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. 2010 Nov 17;99(10):3473-82.
doi: 10.1016/j.bpj.2010.09.058.

Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy

Bela Farago  1 , Jianquan Li, Gabriel Cornilescu, David J E Callaway, Zimei Bu
Affiliations

Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy

Bela Farago et al. Biophys J. .

Abstract

NHERF1 is a multidomain scaffolding protein that assembles signaling complexes, and regulates the cell surface expression and endocytic recycling of a variety of membrane proteins. The ability of the two PDZ domains in NHERF1 to assemble protein complexes is allosterically modulated by the membrane-cytoskeleton linker protein ezrin, whose binding site is located as far as 110 Ångstroms away from the PDZ domains. Here, using neutron spin echo (NSE) spectroscopy, selective deuterium labeling, and theoretical analyses, we reveal the activation of interdomain motion in NHERF1 on nanometer length-scales and on submicrosecond timescales upon forming a complex with ezrin. We show that a much-simplified coarse-grained model suffices to describe interdomain motion of a multidomain protein or protein complex. We expect that future NSE experiments will benefit by exploiting our approach of selective deuteration to resolve the specific domain motions of interest from a plethora of global translational and rotational motions. Our results demonstrate that the dynamic propagation of allosteric signals to distal sites involves changes in long-range coupled domain motions on submicrosecond timescales, and that these coupled motions can be distinguished and characterized by NSE.

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Figures

Figure 1
Figure 1
Multidomain scaffolding protein NHERF1 and NSE experiments. (A) A schematic representation of the different domains in NHERF1. The C-terminal 13-amino-acid residues (aa residue 346–358) of CT, which largely overlap with the ezrin-binding domain (EBD), interact with the ligand-binding pocket of the PDZ2 domain (17). (B) I(Q,t)/I(Q,0) of NHERF1 from NSE in solution. The lines are single exponential fits to I(Q,t)/I(Q,0). The legend on the right gives the Q value at which each I(Q,t)/I(Q,0) is measured. The I(Q,t)/I(Q,0) of NHERF1·hFERM or NHERF1·dFERM also shows single exponential behavior (Fig. S1).
Figure 2
Figure 2
NHERF1 alone can be described by a rigid-body model. (A) Three-dimensional shape of NHERF1 reconstructed from SAXS (14) using DAMMIN (28). For illustration, the structures of the PDZ1 (PDB code: 1I92) and PDZ2 (PDB code: 2KJD) are docked into the three-dimensional shape using UCSF Chimera software (31). EBD that interacts with PDZ2 is not marked. (B) Comparing experimental Deff(Q) of NHERF1 (open squares) with rigid-body calculation performed using dummy atoms (solid line). D0 (solid squares) is from PFG NMR (Table S1).
Figure 3
Figure 3
Activation of domain motion in NHERF1 upon binding to FERM domain. (A) The three-dimensional shape of NHERF1·FERM reconstructed from SANS (14) using the software MONSA (30). The structures of PDZ1, PDZ2, and ezrin FERM (PDB code: 1NI2) are docked into the envelope. Arrows represent motions between PDZ1 and PDZ2. A 60 Å scale bar is shown. (B) Comparing experimental Deff(Q) with rigid-body calculations for NHERF1·dFERM (open red squares and solid red line) and NHERF1·hFERM (open blue squares and blue line). Rigid-body calculations used the dummy-atom coordinates from SANS (14). D0 for NHERF1·dFERM (solid red squares) and NHERF1·hFERM (solid blue squares) are from PFG NMR. D0 (solid black squares), Deff(Q) (open black squares), and the rigid-body calculation (solid black line) of NHERF1 are shown. (C) Comparing NSE data with rigid model calculations for the NHERF1·dFERM and NHERF1·hFERM complexes using the coordinates of the docked domains. Symbols same as in panel B. (D) Comparing experimental Deff(Q) with calculations incorporating interdomain motion (via the mobility tensor) between PDZ1 and PDZ2, for NHERF1·dFERM (dashed red line), and NHERF1·hFERM (dashed blue line). Calculations used the docked structures. Symbols for Deff(Q) and D0 same as panels B and C.
Figure 4
Figure 4
A simplified four-point model can well describe domain motion in the complex. (A) The four-point model represents NHERF1·FERM, with centers of PDZ1, PDZ2, CT, and FERM taken from Fig. 3A. (B) Comparing experimental Deff(Q) with the four-point rigid-body calculations for NHERF1·hFERM (blue open squares are experimental and blue solid line is calculation) and for NHERF1·dFERM (red open squares, experimental and red solid line, calculation). D0 of NHERF1·dFERM (solid red squares) and NHERF1·dFERM (solid blue squares) are shown. (C) Comparing experimental data with calculations assuming interdomain motion between PDZ1 and PDZ2 in NHERF1·dFERM (red dashed line) and NHERF1·hFERM (blue dashed line). Experimental symbols same as in panel B. (D) Comparing the experimental data with calculations incorporating interdomain motion between PDZ1 and PDZ2, as well as assuming a form factor of spheres of 20 Å radius for FERM and both PDZ domains in NHERF1·dFERM (red dash-dot line) and in NHERF1·hFERM (blue dash-dot line).
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