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 Matthias Ullmann: Current Themes in Biomolecular Simulation Ilme Schlichting: X-Ray Crystallography-recent advances (I) Klaus Scheffzek: X-Ray Crystallography-recent advances (II). 4.6.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 - required. Hydrophobic residues in Leu/Val positions - required.  sheet and  turns - required. : Sidedness Hypothesis (Schwyzer, 1958, Kato & Izumiya, 1977)

Molecular Dynamics of Gramicidin S in DMSO Backbone: Stays in one conformation Average deviation from NMR: 18 o NMR: Xu et al 1995.

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 + Perturbations STÉPHANIE HÉRY DANIEL GENEST

Rigid-Body Decomposition Rigid-Body Fit (R-factor re: Full Trajectory = 5.3%) Molecular Dynamics of Lysozyme Unit Cell Experimental Full Trajectory

Protein Hydration. Svergun et al PNAS 1998: First 3Å hydration layer around lysozyme ~10% denser than bulk water FRANCI MERZEL

Geometric R g from MD simulation = 14.1  0.1Å

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

What determines water density variations at a protein surface?

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

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 Water Dipoles Align with Protein E Field Fewer Disorienting Bulk Water Dipoles Water Density Variations Correlated with Surface Topography and Local E Field from Protein

Macromolecular Complexes

Protein 1 Complex Formation Conformational Change Function Protein 2 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 fold

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. Homology Model of Framework Residues. Modelling of Isolated Antibody

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. Initial Generation Low -Resolution Shape Complementarity. > 41,585 models Modelling of Ab:Ag Complex

Toxin  and M  23 Functional Binding Sites Red - >100 fold affinity loss on mutation Yellow 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

Charge Transfer in Biological Systems Ions, Electrons...

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