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Water. Water in and on Proteins. Buried Water Molecules -Binding -Reactions Surface Water Molecules -Structure -Dynamics -Effect on Protein Motions. MD Simulation of Myoglobin. A-inside B-low density C-high density D-bulk. Svergun et al:

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Water


Water in and on Proteins

Buried Water Molecules

-Binding

-Reactions

Surface Water Molecules

-Structure

-Dynamics

-Effect on Protein Motions


MD Simulation of

Myoglobin

A-inside

B-low density

C-high density

D-bulk

Svergun et al:

First 3Å hydration layer around lysozyme ~10% denser than bulk water


Lysozyme in explicit water


Small Angle Neutron Scattering

P(q)

q(Å-1)

Include Higher q :

Chain Configurational

Statistics

Low q :

Size

Radius of Gyration (Rg)


Surface Water Molecules

-Structure

First 3Å hydration layer around lysozyme ~10% denser than bulk water

Svergun et al PNAS 95 2667 (1998)


RADII OF

GYRATION

Geometric Rg from MD simulation

= 14.10.1Å

SMALL-ANGLE

SCATTERING


Bulk

Water

(d)

d

Bulk Water

Average Density

Present Even if

Water UNPERTURBED

from Bulk

o(d)

Bulk

Water

(d)

Water

Protein

o(d)  10% increase

o(d)- (d)

= Perturbation

from Bulk

 5% increase

Radial Water

Density Profiles


What determines variations

in surface water density?


(1) Topography

h=Surface Topographical

Perturbation

Protuberance

L=3

surface

Depression

(2) Electric Field

L=17

surface

qi

qj

qk

Simple View of Protein Surface


Surface Topography, Electric Field and Density Variations

Low 

High

O

High

H

H

High


Physical Picture:

Water Dipoles

Align with

Protein E Field

Water Density Variations

Correlated with

Surface Topography

and Local E Field from Protein


Hydration of hydrophobic molecules

Small molecules

Bulk-like water

“WET”

  • Large Exposed Surface Area

  • Fewer hydrogen bonds

  • “DEWETTING”

Same effect in peptides?


ISABELLA

DAIDONE

Same effect in peptides?

Prion Peptide - MKHMAGAAAAGAVV

Lowest

Free

Energy

density

around hydrophilic

groups

“WET”

Hydration Shell Density (nm-2)

“DRY”

density around

hydrophobic

groups

hydrophobic analog

Exposed Hydrophobic Surface Area (nm2)


Free Energy Profile

Hydrophobic Hydration Shell Density (nm-2)

Stable at High

Hydration Density

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


KEI

MORITSUGU

Effect of Water on Protein Vibrations

1. MD Simulations and

Normal Mode Analysis of Myoglobin

2. Langevin Analysis of each ´´MD normal mode´´

Velocity Correlation Function


Friction changes

Frequency shifts

solvation

vacuum PES

water PES

Effect of Hydration on Protein Vibrational Motions

Shift to high frequencies

Increase of friction


Protein:Protein Interactions.Vibrations at 150K

VANDANA

KURKAL-SIEBERT


KEI

MORITSUGU

Diffusive and Vibrational Components

1. MD Simulation

2. Langevin Analysis of Principal Component

Coordinate Autocorrelation Function.


KEI

MORITSUGU

Assume Height of Barrier given by Vibrational Amplitude.

Find: V~

Diffusion-Vibration Langevin Description of Protein Dynamics

Linear increase of vibrational fluctuations

v.s.

Dynamical transition of diffusive fluctuations


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