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Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition.

Liu Z, Gong Z, Jiang WX, Yang J, Zhu WK, Guo DC, Zhang WP, Liu ML, Tang C - Elife (2015)

Bottom Line: Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits.A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands.This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China.

ABSTRACT
A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

No MeSH data available.


Related in: MedlinePlus

Concentration dependence of small angle X-ray scattering (SAXS) profiles for ligand-free K63-Ub2.The paired-distance curve displays a narrower distribution at lower protein concentration. The larger particle size at higher protein concentration can be attributed to the non-covalent interactions between two or more K63-Ub2.DOI:http://dx.doi.org/10.7554/eLife.05767.013
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fig2s1: Concentration dependence of small angle X-ray scattering (SAXS) profiles for ligand-free K63-Ub2.The paired-distance curve displays a narrower distribution at lower protein concentration. The larger particle size at higher protein concentration can be attributed to the non-covalent interactions between two or more K63-Ub2.DOI:http://dx.doi.org/10.7554/eLife.05767.013

Mentions: The existence of the closed state for ligand-free K63-Ub2 is corroborated by small angle X-ray scattering (SAXS) analysis. The SAXS data collected for K63-Ub2 at higher concentrations display larger particle size than those at lower concentrations, indicative of high-order oligomers for the former (Figure 2—figure supplement 1). At lower concentrations, the Dmax value is smaller, and the data recorded at 1 mM and 500 µM are similar (Dmax = 67.2 and 65 Å, respectively). The Dmax values are smaller than the calculated values for all known open-state structures (84.0 ± 3.3 Å). Significantly, the experimental paired-distance distribution function P(r) at 1 mM is much narrower than those computed for the known open-state structures, with a large probability of distribution at ∼30 Å (Figure 2A). Further, the theoretical scattering profiles for the open-state structure models (Figure 1—figure supplement 8) all differ from the experiment curve (Figure 2—figure supplement 2A).10.7554/eLife.05767.012Figure 2.Small angle X-ray scattering (SAXS) analysis of ligand-free K63-Ub2.


Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition.

Liu Z, Gong Z, Jiang WX, Yang J, Zhu WK, Guo DC, Zhang WP, Liu ML, Tang C - Elife (2015)

Concentration dependence of small angle X-ray scattering (SAXS) profiles for ligand-free K63-Ub2.The paired-distance curve displays a narrower distribution at lower protein concentration. The larger particle size at higher protein concentration can be attributed to the non-covalent interactions between two or more K63-Ub2.DOI:http://dx.doi.org/10.7554/eLife.05767.013
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4507786&req=5

fig2s1: Concentration dependence of small angle X-ray scattering (SAXS) profiles for ligand-free K63-Ub2.The paired-distance curve displays a narrower distribution at lower protein concentration. The larger particle size at higher protein concentration can be attributed to the non-covalent interactions between two or more K63-Ub2.DOI:http://dx.doi.org/10.7554/eLife.05767.013
Mentions: The existence of the closed state for ligand-free K63-Ub2 is corroborated by small angle X-ray scattering (SAXS) analysis. The SAXS data collected for K63-Ub2 at higher concentrations display larger particle size than those at lower concentrations, indicative of high-order oligomers for the former (Figure 2—figure supplement 1). At lower concentrations, the Dmax value is smaller, and the data recorded at 1 mM and 500 µM are similar (Dmax = 67.2 and 65 Å, respectively). The Dmax values are smaller than the calculated values for all known open-state structures (84.0 ± 3.3 Å). Significantly, the experimental paired-distance distribution function P(r) at 1 mM is much narrower than those computed for the known open-state structures, with a large probability of distribution at ∼30 Å (Figure 2A). Further, the theoretical scattering profiles for the open-state structure models (Figure 1—figure supplement 8) all differ from the experiment curve (Figure 2—figure supplement 2A).10.7554/eLife.05767.012Figure 2.Small angle X-ray scattering (SAXS) analysis of ligand-free K63-Ub2.

Bottom Line: Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits.A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands.This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China.

ABSTRACT
A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

No MeSH data available.


Related in: MedlinePlus