proteins are „3d jigsaw-puzzles“ · 2012. 4. 26. · solvent with ionic strength i (high e)...

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Proteins are „3D Jigsaw-Puzzles“

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Page 1: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Proteins are „3D Jigsaw-Puzzles“

Page 2: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Hydrogen Bonds in BPTI

Page 3: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Hydrogen Bonds in BPTI

Page 4: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Protein continuum electrostatics

Page 5: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

X-Ray Crystallography

various protein crystal forms

Page 6: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

X-Ray Crystallography

experimental setup

typical diffraction pattern

Page 7: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

One single atom

real space

Fourier space

phase

Page 8: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

One single atom - shifted

real space

Fourier space

phase

Page 9: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

Two atoms

real space

Fourier space

phase

Page 10: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

One “molecule“

real space

Fourier space

phase

Page 11: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

3 x 3 unit cells

real space

Fourier space

phase

Page 12: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

5 x 5 unit cells

real space

Fourier space

phase

Page 13: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

Electron density from x-ray

10 x 10 unit cells

real space

Fourier space

phase

Page 14: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

X-Ray Crystallography

Levels of resolution

Effect of temperature

Page 15: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

BPTI: Molecular Dynamics (300K)

Page 16: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

A model of Bacteriorhodopsin

Page 17: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

BR photocycle

Page 18: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

t [ps]

C13 – C14

C14 – C15

13-14

14-15

NH

H N

Prot.

Page 19: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

W. Zinth et. al.

Time-resolved Pump-Probe Spectrum of Sensorhodopsin

Page 20: Proteins are „3D Jigsaw-Puzzles“ · 2012. 4. 26. · Solvent with ionic strength I (high e) Ions (mobile) Ion exclusion layer, high e, but 1=0 solvent accessible surface Charges

W. Zinth et. al.

BR J

J K