Limits...
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.


Comparison between all known structures of K63-Ub2 in the open state.With the distal unit superimposed, the positions for the proximal unit are compared. By enforcing negative inter-subunit paramagnetic relaxation enhancement (PRE) restraints, open-state conformations of K63-Ub2 can also be obtained. The atomic probability map plotted at 10% threshold (gray meshes) encompasses the known structures of K63-Ub2 in the open state.DOI:http://dx.doi.org/10.7554/eLife.05767.010
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4507786&req=5

fig1s7: Comparison between all known structures of K63-Ub2 in the open state.With the distal unit superimposed, the positions for the proximal unit are compared. By enforcing negative inter-subunit paramagnetic relaxation enhancement (PRE) restraints, open-state conformations of K63-Ub2 can also be obtained. The atomic probability map plotted at 10% threshold (gray meshes) encompasses the known structures of K63-Ub2 in the open state.DOI:http://dx.doi.org/10.7554/eLife.05767.010

Mentions: K63-Ub2 has been generally considered to only exist in the open state for both ligand-free and many ligand-bound forms. For the known open-state structures of K63-Ub2 (Sato et al., 2008; Datta et al., 2009; Komander et al., 2009; Sato et al., 2009a; Weeks et al., 2009; Yoshikawa et al., 2009; Sekiyama et al., 2012), the intra-molecular inter-subunit PREs calculated with an MTS probe attached at either N25C or K48C site are essentially zero for residues in the proximal unit (Figure 1—figure supplement 7). Alternatively, an open extended conformation of K63-Ub2 can be simply obtained by restraining the inter-subunit PRE target value to zero for residues in the proximal unit—the resulting conformational space encompasses all known K63-Ub2 structures in the open state (Figure 1—figure supplement 8). As such, the large inter-subunit PREs should only arise from the closed state of K63-Ub2, and ligand-free K63-Ub2 should exist in both open and closed states.


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)

Comparison between all known structures of K63-Ub2 in the open state.With the distal unit superimposed, the positions for the proximal unit are compared. By enforcing negative inter-subunit paramagnetic relaxation enhancement (PRE) restraints, open-state conformations of K63-Ub2 can also be obtained. The atomic probability map plotted at 10% threshold (gray meshes) encompasses the known structures of K63-Ub2 in the open state.DOI:http://dx.doi.org/10.7554/eLife.05767.010
© Copyright Policy
Related In: Results  -  Collection

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

fig1s7: Comparison between all known structures of K63-Ub2 in the open state.With the distal unit superimposed, the positions for the proximal unit are compared. By enforcing negative inter-subunit paramagnetic relaxation enhancement (PRE) restraints, open-state conformations of K63-Ub2 can also be obtained. The atomic probability map plotted at 10% threshold (gray meshes) encompasses the known structures of K63-Ub2 in the open state.DOI:http://dx.doi.org/10.7554/eLife.05767.010
Mentions: K63-Ub2 has been generally considered to only exist in the open state for both ligand-free and many ligand-bound forms. For the known open-state structures of K63-Ub2 (Sato et al., 2008; Datta et al., 2009; Komander et al., 2009; Sato et al., 2009a; Weeks et al., 2009; Yoshikawa et al., 2009; Sekiyama et al., 2012), the intra-molecular inter-subunit PREs calculated with an MTS probe attached at either N25C or K48C site are essentially zero for residues in the proximal unit (Figure 1—figure supplement 7). Alternatively, an open extended conformation of K63-Ub2 can be simply obtained by restraining the inter-subunit PRE target value to zero for residues in the proximal unit—the resulting conformational space encompasses all known K63-Ub2 structures in the open state (Figure 1—figure supplement 8). As such, the large inter-subunit PREs should only arise from the closed state of K63-Ub2, and ligand-free K63-Ub2 should exist in both open and closed states.

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.