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Seminario Prof. Joseph Zaccai8 aprile 2010ore 13.15Dipartimento di Fisica
Citation preview
NiPS 2010
I neutroni rivelano la relazione tra dinamica molecolare e funzione
biologica in proteine, membrane e cellule, in vivo
Giuseppe (Joe) Zaccai
Institut Laue-Langevin, GrenobleE-mail: [email protected]
NiPS 2010
> 60 000 strutture nella PDB
NiPS 2010
Capire una struttura è capire le forze che la mantengano
NiPS 2010
Haloarcula marismortuiSale ! Archaeoglobus fulgidus
Temperatura !
Malate dehydrogenase
NiPS 2010
_H +. _S +∆H+ ∆S+
∆H+,-,0 ∆S +,-,0
Privalov and Khechinashvili (1974) J. Mol. Biol., 86, 665-684
Calorimetria
NiPS 2010
BPTI (Go et al., 1983)
3.56 ps-1
0.21 ps-1
Normal M
odes
NiPS 2010
r i (0)
€
S(Q,ω)= 12π
I(Q∫ ,t)exp(−iωt)dt
I(Q,t)= 1N
<eiQ.rk(t)
k, j
∑ e-iQ.rj (0) >
r i (t )
Neutron Incoherent Scattering
Single Particle Scattering
k0
k1 Q
σ (H) >> σ (D and other nuclei)
NiPS 2010
≈ ( 1 / Q ) 2 Å 2
≈ 2 Å 2
on IN13 at ILL
time ≈ 100 pson the backscatteringspectrometer IN13
≈ 25 Å 2
H 2 O diffusing
H on protein
The elast ic scan : a window in length – t ime
NiPS 2010
T ( K )0 40 80 120 160 200 240 280
0.00
0.30
0.60
0.90
1.20
k' = 0.3N/m
k = 2N/m
k = 3N/m
< u
2>
Å2(
)
320
1.50
Data from Doster et al. (1989), Cordone et al. (2000)
hydrated powder
in trehalose glass
Neutron Scattering:Mean square displacements and
Effective Force Constants in Myoglobin
€
<k'>=2kB
d u2
dT
−1
< u2 > and < k’ > are experimental parameters~ flexibility,
~ resilience respectively
T’
IN 13 8 microeV 100 ps
Parametri
« High th
roughput !
»
NiPS 2010
Lavori sul Lisozima di Paciaroni e colleghi:
La dinamica di una proteina dipendefortemente dall’ambiente acquoso !
NiPS 2010Frauenfelder et al. (1988)
Una chiave per capire :
“Energy landscapes
or seascapes”
NiPS 2010
∆G
~ kBT ’ < k >
< k ’ >
quasi-harmonic approximation
√< u2 >
∆G
d
√< u2 >
< k ’ > ~ ∆G / 2d2
Bicout and Zaccai, Biophys. J., 2001Ea
√< u2 >
d
€
<k'>~1/d
dTRate×∆τ×d2
€
< k '>~ 1/d
dTRate × ∆τ × d 2
Rate ~ A exp(− E a
RT)
1/ < k '> ~ 0 ~ E a
RT >> 1 or << 1
< k '> ~ constant ~ E a
RT ~ 2 to 1
Ea
d
Bicout and Zaccai, Biophys. J., 2001
NiPS 2010
Vita colorata del sale
NiPS 2010
1.0
1.5
2.0
2.5
3.0
3.5
4.0
270 280 290 300 310 320 330
0 10 20 30 40 50
Temperature (K)
<u2
> (Å
2 )
(C)
2M NaCl H2 O
2M NaCl D2 O
2M KCl D2 O
< k’ > = 0.1 N/m
< k’ > = 0.2 N/m
< k’ > = 0.5 N/m
200 mg/ml protein
Fluctuations and force constants depend on the solventand correlate with stabil i ty
Tehei et al.(2001)
0.70
0.75
0.80
0.85
0.90
0.95
1.00
1.05
1.10
20 30 40 50 60 70 80 90
300 310 320 330 340 350 360
Aggregation
Temperature (C)
Norm
ali
zed
Ell
ipti
city
222 n
m
(K)
2M NaCl H2 O
2M NaCl D2 O2M KCl D2 O
NiPS 2010
There are
Dynamics-Function-Activity
Relations
Dynamics – Function-Activity
NiPS 2010
Biological Dynamics is not as simple as 'Flexibil i ty is required for activity ' - i t is Function Specif ic !
NiPS 2010Gabel et al., Biophys J, 2009
Human BuChE and Soman
NiPS 2010
Hb e temperatura fisiologica
Hb in …
solution
powder
Stadler et al., Biophys J, 2009Stadler et al., Biophys J, 2008
NiPS 2010
Purple Membrane
H. Salinarum
Bacteriorhodopsin
CP
CP
EC
NiPS 2010
Photocycle
specif ic f lexibil i ty
K
J
LN
O
BR570
M412
hν
ECH+
M412
CP
H+CP
EC
AG
F
E DC
B
H+
NiPS 2010
Dry PM
Wet PM
Harmonic domain
Dynamical transition
Activation of photocyle !
H+
‘transition of methyls’
NiPS 2010
Labelled sample :
In-vivo labelling:Fully deuterated PM with hydrogenated retinal, Trp, Met.
Retinal binding pocketExtracellular moiety of BR
Labelled BR: Sample preparation:
EC
CP
NiPS 2010
2.5
2.0
1.5
1.0
0.5
0.0
300200100
Temp. [K]
B
2.5
2.0
1.5
1.0
0.5
0.0
30025020015010050
Temp. [K]
D
2.5
2.0
1.5
1.0
0.5
0.0
300200100
Temp. [K]
A
2.5
2.0
1.5
1.0
0.5
0.0
30025020015010050
Temp. [K]
C
Large amplitude motions in labelled ↔ unlabelled PM
0 % r.h. 75 % r.h.
86 % r.h. 93 % r.h.
< u2 >, < k’ >Separate f lexibi l i ty and
r igidity
NiPS 2010
<u2 >
[Å
2 ]
<u2 >
[Å
2 ]
Lipids BR
NiPS 2010
Less soft core = valve
H+
Soft body
Softer lipid environment
All are hydration ...
and temperature dependent
Degrees of ‘Softness’
NiPS 2010
Dynamic adaptation to heat
LDH of Rabbit
MDH of Methanocaldococcus
jannaschii
0
20
40
60
80
100
120
0 20 40 60 80 100
Opt
imal
Act
ivit
y (%
)
T(°C)
Tehei, M., D. Madern, B. Franzett i & G. Zaccai, J Biol Chem (2005)
0
20
40
60
80
100
120
0 20 40 60 80 100 120
T(° C)
B
NiPS 2010
0,0
0,5
1,0
1,5
2,0
2,5
3,0
3,5
4,0
270 280 290 300 310 320 330
<u2
> (
Å2)
T(K)
Soft Rabbit muscle LDH Hard Methanocaldococcus jannaschii MalDH
NiPS 2010
Escherichia colimesophile 37°C
Aquaspir i l lum arct icumpsychrophile 4°C
Proteus mirabi l ismesophile 37°C
Thermus thermophilusthermophile 65°C
Aquifex pyrof i lushyperthermophile 85°CTehei et al. (2004)
Adaptation of the Proteome
NiPS 2010
0.5
1.0
1.5
2.0
2.5
3.0
270 280 290 300 310 320
0 10 20 30 40<
u2 >
(Å2 )
T (K)
T (° C)
E. coli : al ive and dead
NiPS 2010
1.0
1.5
2.0
2.5
270 280 290 300 310 320
0 10 20 30 40
<u
2 > (
Å2 )
T(° C)
T (K)
<k'>=(0,21±0,03) N/m A
1,0
1,5
2,0
2,5
270 280 290 300 310 320
0 10 20 30 40
<k'>=(0,39±0,01) N/m
<u2
> (
Å2)
T (K)
B
T (° C)
1.0
1.5
2.0
2.5
270 280 290 300 310 320
0 10 20 30 40
T (K)
<u2
> (
Å2)
<k'>=(0,67±0,11) N/m C
T (° C)
1.0
1.5
2.0
2.5
270 280 290 300 310 320
0 10 20 30 40
<k'>=(0,60±0,01) N/m<
u2 >
(Å2 )
T (K)
DT (° C)
P. mirabi l isA. arct icum
A. pyrofi lusT. thermophilus
NiPS 2010
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8<
k'
> (
N/m
)
Psychrophile Mesophile Thermo / Hyperthermophile
The effective force constant increases to maintain stabil i ty
NiPS 2010
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6¦(
< u
2 >)
(Å
)
Psychrophile Mesophile Thermo / Hyperthermophile
Same rms f luctuation at physiological temperature !
√
NiPS 2010
Una costante di forza adatta per mantere lo stesso valore della
f lutuazione alla temperatura f isiologica
L’evoluzione ha scelto la dinamica !
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
¦(<
u2 >
) (
Å)
Psychrophile Mesophile Thermo / Hyperthermophile
NiPS 2010
< u2
> (Å
2 )
Heparan Sulfate, a cell surface polysaccharide
Jasnin et al., PCCP, 2010
Cartografia dinamica della cellula
NiPS 2010
< u2
> (Å
2 )
Proteine di membrana Lipidi poliSaccaridi <u
2 > [
Å2 ]
1.00
P
L
S
NiPS 2010
Michel Ferrand, Valérie Réat, Uschi Lehnert, Martin Weik, Moeava Tehei, Frank Gabel, Katy Wood, Marion Jasnin, Andreas Stadler…
BacteriorhodopsinDieter Oesterhelt and his Lab, MPI Martinsried
Proteins and CellsDominique Madern et Bruno Franzetti, IBS, Grenoble, Margaret et Ben Zion Ginzburg,
Jérusalem, Martine Moulin et Michael Haertlein, D-LAB, Marie-Thérèse Giudici-Orticoni, Marseille
Red Blood CellsGerhard Artmann and his Lab in Aachen, Georg Bueldt in Juelich
Senza chi …
NiPS 2010
Grazie !