water. buried water molecules -binding -reactions surface water molecules -structure -dynamics...
TRANSCRIPT
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Water
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Buried Water Molecules-Binding-Reactions
Surface Water Molecules-Structure-Dynamics-Effect on Protein Motions
Water in and on Proteins
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A-insideB-low densityC-high densityD-bulk
MD Simulation of Myoglobin
Svergun et al:
First 3Å hydration layer around lysozyme ~10% denser than bulk water
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Lysozyme in explicit water
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Low q :Size
Radius of Gyration (Rg)
Include Higher q :Chain Configurational
Statistics
q(Å-1)
P(q)
Small Angle Neutron Scattering
rijbibj
0 0.1 0.2 0.30
0.2
0.4
0.6
0.8
1
ki
kf
ki
kfq
array detector
Sample
L ~ 5 - 50 m
n
1i
n
1jji qrij
qrsin ijbb
n21
)q(PqR
3
11~)q(P 2
g
0q
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First 3Å hydration layer around lysozyme ~10% denser than bulk water
Surface Water Molecules-Structure
Svergun et al PNAS 95 2667 (1998)
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Geometric Rg from MD simulation = 14.10.1Å
SMALL-ANGLESCATTERING
RADII OF GYRATION
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o(d)- (d) = Perturbation from Bulk
o(d) 10% increase
5% increase
Radial WaterRadial WaterDensity ProfilesDensity ProfilesProtein
Water (d)
(d)
Bulk Water Average Density
Bulk Water
d
Bulk Water
o(d) Present Even if Water UNPERTURBED from Bulk
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What determines variationsin surface water density?
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Simple View of Protein SurfaceSimple View of Protein Surface
(1) Topography
Protuberance
Depression
(2) Electric Field
qi
qj
qk
h=Surface Topographical Perturbation
L=17surface
L=3surface
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Surface Topography, Electric Field and Density VariationsSurface Topography, Electric Field and Density Variations
Low
High
O
H HHigh
High
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Water Dipoles Align withProtein E Field
Water Density Variations Correlated with Surface Topography and Local E Field from Protein
Physical Picture:Physical Picture:
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Hydration of hydrophobic molecules
Small molecules• Bulk-like water • “WET”
Large Exposed Surface Area
• Fewer hydrogen bonds
•“DEWETTING”
Same effect in peptides?
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Prion Peptide - MKHMAGAAAAGAVV
Exposed Hydrophobic Surface Area (nm2)
Hyd
rati
on S
hell
Den
sity
(nm
-2)
densityaround hydrophilicgroups
density around hydrophobicgroups
“DRY”
“WET”
hydrophobic analog
ISABELLADAIDONESame effect in peptides?
LowestFreeEnergy
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Free Energy Profile
Met 109 (H) –Val 121 (O) (nm)
0 0.2 0.4 0.6 0.8 1.0 1.2 1.4
Stable at Low Hydration Density
Stable at High Hydration Density
Hydrophobic Hydration Shell Density (nm-2)
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1. MD Simulations and Normal Mode Analysis of Myoglobin
2. Langevin Analysis of each ´´MD normal mode´´ Velocity Correlation Function
(0) ( ) exp( / 2)(cos sin )2nn
nn nn n nn
v v t t t t
KEIMORITSUGUEffect of Water on Protein Vibrations
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Effect of Hydration on Protein Vibrational Motions
solvation
vacuum PES water PES
Increase of friction Shift to high frequencies
Friction changes Frequency shifts
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Protein:Protein Interactions.Vibrations at 150K
VANDANAKURKAL-SIEBERT
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1. MD Simulation
2. Langevin Analysis of Principal Component Coordinate Autocorrelation Function.
0
0
exp( / 2)(cos( s 10) ( ) ( )1
in ))
2
exp(vv v v
vn n t t tx
t
tx t
KEIMORITSUGUDiffusive and Vibrational Components
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Diffusion-Vibration Langevin
Description of Protein Dynamics
Linear increase of vibrational fluctuationsv.s.
Dynamical transition of diffusive fluctuations
KEIMORITSUGU
Assume Height of Barrier given by Vibrational Amplitude.
Find: V~