Transcript IWCMB09 16, Sept. 09

Neutrons in Biology
IWCMB09 16, Sept. 09
- Nautron Scattering Studies Water & Water around Biomolecules
Dr Jichen Li
Department of Physics & astronomy
The University of Manchester
Manchester, M60 1QD, UK
Topics:
Inelastic neutron scattering investigation of Water/Ice
Water in Biological Systems
Water in porous media, Carbon nanotubes and Nano-materials
Ab initio QM simulations for water and water around amino acids
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Water is still mystery to us
IWCMB09 16, Sept. 09
It’s water to you,
but to science,
it is a still mystery
Source Sunday Telegraph 13/10/1996.
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Water in living cells
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How much do we know water in
biological systems?
We know that water acts as media of
solution,
transportation,
lubrication,
--However, we know very little about
the role of water in bioprocesses:
e.g. formation and stabilization
of DNA, proteins.
bonded water (%)
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Robert C. Ford et al, J. Amer. Chem. Soc. 126 (2004) 4682
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Water in confined spaces
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QENS measurement on water
droplets and nano-clusters:
• The diffusion coefficient is lower
when size of the water droplets
decreases.
• The reduction is partially due to
confined space.
67oC
• The diffusion confident increases
with T discontinuously.
52oC
37oC
Kw
KS
KS
Kw
4
Body temperatures
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Body temperature
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T = 37 oC
+/- 3oC (80%)
+/-5oC (15%)
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Variation of the body temperature of lizard
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37oC
16oC
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Accurate description of water interaction
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hydrogen bond
Two different
potentials
O
H
Covalent bond
Voo ( r ) =
A
12
roo
-
B q+ q +
+ ( pol ).
6
roo
roh
2. Non-rigid water potentials (complicated)
(e.g. KKY, ST2 and etc).
3. Polarisable potentials (more accurate)
(e.g. SK, Pol, BLSL and etc).
q
r
1. The rigid water-water potentials
(simple and effective)
(e.g. MCY, SPC, TIP3P, TIP4P and etc).
-2q
+q
+q
-q
+q
-2q
+q
-q
+q
+q
q = 0.3-0.6 e, D = 2.5-28 D
4. Smear charged polarisable potential (more realistic)
(CJ Burnham, J.C. Li & etc, JCP 110(1999) 4566).
-q
+q
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Measuring the potential surface?
roo
Ice Ih:
2.75 Å
Others: 2.6-2.85 Å
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q
roo
104.5o
75-120o
q
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Structure factors of water
A Soper et al, JCP (1996).
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J. Dore, et al NATO ASI (1998).
OD/OH
1.72
1.78
1.76
1.66
• H/D unequivalence
• Q range measured
• Inelasticity
resulting large differences in G(r)’s.
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Testing water-water potentials
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The test of a water potential
Microscopic properties
Bulk properties
Strcture factors
Vibrational dynamics
Neutron diffraction
SHH(Q)
SOO(Q)
SHO(Q)
Inelastic
neutron scattering
D(w)
Fourier transform
GHH(r)
GOO(r)
GOH(r)
Energy
Heat capacity
density maximum
and etc.
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Vibrational spectra of ice Ih
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220 cm-1 or 28 meV
librational
Internal vibrations
translational
translational
librational
Bending and
strengthening
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Exotic ices (H2O)
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Ice VII
TFXA at ~ 4 K.
.
The samples are recovered phases at >77K.
J.C. Li et al, JCP , 94 (1991) 6770.
J.C.Li et alJ. Phys.:C 4 (1992) 2109.
A.I. Kolesnikov, et al, J. Phy.L. A 168 (1992) 308.
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Properties of a water potential model
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Water potential model:
K
Voo (r ) =
K
A
12
roo
-
B q+ q +
.
6
roo
roh
G
K = d2V(r)/dradra’
K
The vibration frequencies can be
obtained by diagonalsing the dynamics
matrix D(q):
[D(q) –Ω2(q)] A(q) = 0,
where
D(q) = F(q)X(q)
Solutions:
ω = ωk(q).
Density of states:
Diamond-like structure
G(ω) = Σq,k (Ak(q))2(ω-ωk(q)).
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LD simulations for ice Ih
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Potential models (phonon):
(S.L. Dong, thesis, 1999, UMIST)
Using lager super cells (64 molecules)
Large BZ integration (Q points 10x10x10)
Results:
•The features are very sensitive to the
potentials function used.
•The optic peaks at ~30 meV vary.
•Only one dominated optic peaks.
•The librational band shifts from one potential
function to another.
None of them produces the main features
seen in IINS spectrum.
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MD simulations for ice Ih
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Potential models for ice Ih:
(JC Burnham, thesis, 2000, UMIST)
•
super cells (512 molecules)
•
using different potential functions
•
MD step: 0.4fs for 40,000 steps
Results:
•
The features are very similar to LD
results
•
Only one dominated peaks
•
The liberation band shifts from
one potential function to another
•
None of the methods produce the
main features seen in IINS
spectrum
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Translation vibrations
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Estimate of the force act
one the two optic peaks:
w = (K/m)1/2
w1(27) : w2(36) = (K1: K2)1/12
K1: K2 = (27 : 36)2 ~ 1: 1.8
Proposals:
* The force constant difference
comes from orientations of the
ice crystal (Ranker 1972)
Single crystal experiments show no
orientation differences.
•It comes from the relative
orientation of two water
molecules
The difference from charge
interaction is too small to account
for….
…
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2 H-bond model
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(B) & (D)  Kw = 1.1 eV Å-2
(A) & (C)  Ks = 2.1 eV Å-2
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Lattice Dynamics
Lattice dynamic simulation for ice Ih:
* 64 molecules super-unit cell,
* rigid molecules,
* full BZ integration.
Using different ratio of the two
force constants:
Ks : Kw
Results:
• The splitting optic peaks require
two K values.
•
The shapes of the two peaks are also
correlate presented from the
disordered structure.
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Ks : K w
1:1
1 : 1.3
1 : 1.5
1:1.8
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Ab initio calculations
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8 Water molecules
S.S. Xantheas Battele/PNNL…
M. Heggie and S. Maynard, CPL. (1996).
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Summary
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Water models?
q
V=C
Voo ( r ) = (
V = LJ
A
12
roo
-
B
q+ q )
F
(
q
)
+
+ ( pol ).
6
roo
roh
If the model is correction, it may provide:
– necessary mechanism to explain most of water anomalies,
– way to study the structure of water in biology,
– better understanding of water in biological processes.
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Water in bio-molecules
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Studies of water is traditionally difficult:
1. The structures of the hydration water around DNA/proteins
are disordered.
2. Diffraction techniques are less effective,
* X-ray can not see H positions
* neutron has low resolution
* the scattering signal dominates from the bio-molecule
- SPP(Q) + SPW(Q) + SWW(Q)....
IINS is powerful way to identify the local structures of water
by comparing known ice spectra, the local structure of
water inside around DNA/proteins can be identified.
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Water inside and around DNA
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DNA, the most important biomolecule, interacting with water
determines to a large extent its
structure and functions.
Understanding of the interaction
of water inside and around DNA
is fundamentally important.
INS as a complementary
technique has an important role
to play.
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Water in Proteins
•
The different local structures of
water clusters are of difference
vibrational signatures.
•
Change of a proton position could
alter the local proton
configurations and hence H-bond
strengths.
•
These features can be detected by
inelastic incoherent neutron
inelastic neutron scattering
techniques.
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Water
clusters
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Water in DNA at different hydration levels
On TOSCA at ~10K
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Ice Ih
Arbitrary units
On HET at ~10K
DNA 75%
hydrated
Ice Ih
High density
amorphous ice
Intensity (Arbitrary units)
Intensity (Arbitrary units)
O-H strengthening
DNA 100% water
DNA 50% water
DNA 20% water
360
380
400
420
440
460
Energy transfer (meV)
C-H strengthening
DNA 11% water
0
50
100
Energy transfer (meV)
150
200
340
360
380
400
420
440
460
480
Energy difference (meV)
Ilias Michalarias, Ilir Beta, Jichen Li, et al, J Molecular liquid 101 (2002) 19-26.
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INS spectra for amorphous ices (H2O)
hda: density 1.17 g/cm3, prepared at 12 Kbar at >77K.
lda: density 0.98 g/cm3, recovered from hda.
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Dep-lda: deposit water vapor on
cold surfaces (~10K).
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10
50
100
4
2
0
60
75
Energy Transfer (meV)
5
0
0
6
S(Q,w) (abs.units)
S(Q,w) (abs.units)
--- lda ice = ice Ih, Ic
S(Q,w) (abs.units)
*** hda ice
Ice-Ih
HDA®LDA ice
Dep-LDA ice
hda ice
ice Ih
0
30
60
90
120
Energy Transfer (meV)
Energy Transfer (meV)
A. Kolesnikov, J.C. Li, S.L. Dong, I. Balley, W. Hahn. R. Eccelston and S. Parker, PRL. 79 (1997) 1869.
A. Kolesnikov, J.C. Li, S. Parker, R. Eccleson and C-H. Loong, Phys. Rev. B. 59 (1999) 3569.
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Water in a protein (PSII)
We chose PSII because it is
• easily obtained from plant leaves,
• easily purified.
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TOSCA spectrum at 10K
PSII 70% water
IINS spectra show:
• the bonded water is very much like ice
V and VI.
• the bonded water extended to single
layer up to 50% water by weight.
PSII 50% water
PSII 10% water
Ice Ih
Stuart V. Ruffle, Ilias Michalarias, Jichen Li and Robert C.
Ford, J. Amer. Chem. Soc. 124 (2002) 565-569.
Ilias Michalarias, Ilir Beta, Robert Ford, Stuart Ruffle, 0
Jichen Li, Applied Physics A 74 (2002) S1242-1244.
50
100
150
200
Energy transfer (meV)
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Bulk water and bound water
(a) Water around protein
(Photosystem II)
(b) Water around DNA
7
4
3.5
6
bulk
3
arbitrary units
5
arbitrary units
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4
3
2
2.5
2
bound
1.5
bound
1
1
bulk
0.5
0
0
0
20
40
60
80
g w ater/ 100g m em branes
100
0
20
40
60
80
100
g water/100g DNA
SV Ruffle, I Michalarias, JC Li and RC. Ford, JACS 124 (2002) 565-569.
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Water in biopolymers
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Gelatin is widely found in skin, bones and
tissue.
Gelatin with water
Water content effects its structure and hence
physical properties.
80
Features seen in the polymers are very much
close to ice Ih at very low hydration level
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CHOH
CH2
CH2
H 2C
CH2
CO
NH
N
CH
CH2
NH
CO
CO
CH2
H2C
CH
NH
CO
CO
R
N
NH
CH
CO
R
Gelatin
CH2OH
CO
ice
40
50%water
20
0
20%water
0
50
100
150
200
Energy transfer E1-E2 (mev)
CH2OH
O
OH
CH
neutrons/mev transfer
- indicating the water within the layer structure
of polymer is very well structured.
50%-18%
75%-18% + 12
ice
O
O
NHCOCH3
chitosan
OH
G.L. Wu, I.A. Beta, J.B. Ma and J.C. Li,
Applied Physics A 74 (2002) S1267.
NHCOCH3
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Summary
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From these exercise, we can learn:
1. We can obtain the percentage of the bonded water and free water.
2. The local structures of water around these biomolecules studies.
However, we can not tell how the water molecule bonded with these
molecules and their exact bonding sites.
To answer this question or to get more precise informational about
water bonding sites, we would like to study:
- hydration of water in amino acids – the building block of proteins…
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Proteins and 20 amino acids
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Proteins are large
Peptides of defined
amino acids sequence.
(The sequences is
predetermined by gene).
Third and forth
level of structures
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Amino acids – the building blokes proteins
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Alanine
Amino group
carboxyl group
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IINS spectra for amino acids (dry) at T~10K
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Am ino Acide (dr y)
IINS spectra show:
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Alanine
1.Sharp features in E<200meV.
The features are about 200
meV are mainly O-C and O-H
vibrations.
50
40
Glutamate
2.These are H wagging, rotating.
i.e. 1D/2D motions of H atoms.
3.The features are very
different from IR/Raman
spectra. Very little known
these vibrations from
literature.
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Glycine
20
10
Serince
0
0
50
100
150
200
Ene r gy Tr ans fe r (m e v)
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Glycine: dry and wet (1 mol water)
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gly(wet-dry*20%)
dry
8
gly-dry
18
6
Intensity
20
gly-wet
4
2
0
16
-10
10
30
50
70
90
110
130
150
Energy difference (m ev)
14
5
12
Intensity
4
10
wet
3
2
1
0
8
-10
10
30
50
70
90
110
130
150
Energy difference (m ev)
6
gly(wet-dry*80%)
4
4
3
Intensity
Intensity
gly(w et-dry*60%)
2
0
-10
10
30
50
70
90
110
Energy difference (mev)
130
150
2
1
0
-10
-1
10
30
50
70
90
110
130
150
Energy difference (mev)
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Serince: dry and wet (1 mol water)
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16
ser-wet
wet
12
14
12
10
8
6
4
2
0
Intensity
14
10
-10
10
30
8
50
70
90
110
130
150
Energy difference (mev)
wet-1.5*dry
6
12
10
4
dry
2
0
-10
Intensity
Intensity
wet-dry
ser-dry
8
6
4
2
0
-10
10
30
50
70
90 110 130 150
10
30
50
70
90
110
130
150
Energy difference (mev)
Energy difference (mev)
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Glutamate: dry and wet (1 mol water)
18
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glu(w-d*20%)
glu-dry
14
glu-wet
8
Intensity
16
6
4
2
0
-10
10
10
30
50
70
90
110
130
150
110
130
150
Energy difference (mev)
dry
8
glu(w-d*50%)
6
5
4
4
Intensity
Intensity
12
2
0
-10 10
wet
3
2
1
0
-10
-1
10
30
50
70
90
Energy difference (mev)
30
50
70
90 110 130 150
Energy difference (mev)
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Typical IR/Raman spectra
For glycine, hydration shows very
little effect on the spectra
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For serine, the hydration affects
the spectra considerably.
COH bending
+
NH3 deformation
5mol water
Intensity(a.u.)
Intensity(a.u.)
5mol water
3mol water
2mol water
3mol water
2mol water
1mol water
1mol water
dry serine
dry glycine
400
600
800
1000
1600
-1
Raman shift (cm )
1800
1100
1200
1300
1400
1500
1600
1700
1800
1900
-1
Raman shift (cm )
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Ab initio simulations
IWCMB09 16, Sept. 09
•
Do not require pre-knowledge about the
interactions.
•
Large number of academic and commercial
packages avaliable:
- Guassian 03, DMol3 (Basis sets to present ψ)
- CASTEP, VASP (wavefunction to present ψ)
To calculate vibrational spectrum
requires ab initio MD
16
8
- slow (need very powerful HPC)
14
- can not deal with large systems
12
10
Intensity (arb. units)
(a)
Intensity (arb. units)
•
120.99
6
124
114.31
55.15
106.02
4
18.67
32.92 45.45
59.51
71.74
77.23
2
64.85
109.15
37.77
8
0
20
40
60
150
107
100.69
80
100
120
140
148
143
Energy transfer (meV)
6
109
77
71
4
54
28
2
10
23
6
37
66
48 59
114
141
137
135
99
121
176
171
180
182
166
163
0
0
50
100
150
Vibrational Energy (meV)
200
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Animation results
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39
Conclusion
IWCMB09 16, Sept. 09
• IINS is very powerful tool for the studies of the structures and dynamics
of water around biological systems:
* It does not need high quality single crystals
* The H-bond vib. frequencies is lower than others, easily to be studied.
* Deuteration of samples provides exclusion/selection of modes.
• A large number of spectra and knowledge of water cumulated in the
past put us in a unique position to attack the very interesting question
about the role of water in biological systems.
- the role of water in biological systems,
- the body temperatures for mammals (~37oC).
• The work was supported by both EPSRC and BBSRC.
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Acknowledgement
Experimental work:
Professor D.K. Ross (ices)
Professor J.C. Finney (ices)
Professor W. Sherman (ices)
Dr R.W. Whitworth (ices)
Dr D. Blake (Ice in space)
Dr B. Ford (biology)
Dr A. Kolesnikov
Dr C. Loong
Dr I. Beta
Dr Y. Wang
Mr I. Michalarias
•
•
Univ. of Salford
UCL
King’s College
Univ. of Birmingham
NASA/Ames
BMS/UMIST
IPNS/ANL
PINS/ANL
UMIST
UMIST
UMIST
IWCMB09 16, Sept. 09
Ab intio (water clusters and ice):
Dr M. Panye
University of Cambridge
Dr S.S. Xantheas
Battelle/PNNL, Richland
Dr I. Morrison
University of Salford
MD/LD simulations (water clusters and ice):
Dr M. Leslie
Daresbury Laboratory
Dr W. Smith
Daresbury Laboratory
Dr C.J. Burnham
UMIST, Battelle/PNNL
Mr R. Aswani
UMIST
EPSRC funding of ~£1.5M (AF/94/1868, GR/K57121, GR/K32562, GR/K54717, GR/L41653,
35775, 94932, GR/M74689, GR/R98778…)
ISIS, ILL, LLB and IPNS for providing the neutron beam time.
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