water. buried water molecules -binding -reactions surface water molecules -structure -dynamics...
TRANSCRIPT
Water
Buried Water Molecules-Binding-Reactions
Surface Water Molecules-Structure-Dynamics-Effect on Protein Motions
Water in and on Proteins
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
Lysozyme in explicit water
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
First 3Å hydration layer around lysozyme ~10% denser than bulk water
Surface Water Molecules-Structure
Svergun et al PNAS 95 2667 (1998)
Geometric Rg from MD simulation = 14.10.1Å
SMALL-ANGLESCATTERING
RADII OF GYRATION
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
What determines variationsin surface water density?
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
Surface Topography, Electric Field and Density VariationsSurface Topography, Electric Field and Density Variations
Low
High
O
H HHigh
High
Water Dipoles Align withProtein E Field
Water Density Variations Correlated with Surface Topography and Local E Field from Protein
Physical Picture:Physical Picture:
Hydration of hydrophobic molecules
Small molecules• Bulk-like water • “WET”
Large Exposed Surface Area
• Fewer hydrogen bonds
•“DEWETTING”
Same effect in peptides?
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
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)
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
Effect of Hydration on Protein Vibrational Motions
solvation
vacuum PES water PES
Increase of friction Shift to high frequencies
Friction changes Frequency shifts
Protein:Protein Interactions.Vibrations at 150K
VANDANAKURKAL-SIEBERT
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
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~