1. Water

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

3. A-inside B-low density C-high density D-bulk MD Simulation of Myoglobin Svergun et al: First 3Å hydration layer around lysozyme ~10% denser than bulk water

4. Lysozyme in explicit water

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

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

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

8.  o (d)-  (d) = Perturbation from Bulk  o (d)  10% increase  5% increase Radial Water Density Profiles Protein Water  (d) Bulk Water Average Density Bulk Water d Bulk Water  o (d) Present Even if Water UNPERTURBED from Bulk

9. What determines variations in surface water density?

10. Simple View of Protein Surface (1) Topography Protuberance Depression (2) Electric Field qiqi qjqj qkqk h=Surface Topographical Perturbation L=17 surface L=3 surface

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

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

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

14. Prion Peptide - MKHMAGAAAAGAVV Exposed Hydrophobic Surface Area (nm 2 )Hydration Shell Density (nm -2 ) density around hydrophilic groups density around hydrophobic groups “DRY” “WET” hydrophobic analog ISABELLA DAIDONE Same effect in peptides? Lowest Free Energy

15. Free Energy Profile Met 109 (H) –Val 121 (O) (nm) 00.20.40.60.81.01.21.4 Stable at Low Hydration Density Stable at High Hydration Density Hydrophobic Hydration Shell Density (nm -2 )

16. 1. MD Simulations and Normal Mode Analysis of Myoglobin 2. Langevin Analysis of each ´´MD normal mode´´ Velocity Correlation Function KEI MORITSUGU Effect of Water on Protein Vibrations

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

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

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

20. Diffusion-Vibration Langevin Description of Protein Dynamics Linear increase of vibrational fluctuations v.s. Dynamical transition of diffusive fluctuations KEI MORITSUGU Assume Height of Barrier given by Vibrational Amplitude. Find:  V~ 