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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


Water

Water in and on Proteins

Buried Water Molecules

-Binding

-Reactions

Surface Water Molecules

-Structure

-Dynamics

-Effect on Protein Motions


Water

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


Water

Lysozyme in explicit water


Water

Small Angle Neutron Scattering

P(q)

q(Å-1)

Include Higher q :

Chain Configurational

Statistics

Low q :

Size

Radius of Gyration (Rg)


Water

Surface Water Molecules

-Structure

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

Svergun et al PNAS 95 2667 (1998)


Water

RADII OF

GYRATION

Geometric Rg from MD simulation

= 14.10.1Å

SMALL-ANGLE

SCATTERING


Water

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


Water

What determines variations

in surface water density?


Water

(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


Water

Surface Topography, Electric Field and Density Variations

Low 

High

O

High

H

H

High


Water

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

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

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

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


Water

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


Effect of hydration on protein vibrational motions

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

Protein:Protein Interactions.Vibrations at 150K

VANDANA

KURKAL-SIEBERT


Water

KEI

MORITSUGU

Diffusive and Vibrational Components

1. MD Simulation

2. Langevin Analysis of Principal Component

Coordinate Autocorrelation Function.


Diffusion vibration langevin description of protein dynamics

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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