nanoscale protein dynamics and long- range allostery in cell signaling zimei bu 1 and david j. e....
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NANOSCALE PROTEIN DYNAMICS AND LONG-RANGE ALLOSTERY IN CELL SIGNALING
Zimei Bu1 and David J. E. Callaway1,2 1 City College of New York and
2New York University School of Medicine
• Multiple domains in proteins give rise to a great deal of flexibility and mobility, leading to protein domain dynamics.
• Nanoscale domain motions can only be directly observed using spectra measured by neutron spin echo spectroscopy (our new frontier!). They are essential for:
• nanoscale allostery• catalysis• regulatory activity• transport of metabolites• formation of protein assemblies• cellular locomotion
90O
NHERF1 is an elongated protein with multiple modular domains
PDZ1
PDZ2
CT
PDZ1
PDZ2
CT
57.1 Å
45.8 Å
NHERF1 from SAXS
PDZ domains
0 20 40 60 80 100 120 140 1600.0000
0.0002
0.0004
0.0006
0.0008
0.0010
0.0012
dNHERF1 in complex NHERF1 in solution
P(r
)
r(Å)
Structural changes in NHERF1 upon binding to ezrin
110 Å
Ezrin
PDZ2PDZ1
NHERF1
Ezrin-induces long-range interdomain allostery in NHERF1
Applying neutron spin echo spectroscopy to study long-range coupled protein domain motion
Velocity selector
Polarizerπ/2 coil
Guide field 1
π coil
Sample
Guide field 2
π/2 coil
Analyzer
Detector
Velocity selector
Polarizerπ/2 coil
Guide field 1
π coil
Sample
Guide field 2
π/2 coil
Analyzer
Detector
Ferenc Mezei
Nanosecond to microsecond time scales
10-1000 Å: nano length scales
0 100 200 300 400 500
0.0
0.2
0.4
0.6
0.8
1.0 Q=0.0254 Å-1
Q=0.0302 Å-1
Q=0.0350 Å-1
Q=0.0459 Å-1
Q=0.0531 Å-1
Q=0.0608 Å-1
Q=0.0758 Å-1
Q=0.0882 Å-1
Q=0.1100 Å-1
Q=0.1212 Å-1
Q=0.1538 Å-1
I(Q
,t)/
I(Q
,0)
time (ns)
Shape fluctuations in a protein that ONLY NSE can
see!
Protein motion—low Reynolds number
Overdamped creeping motions--(badminton at bottom of molasses pool, not a cruise ship crossing the Atlantic!)
Effective diffusion constant Deff(Q)
2
0
)()(
)0,(/),(lnlim)(
Q
QQD
QItQIt
Q
eff
t
Mobility tensor H defines dynamics—
our new technique!
The Q dependence of the decay rates of the NSE measured
correlation functions is defined by the mobility tensor
jl
rriQlj
jl
rriQl
Rjlj
Tjllj
Beff
lj
lj
ebb
eLHLQHQbb
Q
TkQD
)(
)(
2)(
Mobility tensor v = H F
H is the mobility tensor, and yields the velocity of a domain given the force
applied on it or another subunit. NSE yields H, given structure.
(Bu et al, PNAS, 2005)
0.00 0.05 0.10 0.15 0.201.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
5.5
Def
f(Q)
(Å2 /n
s)
Q (Å-1)
PDZ1
PDZ2
CT
NHERF1
The dynamics of (unbound) NHERF1 alone is well described by a rigid-body model
Only inputs to calculations are diffusion constant from PFG NMR and SANS
coordinates—no need to fit NSE data or use MD!
Farago et al Biophys J 2010
PDZ1
PDZ2
FERM
CT
0.00 0.05 0.10 0.15 0.201.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
5.5
Def
f(Q)
Q(Å-1)0.00 0.05 0.10 0.15 0.20
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
5.5
Def
f(Q)
Q(Å-1)
Binding to ezrin activates inter-domain motions in NHERF1 more than 100 Å away!!
Rigid body
Farago et al Biophys J 2010
PDZ1
PDZ280 Å 59 Å
110 Å
0.00 0.05 0.10 0.15 0.201.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
Def
f(Q)
(Å2 /n
s)
Q(Å-1)
Binding to FERM activates inter-domain motions in NHERF1 - A simple four-point
model describes all
0.00 0.05 0.10 0.15 0.201.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
De
ff(Q)
(Å2 /n
s)
Q(Å-1)
110 Å
Ezrin
PDZ2PDZ1
NHERF1
Binding to ezrin activates nanoscale inter-domain motions in
NHERF1
• Neutron spin echo spectroscopy allows us to see coupled interdomain motion in proteins for the very first
time
• Our analyses show that these motions can be revealed by utilizing nonequilibrium statistical mechanics
(mobility tensor)—no need for mnolecular dynamics or
multiparameter fits
Acknowledgements
NIH
ILL, NIST, and ORNL