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COMPUTERSIMULATION OF COMPLEX. (BIO-)MOLECULAR SYSTEMS. Possibilities, Impossibilities and Perspectives. Thales 600 B.C. observe. model. design experiment. Galileo 1500 A.D. model. observe. model. mimic reality on a computer. Rahman1980 A.D. model. observe. model. - PowerPoint PPT Presentation
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Computersimulation of reality
real world experimentexperimental
data
predictionscomputational
methodsmodel
of the world
classificationabstractionsimplificationapproximationgeneralisation
comparingis
testing
Three important turns in science:
Thales 600 B.C.design experiment
observe modelmodelmodel
model model
Galileo 1500 A.D.
Rahman 1980 A.D.mimic reality on a computer
observe
observe
Computersimulation of biomolecular systems
1) Why
2) How
3) What
4) And the future …
do we simulate ?
1) Why
2) How
3) What
4) And the future …
do we simulate ?
Computersimulation of biomolecular systems
For which problems are simulations useful ?
Simulation can replace or complement the experiment:
1. Experiment is impossible Inside of starsWeather forecast
2. Experiment is too dangerous Flight simulationExplosion simulation
3. Experiment is expensive High pressure simulationWindchannel simulation
4. Experiment is blind Some properties cannot beobserved on very short time-scales and very small space-scales
Simulations can complement the experiment:
Simulation explains experiments Properties of waterFolding of protein molecules
Simulation suggests Design of drugsnew experiments enzymes
less experimentsbetter chance of success
knowledgenew ideas
For which problems are simulations useful ?
The world of molecular simulation and experiment
Simulation and experiment are complementing methodsto study different aspects of nature
experiment simulation
Typical space / time scales
size : 10-3 meter 10-9 meter
time : 103 seconds 10-6 seconds
Resolution*
size : 1023 molecules 1 molecule
time : 1 second 10-15 seconds
*: Single molecules / 10-15 seconds possible (but not both in the liquid phase)
(restricted) (unrestricted)
1) Why
2) How
3) What
4) And the future …
do we simulate ?
Computersimulation of biomolecular systems
Definition of a model for molecular simulation
MOLECULARMODEL
Degrees of freedom: atoms are the elementary particles
Forces or interactions between atoms Boundary conditions
Methods to generate configurations of
atoms: Newton
systemtemperature
pressure
Every molecule consists of atoms that are very strongly bound to each other
Force Field =physico-chemical
knowledge
Choose relevant degrees of freedom: elementary particles
. . .. . .
atomic nuclei + electrons
quantummechanics
electrostatics
all atoms(excluding solvent)
classicalmechanics
Force Field(including solvent)
monomers
classicalmechanics
Force Field(statistic)
Particles:
Description:
all atoms
classicalmechanics
Force Field(atomistic)
Interactions:
Broader applicabilityLess model parameters Physical parametersMore expensive
Restricted applicabilityMore model parameters
Empirical parametersLess expensive
=
Definition of a model for molecular simulation
MOLECULARMODEL
Degrees of freedom: atoms are the elementary particles
Forces or interactions between atoms Boundary conditions
Methods to generate configurations of
atoms: Newton
systemtemperature
pressure
Force Field =physico-chemical
knowledge
Every molecule consists of atoms that are very strongly attached
Interactions in atomic simulaties : Force Field physico-chemical knowledge
Rotation aroundbond
Planaratomgroups
van der Waalsinteractions
Electrostaticinteractions
-+
-
-
Bond stretching
non-bonded interactions
bonded interactions
Angle bending
Definition of a model for molecular simulation
MOLECULARMODEL
Degrees of freedom: atoms are the elementary particles
Forces or interactions between atoms Boundary conditions
Methods to generate configurations of
atoms: Newton
systemtemperature
pressure
Force Field =physico-chemical
knowledge
Every molecule consists of atoms that are very strongly attached
Situation at time t+t
Classical dynamicsSituation at time t
Force is determined by relative positions
acceleration = force / mass
velocity = acceleration × t
position = velocity × tforce
velocity
position
Determinism …Sir Isaac Newton
1642 -1727
Generating configurations in atomic simulations: molecular dynamics
new positions
Time t
Time (t+t)
positionsvelocities
forces
new velocities
... comparable to shooting a movieof a molecular system...
t 10-15 seconds
Definition of a model for molecular simulation
MOLECULARMODEL
Degrees of freedom: atoms are the elementary particles
Forces or interactions between atoms Boundary conditions
Methods to generate configurations of
atoms: Newton
systemtemperature
pressure
Force Field =physico-chemical
knowledge
Every molecule consists of atoms that are very strongly attached
Boundary conditions in atomic simulations
Vacuum
Droplets
Periodic: rectangular system is surrounded by copies of itself
• Surface effects (surface tension)
• No dielectric screening
• Still surface effects
• Only partial dielectric screening
• Evaporation of the solvent
Advantage:• No surface effectsDisadvantage:
• Artificial periodicity
• High effective concentration
Probably still the best approach…
1) Why
2) How
3) What
4) And the future…
do we simulate ?
Methods Applications
in my research group
Computersimulation of biomolecular systems
1. stable structures binding equilibrium energetically favourable structures between two small
organic molecules
2. Relation between structure and function water transport in the enzymes binding cavity of a
protein (FABP)
3. Motions en mechanisms prediction of the three-
protein folding dimensional structure or
the folding of proteins(polypeptides)
4. Design of new compounds binding strength of design of drugs hormone replacing
molecules to theestrogenreceptor
What do biochemists or molecular biologistswant to know of molecules?
Example 1
Structural interpretation ofthermodynamic properties:
Binding equilibrium between two smallorganic molecules
Applications of molecular dynamics simulation:
Binding equilibrium
Hydrogen bonds
NH2
NH2
HO
HOH
H
OH
N
H
H
H
O
N?Cyclohexane-
diamineCyclopentane-
diol
+ -
- +
Complex :
Experimental MD simulation Benzene CCl4
Gb [kJ/mol] -9.3 -11.5 -10.4
Average binding strength (free enthalpy) :
Many different bindingmodes
Formation of the complex(camera focuses on the diamine)
Diol + Diamine + 252 CCl4 Molecules 2.1 – 2.2.10-9 seconds
Complex formed
Diol + Diamine + 252 CCl4 Molecules 3.2 – 4.0.10-9 seconds
… and a nanosecond later …the molecules are free again…
Hydrogen bonds
O N
N O
NH2
NH2
HO
HO
NH2
NH2
HO
HO
NH2
NH2
HO
HO
NH2
NH2
HO
HO
NH2
NH2
HO
HO
NH2
NH2
HO
HO
54%
21%
8%
7%
4%
3%
Occurrence of different binding modes :
Life time :
• Average life time of the complex: 2.10-10 sec (max. 3.10-9 sec)• Average life time of a hydrogen bond: 5 .10-12 sec
Results of the simulation (over 10-7 sec) :
Experimentally hardly (or not) possible !
What do biochemists or molecular biologistswant to know of molecules?
1. stable structures binding equilibrium energetically favourable structures between two small
organic molecules
2. Relation between structure and function water transport in the enzymes binding cavity of a
protein (FABP)
3. Motions en mechanisms prediction of the three-
protein folding dimensional structure or
the folding of proteins(polypeptides)
4. Design of new compounds binding strength of design of drugs hormone replacing
molecules to theestrogenreceptor
Boundaries: membranes consist of lipids with pores of proteins
Hereditary information in the nucleus: DNA
Proteins: e.g. haemoglobin
for oxygen transport
Carbohydrates:storage of energyand molecularstamps
Biomolecules
• Important to understand enzymatic reactions: the dynamics of the binding cavity
• Simulation allows one to follow the movements of individual molecules
Example 2The watertransport in the binding cavity of a protein (FABP)
Applications of molecular dynamics simulation:
What do biochemists or molecular biologistswant to know of molecules?
1. stable structures binding equilibrium energetically favourable structures between two small
organic molecules
2. Relation between structure and function water transport in the enzymes binding cavity of a
protein (FABP)
3. Motions en mechanisms prediction of the three-
protein folding dimensional structure or
the folding of proteins(polypeptides)
4. Design of new compounds binding strength of design of drugs hormone replacing
molecules to theestrogenreceptor
Example 3
Protein folding the challenge
Proteins consist of chains of amino acids (primary structure)
In an organism proteins only function if they have been correctly folded three- dimensionally. (secondary and tertiary structure)
• What is the relation between amino acid sequence and folded spatial structure?• How does the folding process take place?
20 kinds
Applications of molecular dynamics simulation:
• Proteins are too large systems to simulate the slow folding process.
• Smaller model compounds can be correctly folded on the computer.
Information about folding mechanisms and the unfolded state:
surprise
Foldingsimulation
t [ns]
RM
SD
[nm
]
00 50 100 150 20000
0.1
0.2
0.3
0.4
Unfolded structures
all different?how different?
321 1010 possibilities!!
Folded structures
all the same
Surprising result after simulations of many polypeptides
number of amino acids in
the protein
10
100
Folding time (exp/sim) in
seconds
10-8
10-2
possible structures
320 109
3200 1090
relevant (observed) structures
103
109
number of
peptide
protein
The number of relevant unfolded structures is much and much smaller than the number of possible unfolded structures
Assuming that the number of relevant unfolded structures is proportional to the folding time, only 109 protein structures need to be simulated instead of 1090 structures.
Folding mechanism is simpler than generally expected: searching through only 109 structures
Protein folding on a computer is possible before 2010
Simulations can complement the experiment:
Simulation explains experiments Properties of waterFolding of protein molecules
Simulation suggests Design of drugsnew experiments enzymes
less experimentsbetter chance of success
knowledgenew ideas
For which problems are simulations useful ?
What do biochemists or molecular biologistswant to know of molecules?
1. stable structures binding equilibrium energetically favourable structures between two small
organic molecules
2. Relation between structure and function water transport in the enzymes binding cavity of a
protein (FABP)
3. Motions en mechanisms prediction of the three-
protein folding dimensional structure or
the folding of proteins(polypeptides)
4. Design of new compounds binding strength of design of drugs hormone replacing
molecules to theestrogenreceptor
Example 4Design of drugs
testing compounds with the computer
Enzymes work according to the “lock and key”-principle
Applications of molecular dynamics simulations:
the “key hole”: the active site in the
protein
containing a “fitting key”: the active site with an active molecule
the active and a new molecule (to
be tested) superimposed
a “new key”?: The active site with the molecule to be
tested
HO
Cl
Cl
HO
Cl
Cl
HO Cl
Cl
Cl
HO Cl
ClCl
Cl
HO
Cl ClCl
Cl
Cl
Cl
HO
Cl
Cl
Cl
ClCl
Cl
HO
Cl
Cl
Cl
Cl Cl
HO
Cl
Cl
Cl
Cl
Cl
HO
Cl
Cl
Cl
Cl
Cl
HO
Cl
Cl
Cl
Cl
Cl
HO
Cl
ClCl
Cl
HO
Cl
Cl
Cl
16 hydroxylated PCB’s
Unphysical reference state
Polychlorinated biphenyls
Binding to the estrogen receptor
16 hydroxylated PCB’s: 10 < kBT 2.5 kJ mol-1
13 < 1 kcal mol-1
Average deviation: 2.5 kJ mol-1
Variation exp. values: 4.2 kJ mol-1
Year molecular system: type, size length of the simulation in seconds
1957 first molecular dynamics simulation (hard discs, two dimensions)
1964 atomic liquid (argon) 10-11
1971 molecular liquid (water) 5 .10-12
1976 protein (no solvent) 2 .10-11
1983 protein in water 2 .10-11
1989 protein-DNA complex in water 10-10
1997 polypeptide folding in solvent 10-7
2001 micelle formation 10-7
200x folding of a small protein 10-3
History: classical molecular dynamics simulationsof biomolecular systems
And the future ...
2001 Biomolecules in water (~104 atomen) 10-8 sec
2029 Biomolecules in water 10-3 sec
2034 E-coli bacteria (~1011 atoms) 10-9 sec
2056 Mammalian cell (~1015 atoms) 10-9 sec
2080 Biomolecules in water 106 sec
2172 Human body (~1027 atoms) 1 sec
As fast as nature !
Protein folding sooner?
Standard classical simulations :
Computer speed increases with a factor 10 about every 5½ year!
• Upper limit to computer speed ?• Accuracy of classical models and force fields ?• Better approximations and simplifications
But :
Computersimulation of reality
real world experimentexperimental
data
predictionscomputational
methodsmodel
of the world
classificationabstractionsimplificationapproximationgeneralisation
comparingis
testing
Acknowledgements
Gruppe informatikgestützte Chemie (igc) http://www.igc.ethz.ch
Dirk Bakowies (Germany)
Riccardo Baron (Italy)
Indira Chandrasekhar (India)
Markus Christen (Switzerland)
Peter Gee (England)
Daan Geerke (Holland)
Daniela Kalbermatter (Switzerland)
Alice Glättli (Switzerland)
David Kony (France)
Chris Oostenbrink (Holland)
Daniel Trzesniak (Brasil)
Alex de Vries (Holland)
Haibo Yu (China)