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Water

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

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  1. Water

  2. Water in and on Proteins Buried Water Molecules -Binding -Reactions Surface Water Molecules -Structure -Dynamics -Effect on Protein Motions

  3. 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

  4. Lysozyme in explicit water

  5. Small Angle Neutron Scattering P(q) q(Å-1) Include Higher q : Chain Configurational Statistics Low q : Size Radius of Gyration (Rg)

  6. Surface Water Molecules -Structure First 3Å hydration layer around lysozyme ~10% denser than bulk water Svergun et al PNAS 95 2667 (1998)

  7. RADII OF GYRATION Geometric Rg from MD simulation = 14.10.1Å SMALL-ANGLE SCATTERING

  8. 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

  9. What determines variations in surface water density?

  10. (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

  11. Surface Topography, Electric Field and Density Variations Low  High  O High  H H High 

  12. Physical Picture: Water Dipoles Align with Protein E Field Water Density Variations Correlated with Surface Topography and Local E Field from Protein

  13. Hydration of hydrophobic molecules Small molecules Bulk-like water “WET” • Large Exposed Surface Area • Fewer hydrogen bonds • “DEWETTING” Same effect in peptides?

  14. 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)

  15. 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

  16. 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

  17. Friction changes Frequency shifts solvation vacuum PES water PES Effect of Hydration on Protein Vibrational Motions Shift to high frequencies Increase of friction

  18. Protein:Protein Interactions.Vibrations at 150K VANDANA KURKAL-SIEBERT

  19. KEI MORITSUGU Diffusive and Vibrational Components 1. MD Simulation 2. Langevin Analysis of Principal Component Coordinate Autocorrelation Function.

  20. 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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