Biochemie IV

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Biochemie IV Struktur und Dynamik von
Biomolekülen II. (Mittwochs 8-10 h, INF 230,
klHS) 30.4. Jeremy Smith Intro to Molecular
Dynamics Simulation. 7.5. Stefan Fischer
Molecular Modelling and Force Fields. 14.5. Matthi
as Ullmann Current Themes in Biomolecular
Simulation. 21.5. Ilme Schlichting X-Ray
Crystallography-recent advances (I). 28.5. Klaus
Scheffzek X-Ray Crystallography-recent advances
(II). 4.6. Irmi Sinning Case Study in Protein
Structure. 11.6. Michael Sattler NMR
Applications in Structural Biology. 18.6. Jörg
Langowski Brownian motion basics. 25.6. Jörg
Langowski Single Molecule Spectroscopy. 2.7.
Karsten Rippe Scanning Force Microscopy. 9.7.
Jörg Langowski Single Molecule
Mechanics. 16.7. Rasmus Schröder Electron
Microscopy. 23.7. Jeremy Smith Biophysics, the
Future, and a Party.
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PeptideMembrane Interactions
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GRAMICIDIN
S - cyclo(Leu-DPhe-Pro-Val-Orn)2 -
Powerful but nonspecific antimicrobial agent. -
Principal target bacterial or erythrocyte
membranes.
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Structure- Antimicrobial Activity
Relationships Two basic residues
(e.g. Orn) on same face -
required. Hydrophobic residues in Leu/Val
positions - required. ? sheet and ?
turns - required. Sidedness
Hypothesis (Schwyzer, 1958, Kato
Izumiya, 1977)
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Molecular Dynamics of Gramicidin S in
DMSO Backbone Stays in one conformation
Average deviation from NMR 18o
NMR Xu et al 1995.
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Order parameters of the sn-2 chains of DMPC.
Hydrated DMPC -Douliez et al 1975
Bound Lipids - Disordered
?Free lipids - more ordered
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Scattering Experiments
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Lysozyme in explicit water
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Scattering of X-Rays by Protein Crystals
STÉPHANIE HÉRY DANIEL GENEST
Real Crystal
Ideal Crystal

Perturbations

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Molecular Dynamics of Lysozyme Unit Cell
Full Trajectory
Experimental
Rigid-Body Decomposition
Rigid-Body Fit (R-factor re Full Trajectory
5.3)
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FRANCI MERZEL
Protein Hydration.
Svergun et al PNAS 1998 First 3Å hydration
layer around lysozyme 10 denser than bulk
water
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Geometric Rg from MD simulation 14.1?0.1Å
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Bulk Water
d
Bulk Water Average Density
Present Even if Water UNPERTURBED from Bulk
?o(d)
Bulk Water
Radial Water Density Profiles
Water
Protein
?o(d) ? 10 increase
?o(d)- ?(d) Perturbation from Bulk
? 5 increase
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What determines water density variations at a
protein surface?
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Simple View of Protein Surface
(1) Topography
hSurface Topographical Perturbation
Protuberance
L3 surface
Depression
L17 surface
(2) Electric Field
qi
qj
qk
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Surface Topography, Electric Field and Density
Variations
Low ?
High ?
O
High ?
H
H
High ?
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Conclusions
(1) Simulation and Experimental I(q) in Good
Agreement
(2) First Hydration Layer (0-3Å) 15
Density Increase of which - 10
Unperturbed - 5 Perturbed
Fewer Disorienting Bulk Water Dipoles
Water Dipoles Align with Protein E Field
Water Density Variations Correlated with
Surface Topography and Local E Field from
Protein
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Macromolecular Complexes
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More Proteins
Protein 1
Protein 2
Complex Formation
Conformational Change
Function
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Structures of Macromolecular Complexes

• Very few experimentally determined
• e.g. antibodiesantigens
• 1000 antibody sequences known
• 100 antibody structures known
• 10 antibodyantigen complex structures known
• Can we use calculation?

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Homology Modelling

• Can derive structures for sequences with
• gt20-30 sequence identity when aligned with
• sequence of known structure.

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• Structures of Isolated Components?
• - crystallography
• - NMR
• - Homology Modelling

• Structure of Complex?
• Rigid-Body Shape Complementarity
• (based on hydrophobic effect and van der Waals
  packing)
• Conformational Change on Complexation?
• Electrostatic Complementarity?
• Solvation Effects?
• Experiment?

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Functional Binding Site on Toxin ? Red Affinity
Lowered gt100-fold Yellow Affinity Lowered 10-100
fold
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Modelling of Isolated Antibody
Homology Model of Framework Residues.
Complementarity Determining Region Loops
(CDRs) (i) Uniform Conformational Searching (ii)
Canonical Loop Modelling (iii) Data-Base
Searching of Loop Conformations (iv) Molecular
Dynamics in vacuo and with solvated CDRs. gt 90
models.
Clustering and Screening for Consistency with
Experimental Antibody Structures.
4 Dynamically Interconvertible Models.
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Modelling of AbAg Complex
Initial Generation Low -Resolution Shape
Complementarity. gt 41,585 models
Clustering and Screening for (i) Buried Surface
Area. (ii) Electrostatic Complementarity. (iii)
Consistency with existing AbAg complex
structures. gt 18 models.
Refinement of Atomic-Detail Models with Molecular
Dynamics in Explicit Solvent.
6 Models.
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Toxin ? and M ?23 Functional Binding Sites
Red - gt100 fold affinity loss on mutation
Yellow - 10-100 fold affinity loss on mutation
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Three Models of Calculated M?23 Paratope Red
Residues contacting antigen energy core Yellow
Residues contacting functional epitope
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Orientation of toxin ? on M?23 combining site in
the two remaining models.
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Annexin V - Pathway for Conformational Transition
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Charge Transfer in Biological Systems

• Ions, Electrons...

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NICOLETA BONDAR MARCUS ELSTNER STEFAN
FISCHER SANDOR SUHAI
Proton Transfer Step 1 in Bacteriorhodopsin