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Biochemie IV – Struktur und Dynamik von Biomolekülen II. (Mittwochs 8-10 h, INF 230, klHS)
30.4.
7.5.
14.5.
21.5.
28.5.
4.6.
11.6.
18.6.
25.6.
2.7.
9.7.
16.7.
23.7.
Jeremy Smith: Intro to Molecular Dynamics Simulation.
Stefan Fischer: Molecular Modelling and Force Fields.
Matthias Ullmann: Current Themes in Biomolecular Simulation.
Ilme Schlichting: X-Ray Crystallography-recent advances (I).
Klaus Scheffzek: X-Ray Crystallography-recent advances (II).
Irmi Sinning: Case Study in Protein Structure.
Michael Sattler: NMR Applications in Structural Biology.
Jörg Langowski: Brownian motion basics.
Jörg Langowski: Single Molecule Spectroscopy.
Karsten Rippe: Scanning Force Microscopy.
Jörg Langowski: Single Molecule Mechanics.
Rasmus Schröder: Electron Microscopy.
Jeremy Smith: Biophysics, the Future, and a Party.
Peptide:Membrane Interactions
GRAMICIDIN S
- cyclo(Leu-DPhe-Pro-Val-Orn)2
- Powerful but nonspecific antimicrobial agent.
- Principal target : bacterial or erythrocyte membranes.
Structure- Antimicrobial Activity Relationships:
Two basic residues (e.g. Orn) on same face
Hydrophobic residues in Leu/Val positions
 sheet and  turns
- required.
- required.
- required.
: Sidedness Hypothesis (Schwyzer, 1958,
Kato & Izumiya, 1977)
Molecular Dynamics of Gramicidin S in DMSO
Backbone: Stays in one conformation
Average deviation
from NMR: 18o
NMR: Xu et al 1995.
Peptide:Membrane
Interactions
•
•
•
Where does the peptide position itself in the
membrane?
What are its structure and dynamics?
What effect does it have on the lipid structure
and dynamics?
Lipid Order Param eters.
SCD =1/2[3<cos 2q(t)> -1)]
q
C
Etc.
D
Order parameters of the sn-2 chains of DMPC.
Hydrated DMPC
-Douliez et al 1975
Bound Lipids Disordered
Free lipids
- more ordered
Scattering Experiments
Lysozyme in explicit water
Scattering of X-Rays by
Protein Crystals
Real
Crystal
=
Ideal
Crystal
STÉPHANIE HÉRY
DANIEL GENEST
+ Perturbations
Molecular Dynamics of Lysozyme Unit Cell
Experimental
Rigid-Body
Decomposition
Full Trajectory
Rigid-Body Fit
(R-factor re: Full Trajectory = 5.3%)
Protein Hydration.
FRANCI MERZEL
Svergun et al PNAS 1998:
First 3Å hydration layer around lysozyme ~10% denser than bulk water
Geometric Rg from
MD simulation
= 14.10.1Å
Bulk
Water
(d)
d
Bulk Water
Average Density
o(d)
Bulk
Water
Protein
Water
o(d)  10% increase
o(d)- (d)
= Perturbation
from Bulk
 5% increase
(d)
Present Even if
Water UNPERTURBED
from Bulk
Radial Water
Density Profiles
What determines water density
variations
at a protein surface?
Simple View of Protein Surface
(1) Topography
Protuberance
h=Surface Topographical
Perturbation
L=3
surface
Depression
+ (2) Electric Field
qi
qj
qk
L=17
surface
Surface Topography, Electric Field and Density Variations
Low 
High

O
H
H
High

High

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
Macromolecular Complexes
Protein 1
Protein 2
Complex
Formation
Conformational
Change
Function
More
Proteins
Structures of Macromolecular Complexes
• Very few experimentally determined
– e.g. antibodies:antigens
• ~1000 antibody sequences known
• ~100 antibody structures known
• ~10 antibody:antigen complex structures known
• Can we use calculation?
Homology Modelling
Can derive structures for sequences with
>20-30% sequence identity when aligned with
sequence of known structure.
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?
Functional Binding Site on Toxin 
Red: Affinity Lowered >100-fold
Yellow: Affinity Lowered 10-100 fold
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.
> 90 models.
Clustering and Screening for Consistency with
Experimental Antibody Structures.
4 Dynamically Interconvertible Models.
Modelling of Ab:Ag Complex
Initial Generation
Low -Resolution Shape Complementarity.
> 41,585 models
Clustering and Screening for:
(i) Buried Surface Area.
(ii) Electrostatic Complementarity.
(iii) Consistency with existing Ab:Ag complex structures.
> 18 models.
Refinement of Atomic-Detail Models with Molecular Dynamics
in Explicit Solvent.
6 Models.
Toxin  and M 23 Functional Binding Sites
Red - >100 fold affinity loss on mutation
Yellow - 10-100 fold affinity loss on mutation
Three Models of Calculated M23 Paratope
Red: Residues contacting antigen energy core
Yellow: Residues contacting functional epitope
Orientation of toxin  on M23
combining site in the two remaining
models.
Annexin V Pathway for Conformational Transition
W187
A
E228
A
20.0
Phase II
Phase I
Phase III
IV
10.0
ENERGY (kcal/mol)
W187
B
0.0
E234
-10.0
-20.0
-30.0
-40.0
W187
0
0.2
0.4
0.6
REACTION COORDINATE
0.8
1
l
S 7 9
S 7 6
Helix E
S 7 3
S 7 0
S 6 7
S 6 4
S 6 1
Helix D
S 5 8
S 5 5
S 5 2
S 4 9
 helix
coil
B
D226
C
Charge Transfer in Biological Systems
• Ions, Electrons...
NICOLETA BONDAR
Proton Transfer Step #1 in Bacteriorhodopsin
MARCUS ELSTNER
STEFAN FISCHER
SANDOR SUHAI