Activation of human biliverdin-IXα reductase by urea: Generation of kinetically distinct forms during the unfolding pathway

Franklin, Edward; Mantle, Timothy J.; Dunne, Aisling

doi:10.1016/j.bbapap.2013.09.009

Cited by 5 publications

(3 citation statements)

References 17 publications

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“…This interpretation is qualitatively in agreement with that urea generally has a larger effect on the unfolding rate constant compared to the refolding rate-constant in protein folding studies (30). Urea activation of other enzymes has also been observed-including dihydrofolate reductase (13,14), prostaglandin D synthase (16,17), and biliverdin-Ixa (18). Possibly, the increased activities in these other enzymes are also mediated by a redistribution of existing structural states.…”

Section: Discussionsupporting

confidence: 85%

“…It has been observed that common denaturants like urea can increase activities of certain enzymes, including dihydrofolate reductase (13,14), Adk (15), prostaglandin D synthase (16,17), and biliverdin-Ixa (18). Various mechanisms for these increases have been proposed, for example removal of inhibition in biliverdin-Ixa (18) and structural reorganization in prostaglandin D synthase (16).…”

Section: Introductionmentioning

confidence: 99%

“…Various mechanisms for these increases have been proposed, for example removal of inhibition in biliverdin-Ixa (18) and structural reorganization in prostaglandin D synthase (16). Exposure to 1 M urea has been shown to increase activity of Adk bỹ 50% (15), putatively due to an increase in conformational flexibility in the active site.…”

Section: Introductionmentioning

confidence: 99%

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Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States

Rogne

Wolf‐Watz

2016

Biophysical Journal

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Proteins are often functionally dependent on conformational changes that allow them to sample structural states that are sparsely populated in the absence of a substrate or binding partner. The distribution of such structural microstates is governed by their relative stability, and the kinetics of their interconversion is governed by the magnitude of associated activation barriers. Here, we have explored the interplay among structure, stability, and function of a selected enzyme, adenylate kinase (Adk), by monitoring changes in its enzymatic activity in response to additions of urea. For this purpose we used a 31 P NMR assay that was found useful for heterogeneous sample compositions such as presence of urea. It was found that Adk is activated at low urea concentrations whereas higher urea concentrations unfolds and thereby deactivates the enzyme. From a quantitative analysis of chemical shifts, it was found that urea redistributes preexisting structural microstates, stabilizing a substrate-bound open state at the expense of a substrate-bound closed state. Adk is rate-limited by slow opening of substrate binding domains and the urea-dependent redistribution of structural states is consistent with a model where the increased activity results from an increased rate-constant for domain opening. In addition, we also detected a strong correlation between the catalytic free energy and free energy of substrate (ATP) binding, which is also consistent with the catalytic model for Adk. From a general perspective, it appears that urea can be used to modulate conformational equilibria of folded proteins toward more expanded states for cases where a sizeable difference in solvent-accessible surface area exists between the states involved. This effect complements the action of osmolytes, such as trimethylamine N-oxide, that favor more compact protein states.

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Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

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Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States

Rogne

Wolf‐Watz

2016

Biophysical Journal

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Purification and characterization of a urea sensitive lactate dehydrogenase from the liver of the African clawed frog, Xenopus laevis

2014

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The African clawed frog, Xenopus laevis, is able to withstand extremely arid conditions by estivating, in conjunction with dehydration tolerance and urea accumulation. Estivating X. laevis reduce their metabolic rate and recruit anaerobic glycolysis, driven by lactate dehydrogenase (LDH; E.C. 1.1.1.27) enzymes that reversibly convert pyruvate and NADH to lactate and NAD(+), to meet newly established ATP demands. The present study investigated purified LDH from the liver of dehydrated and control X. laevis. LDH from dehydrated liver showed a significantly higher K m for L-lactate (1.74 fold), NAD(+) (2.41 fold), and pyruvate (1.78 fold) in comparison to LDH from the liver of control frogs. In the presence of physiological levels of urea found in dehydrated animals, the K m values obtained for dehydrated LDH all returned to control LDH K m values. Dot blot analysis showed post-translational modifications may be responsible for the kinetic modification as the dehydrated form of LDH showed more phosphorylated serine residues (1.54 fold), less methylated lysine residues (0.43 fold), and a higher level of ubiquitination (1.90 fold) in comparison to control LDH. The physiological consequence of dehydration-induced LDH modification appears to adjust LDH function in conjunction with urea levels in dehydrated frogs. When urea levels are high during dehydration, LDH retains its normal function. Yet, as urea levels drop during rehydration, LDH function is reduced, possibly shunting pyruvate to the TCA cycle.

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Towards the energy landscape of adenylate kinase in crowded milieu: Activity, conformation, structure and dynamics in sequence

Rastogi

Singh

Chowdhury

2023

Archives of Biochemistry and Biophysics

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Activation of human biliverdin-IXα reductase by urea: Generation of kinetically distinct forms during the unfolding pathway

Cited by 5 publications

References 17 publications

Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States

Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States

Purification and characterization of a urea sensitive lactate dehydrogenase from the liver of the African clawed frog, Xenopus laevis

Towards the energy landscape of adenylate kinase in crowded milieu: Activity, conformation, structure and dynamics in sequence

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