Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A

Tsytlonok, Maksym; Hemmen, Katherina; Hamilton, George L.; Kolimi, Narendar; Felekyan, Suren; Seidel, Claus A. M.; Tompa, Péter; Sanabria, Hugo

doi:10.1016/j.jmb.2020.02.010

Cited by 29 publications

(29 citation statements)

References 58 publications

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“…The N-terminal kinase inhibitory domain (KID) of p27, comprising D1, D2, and LH subdomains, is disordered, and folds through interactions with CDK2 and cyclin A [ 81 ]. Using a model protein containing only the p27 KID, one-dimensional 1 H WaterLOGSY and STD NMR methods were used to screen a chemical library of 1100 compounds from the Ro3 collection and an in-house library of 1222 compounds [ 66 ].…”

Section: Inhibitors Of Intrinsically Disordered Proteinsmentioning

confidence: 99%

Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Hosoya

Ohkanda

2021

Molecules

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Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid–liquid phase separations—which critically involve both intermolecular interactions between IDPs and their posttranslational modification—are analyzed to understand the potential of IDPs as new drug targets.

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Section: Inhibitors Of Intrinsically Disordered Proteinsmentioning

confidence: 99%

Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Hosoya

Ohkanda

2021

Molecules

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“…Nonequilibrium systems exacerbate the need to improve representations of multidimensional energy landscapes. Nonequilibrium processes, including the application of external force, 68 allosteric cofactors, 69 protein–protein interactions, 70 post-translational modifications, 54 and temperature 71 and pH changes, 72 as well as other energy transfer mechanisms 73 and environmental perturbations, 74 can impact biomolecular systems in ways that nonuniformly distort the multidimensional free energy landscape. Consider a biomolecular system subject to external loading that displaces its atoms along dimensions other than the direction of the force due to its anisotropic nature.…”

Section: Multidimensional Energy Landscapesmentioning

confidence: 99%

“…Specifically, MD simulations allow one to calculate multiple possible conformational and configurational trajectories through highly multidimensional (all 3 N – 6 dimensions) energy landscapes. MD simulations can be used to predict and validate experimental observables made with complementary techniques, such as NMR, 96 FRET, 27 , 70 force spectroscopy, 97 and other biophysical tools. MD simulation packages, including CHARMM, 124 AMBER, 125 NAMD, 126 and GROMACS, 127 can include external forces with the conventional force fields and other external perturbations in targeted and steered MD simulations.…”

Section: Mapping the Multidimensional Functional Energy Landscape In Equilibrium And Nonequilibrium Systemsmentioning

confidence: 99%

Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches

et al. 2021

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Out-of-equilibrium processes are ubiquitous across living organisms and all structural hierarchies of life. At the molecular scale, out-of-equilibrium processes (for example, enzyme catalysis, gene regulation, and motor protein functions) cause biological macromolecules to sample an ensemble of conformations over a wide range of time scales. Quantifying and conceptualizing the structure–dynamics to function relationship is challenging because continuously evolving multidimensional energy landscapes are necessary to describe nonequilibrium biological processes in biological macromolecules. In this perspective, we explore the challenges associated with state-of-the-art experimental techniques to understanding biological macromolecular function. We argue that it is time to revisit how we probe and model functional out-of-equilibrium biomolecular dynamics. We suggest that developing integrated single-molecule multiparametric force–fluorescence instruments and using advanced molecular dynamics simulations to study out-of-equilibrium biomolecules will provide a path towards understanding the principles of and mechanisms behind the structure–dynamics to function paradigm in biological macromolecules.

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“…Next, we set out to determine if NADH-stabilized 26S PC are capable of facilitating the degradation of IDPs. Initially, we used bacterially expressed and purified p27, a highly disordered protein [33,34] (Figure 3a). NADH 26S-PC were very efficient at promoting the degradation of p27, kinetically even faster than ATP-26S PC (Figure 3b).…”

Section: Nadh-26s Proteasomes Can Degrade Idpsmentioning

confidence: 99%

Degradation of Intrinsically Disordered Proteins by the NADH 26S Proteasome

et al. 2020

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The 26S proteasome is the endpoint of the ubiquitin- and ATP-dependent degradation pathway. Over the years, ATP was regarded as completely essential for 26S proteasome function due to its role in ubiquitin-signaling, substrate unfolding and ensuring its structural integrity. We have previously reported that physiological concentrations of NADH are efficient in replacing ATP to maintain the integrity of an enzymatically functional 26S PC. However, the substrate specificity of the NADH-stabilized 26S proteasome complex (26S PC) was never assessed. Here, we show that the binding of NADH to the 26S PC inhibits the ATP-dependent and ubiquitin-independent degradation of the structured ODC enzyme. Moreover, the NADH-stabilized 26S PC is efficient in degrading intrinsically disordered protein (IDP) substrates that might not require ATP-dependent unfolding, such as p27, Tau, c-Fos and more. In some cases, NADH-26S proteasomes were more efficient in processing IDPs than the ATP-26S PC. These results indicate that in vitro, physiological concentrations of NADH can alter the processivity of ATP-dependent 26S PC substrates such as ODC and, more importantly, the NADH-stabilized 26S PCs promote the efficient degradation of many IDPs. Thus, ATP-independent, NADH-dependent 26S proteasome activity exemplifies a new principle of how mitochondria might directly regulate 26S proteasome substrate specificity.

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Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A

Cited by 29 publications

References 58 publications

Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches

Degradation of Intrinsically Disordered Proteins by the NADH 26S Proteasome

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