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Basics of Molecular modelling _2History,Interdisciplinary classification, Goals, Model definition,Molecular mechanics forcefields,Energy minimization algorithmsMolecular dynamics simulationComparative modelling (homology modelling)Simulated annealingScanning conformational space of a moleculeMolecular properties as recognition patterns

Gerd Krause, Structural bioinformatics and protein design Leibniz-Institute of molecular Pharmacologywww.fmp-berlin.de/GKrause.html

G Krause

Molecular dynamic simulations

-enablescharacterizing of molecule properties and movementover a time scale

G Krause

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- Evaluation of geometric stability larger molecular structures (Protein (Homology models)

- conformational change of molecules at room temperature- since all biological processes are running at 310 Kelvin,

( but potential energy of force field are calculated at 0 K !!)

- considering of kinetic energy.

- geting over theproblem of multiminima of proteins(Simulated Annealing)

- study of structural and thermal energies- study of functional properties of fast biological processes(10–12 –10-9 sec)

tasks for molecular dynamic Simulations

G Krause

F = m a

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Newtons equationis used to simulate atom movement

G Krause

force At each atomcalculated from energy changebetween current position and a position in a small distance

Energy caculation from molecular mechanics

By means of Atom forces and massesarepositions of each atom calculated along a

series of extreme short time steps(femto Second=1015 Second) .

Resulting snapshots of structural changes:

Trajectory

F = m a

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TrajectorySubdivide between two states into large number of sub-statesBy extreme small time steps ( 1 femto Seconds)

Initiale Atom position at time t is used predictingAtom positions at time t + delta t Atom position at time t + delta t is used predictingatom position at tie t + 2 delta t etc.

G Krause

Dynamic Trajectory: - resting at start point a -> after initial movement going with constant total energy

(kinetic E. + potential E.), - initialer Gradient pulls Particle in the valley- portion of accelaration inceases in direction of d (potential Energy decreases)- kinetic energy moves particle forth and back,

therfore running through many points at the surface (b, c)

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2. Initial movement assigned to all atoms , is dictated by choosen temperature

3. Equilibration phase: slow heating e.g. from 0K to 310 KEnergy compensation between the atoms

4. Data production phase: Trajektory e. g. at constant temperature.

1. Start structure: conformation of low energy

Phases of MDEpot

time 1.2. 3. 4.

G Krause

Statistic EnsemblesN: number ParticlesV: VolumenT: TemperatureE: EnergyP: pressure

Canonical : constant –NVT Temp-Bath couplingVacuo without periodic conditions

Micro-canonical: : constant –NVE Energy-couplingsurface const. Energy

Isothermal-isobaric : constant –NPT constant pressure and temp

Randbedingungen der MD - Statistische Ensembles- Periodic boundary conditions- Explicit image model- Nonbond cutoff

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Periodic boundary conditions

Randbedingungen der MD

G Krause

ETA RECEPTOR

Docking strategy –constrained

MD supported dockingof peptide ligand

J. LättigG Krause

ET1

experimentally determined contact points(mutants)

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de Groot B, Grubmüller H, Science 2001

MD water channel Aquaporin

G Krause

de Groot B, Grubmüller H, Science 2001 G Krause

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Molecular modelling _2History,Interdisciplinary classification, Goals, Model definition,Molecualr mechanics forcefields,Energy minimization algorithmsMolecular dynamics simulationComparative modelling (homology modelling)

G Krause

Application ofProtein Structure Models

Depending much on accuracy and reliability of the model:– Studying catalytic mechanism– Designing and improving ligands– Docking of macromolecules– Prediction of interacting protein partners– Virtual screening of small ligands– Defining antibody epitopes– Designing chimeras, stable and crystallizable variants– Supporting site-directed mutagenesis– Refining NMR structures– Fitting proteins into low-resolution electron density maps– Functional site identification by 3D Motif searching– Fold assignment => annotating function & establishing evol. Relationships– Facilitate prediction of genes e.g. Drosophila

In principle: every application for structuresIn principle: every application for structuresG Krause

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structuralbioinformatics

Comparative modelling

G Krause

Comparative modeling

Target sequence

Homologous Proteine(s)

Alignment

Model building

Refinement

Model evaluationG Krause

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Similar/common Sequence function

Sequence -> fold -> function

Sequence fold -> function

fold function

qerry: homolog

protein, proteindomain, domainmotif motif

G Krause

Comparative Modeling

-Studying catalytic mechanismactivation mechanism

-Designing and improove ligands-Docking of macromolecules

Prediction of protein partners-Virtual screening and docking of small molecules-Defining antibody epitopes-Support site directed mutagenesis

-Refining NMR structures-Structures from sparse experimental restraints

-Functional relationships from structural similarity-Finding functional sites by 3D –motif searches

qerryhomolog Application of Protein Structure Models

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hTSHR 3.32TVFASELSV3.40 4.57ALLP4.60 560ISSYAKVSICLPMD573hLHCGR 3.32TVFASELSV3.40 4.57ALLP4.60 505VSNYMKVSICFPMD518

hTSHR 5.34PLALAYIVFVLTLN5.47 6.48MAPISFYALSAI6.59 7.39VLFY7.42hLHCGR 5.34TLSQVYILTILILN5.47 6.48MAPISFFAISAA6.59 7.39VLFY7.42

TMH3 TMH4 ECL2

TMH5 TMH6 TMH7

A

B

Jaeschke et al. JBC 2006

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AminosäurenZu überprüfende Backbone Struktur

phi / psi Winkel-Bereiche typischer Sekundärstrukturelemente

Progamm PROCHECK

Comparative Modelling

G Krause

Molecular modelling _2History,Interdisciplinary classification, Goals, Model definition,Molecualr mechanics forcefields,Energy minimization algorithmsMolecular dynamics simulationComparative modelling (homology modelling)Simulated annealing

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Datensammlung (n Konformationen)Satz von n Konformationeneine Konformationsfamilie

Temp

Zeit

n x ( Aufheizen + Abkühlung )Überwindung

Energiebarrieren

Wirkung des Kraftfeldes+ experimentelle Restraints(Standardgeometrien) (zB. NOE Abstands-Bereich)

Simulated annealing

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NMR spectroscopy

Austausch der Magnetisierungszuständeführt zuexp. Atomabständen zB. NuclearOverhauserEffects

(NOE)

(blau gestrichelt)

werdenals restraintsbenutzt

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NMR spectroscopy

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Konformationsensemblenach Simmulated Annealing

Cα Atom trace

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NMR spectroscopy

Figure 2. a) Surface representation of the AF6 PDZ domain without ligand, 1XZ9. Surface coloring indicates hydrophobic (yellow) and hydrophilic (green) areas. b) AF6 PDZ domain in complex with 5 f. Surface coloring indicates hydrophobic (yellow) and hydrophilic (green) areas. The hydrogen bonding interaction between the PDZ domain and 5 f are shown as yellow-dotted lines. c) Schematic representation of the AF6 PDZ-5 f interaction. Hydrogen bonds are shown as green-dotted lines. Hydrophobic interactions are highlighted by red line fences.Joshi et al. 2006 Angew. Chemie Intern. Ed

Protein-protein interaction profiles ofPDZ domain and C-terminal peptides of proteins

lead to patterns for preferreddocking poses of small molecules into binding pocket