronutrient essential for all eukaryotic organisms as it plays a crucial role in coordinating different physiological activities of cells (1)(2)(3)(4). Copper shuttles between its two primary oxidation states, Cu(I) and Cu(II).…”

Section: Introductionmentioning

confidence: 99%

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Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1

Kar

Sen

Maji

et al. 2022

Journal of Biological Chemistry

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Section: Methodsmentioning

confidence: 99%

Section: Cu(i) and Not Cu(ii) Triggers Hctr1 Endocytosismentioning

confidence: 99%

See 1 more Smart Citation

Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1

Kar

Sen

Maji

et al. 2022

Journal of Biological Chemistry

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show abstract

“…Initially each system is energy minimized using the steepest descent method (Fritsch et al, 1988) for 10000 steps, followed by heating it to 300K in 200 ps using Berendsen thermostat and barostat (Berendsen et al, 1984) with a coupling constant of 0.5 ps each. Restraints of 25 kcal/mol/Å are applied on heavy atoms during the heating process.…”

Section: B Equilibration and Simulationmentioning

confidence: 99%

“…Copper is a micronutrient essential for all eukaryotic organisms as it plays a crucial role in coordinating different physiological activities of cells (Fritsch et al, 1988;Linder, 1991;Labbé et al, 1999;Puig et al, 2002). Copper shuttles between its two primary oxidation states, Cu(I) and Cu(II).…”

Section: Introductionmentioning

confidence: 99%

Redox state and cellular uptake of copper is regulated by N-terminus of human Copper Transporter-1

Kar¹,

Sen²,

Maji³

et al. 2021

Preprint

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Copper(I) is essential for all life forms. Though Cu(II) is the most abundant state in environment, its reduction to Cu(I) is a prerequisite for bio-utilization, the mechanism of which is still uncharacterized. We show that in the human Copper Transporter-1, two amino-terminal methionine-histidine clusters and neighbouring aspartates distinctly binds Cu(II) to Cu(I) preceding its import. The endocytosis of hCTR1 from the basolateral membrane of polarized epithelia to Common-Recycling-Endosomes is dependent on copper reduction and coordination of Cu(I) by methionine residues. The transient binding of both Cu(II) and Cu(I) during the reduction process facilitated by aspartates also acts as another crucial determinant of hCTR1 endocytosis. Mutating 7Met-Gly-Met9 and Asp13 abrogates copper uptake and endocytosis, which was corrected by reduced and non-reoxidizable Cu(I). Histidine motifs, on the other hand, are crucial for hCTR1 functioning at limiting copper. Finally, we show that the two N-terminal His-Met-Asp clusters exhibit functional complementarity in regulating Cu(I)-induced hCTR1 endocytosis. This study proposes a model where His-Met-Asp residues of hCTR1 amino-terminal not only coordinate copper but also maintains its reduced state crucial for intracellular uptake.

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Quantifying the effects of dynamical noise on the predictability of a simple ecosystem model

2004

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SUMMARYThe need to understand the effects of anthropogenic perturbations on ocean biology has renewed interest in ecosystem and biogeochemical models in recent years. We develop a nonlinear time series approach to quantify the effects of different types of noise on ecosystem dynamics. Different types of noise can alter the local predictability of the system, induce qualitative regime shifts in model dynamics, and destroy (create) internal nonlinear oscillations and chaos. The ecosystem model we use in our article is a model of plankton dynamics and nitrogen cycling. It is a compartmental model (NPZD) consisting of compartments for nitrogen (N), phytoplankton (P), zooplankton (Z), and detritus (D). The flows or intercompartmental exchanges are modeled as a nonlinear system of four first-order differential equations. The types of noise of interest are both independent and correlated. Because the noise is an integral part of the system's dynamics, a nonlinear time series approach is used to quantify the dynamics and predictability of the system. This involves fitting neural network models and estimating dynamical system quantities of interest such as global and local Lyapunov exponents, along with measures of uncertainty for these estimates.

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Numerical Recipes--The Art of Scientific Computing.

Cited by 992 publications

References 0 publications

Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1

Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1

Redox state and cellular uptake of copper is regulated by N-terminus of human Copper Transporter-1

Quantifying the effects of dynamical noise on the predictability of a simple ecosystem model

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