Simulations in Biology and Biophysics
How to bring Physics to Life?
Péter Maróti
Department of Biophysics,
University of Szeged, Hungary
Topics
- (Young) physicists: face to biology (related problems)
- (Bio)Molecules in motion: brief tutorial on molecular dynamics
(MD)
- Applications
- K+ channel protein
- aquaporin
- titin
- photosynthetic apparatus of bacteria
- harvesting the sun
- temperature dependence of intraprotein
electron transfer
- interquinone electron transfer coupled to
proton uptake
- protein and lipid control of energetics of QA
(effect of mutations)
Physics in Biology, Biological Physics,
Biophysics
In 1944, the physicist Erwin Schrödinger, published a short book
that changed the course of modern biology.
"What is Life?" he asked famously in his title. Could the events
inside a living organism be explained solely by physics and
chemistry? Yes, they could, Schrödinger answered. "The
obvious inability of present-day physics and chemistry to
account for such events is no reason at all for doubting that
they can be accounted for by those sciences.„
At that time, there was a wide disconnect between physics and
biology. No one knew
- the physical nature of a gene,
- the molecular biology, and
- many of the smartest scientists went into elementary particle
physics.
No more today.
''Ask not what physics can do for biology,'‘
said Hans Frauenfelder, one of the field's pioneers,
''Ask what biology can do for physics.'' .
(Adaptation of famous phrase from J.F. Kennedy)
''Biology has provided physics with its new frontier,'‘
said Robert Laughlin, who won the 1998 Nobel prize in physics
(quantum Hall effect) and now devotes himself to theoretical
problems in biology.
''The whole problem is that we are living in the 21st century with
these 19th century guilds.''
said John Hopfield, a Princeton scientist, one of the first
physicists to move into biology.
Molecules in Motion
Structural biologists have long determined the detailed threedimensional structures of proteins and the cell's other
macromolecules, pinpointing the position of the thousands of
component atoms. Those structures offer clues about how
proteins act as
• motors,
• channels,
• solar cells, or
• genetic switches.
But the structure is just a starting point. To begin explaining how a
protein functions, it's important to see how it moves. The need
is large to make successful simulations of macromolecules at
work: Molecular Dynamics (MD).
Experiments that show protein dynamics
Hemoglobin
Bacterial Reaction Center
O2
H+
The oxygen would need seconds to
diffuse through the protein matrix to
the hem groups in rigid protein.
However, the time scale of oxygen
uptake is ms!
Hans Frauenfelder, PNAS 1979
The rate of proton uptake from the
aqueous bulk phase is governed by the
dynamics of exposure of the
protonatable group of the protein.
P. Maróti and C.A: Wraight, Biophys. J. 1997
Speed up
Use of Molecular Dynamics in Biophysics
A Brief Tutorial on MD Simulations
MD: The Verlet Method
Double V-shape
Obtaining files
Files can be downloaded
through the Web
First, you need a PDB File
What you need to know
to build a realistic atomistic model
of your system?
What you need to know
to build a realistic atomistic model
of your system?
MD Simulations of the K+ Channel Protein
Temperature fluctuation
Water Transport in Aquaporins
Aquaporins are membrane water channels that play critical roles
in controlling the water contents of cells.
The Nobel Prize in Chemistry for 2003
Peter Agre
Johns Hopkins University School of Medicine,
Baltimore, USA
“for the discovery of water channels”
Fundamental molecular understanding of how the kidneys recover water from
primary urine.
Several diseases, such as congenital cataracts and nephrogenic diabetes
insipidus, are connected to the impaired function of these channels.
Aquaporins facilitate the transport of water and, in some cases, other small
solutes across the membrane. However, the water pores are completely
impermeable to charged species, such as protons, a remarkable property that
is critical for the conservation of membrane's electrochemical potential, but
paradoxical at the same time, since protons can usually be transferred readily
through water molecules.
Water Transport in Aquaporins
Emad Tajkhorshid, Peter Nollert, Morten Ø.
Jensen, Larry J. W. Miercke, Joseph O'Connell,
Robert M. Stroud, and Klaus Schulten. Control
of the selectivity of the aquaporin water
channel family by global orientational tuning.
Science, 296:525-530, 2002.
12-nanosecond molecular dynamics
simulations were carried out that define the
spatial and temporal probability distribution and
orientation of a single file of seven to nine
water molecules inside the channel. Two
conserved asparagines (Asn 68 and 203) force
a central water molecule to serve strictly as a
hydrogen bond donor to its neighboring water
molecules. Assisted by the electrostatic
potential generated by two half-membrane
spanning loops, this dictates opposite
orientations of water molecules in the two
halves of the channel, and thus prevents the
formation of a "proton wire," while permitting
rapid water diffusion.
Yellow ball: selected water molecule (or small
salute).
Dozens of rounded red and white water molecules swarm around
the much-larger channel like bees; a line of them squeeze singlefile through a narrow hole in the channel’s center. Halfway through,
each water molecule flips 180 degrees.
In the extreme sport of bungee jumping, a daring athlete leaps from a great height and free-falls
while a tethered cord tightens and stretches to absorb the energy from the descent. The bungee
cord protects the jumper from serious injury, because its elasticity allows it to extend and provide
a cushioning force that opposes gravity during the fall. Amazingly, nature also uses elasticity to
dampen biological forces at the molecular level, such as during extension of a muscle fiber under
stress. The molecular bungee cord that serves this purpose in the human muscle fiber is the
protein titin, which functions to protect muscle fibers from damage due to overstretching.
Forced
unfolding of
titin Z1Z2
Molecular
Bungee Cord
750 pN
Photosynthetic Apparatus
of Purple Bacteria.
Some problems for MD simulations
1. Harvesting the Sun
The light harvesting
system displays a
hierarchy of integral,
functional units
How does the Light
Harvesting System function
with thermal disorder?
How does Q/QH2 pass
through LH-I to/from RC
within reasonable time
(≈1 ms)?
2. Temperature-dependence of the rate
of the initial electron transfer
The electron transfer is coupled to the thermal motion of the surrounding
protein.
3. Interquinone Electron Transfer.
Effects of Mutations
HisM219
QB
HisL190
e-
QA
Fe
HisL230
M266His
M234Glu
H+/QA- proton uptake
0.5
WT
0.25
Mutants
0
1
H+/QB- proton uptake
Extended network of
strongly interacting
protonatable groups
a
b
WT
0.5
Mutants
0
6
H. Cheap et al. Biochemistry
(submitted)
7
8
9
pH
10
11
WT
■
M266HA
O
M266HL
□
Delocalized proton
uptake: the cytoplasmic
part of the RC acts as
proton sponge.
The high pH band of
proton uptake reflects
interaction among
protonatable residues.
4. Protein (M265ILE and M252TRP) and lipid
(cardiolopin) control of QA/QA- midpoint potential
László
Rinyu et al.
Biochim.
Biophys.
Acta 2004.
The free energy drop from P* to P+QA- in mutants
at residue M265 of the QA binding site.
ΔGP*A was determined from the intensity of delayed fluorescence.
The effect of cardiolipin and M252WF mutation on the
delayed fluorescence emission (DF) from RCs.
Trp→Phe
mutant
Wild type
Thermodynamic box
QA
Gdissociation
RC-QA
Q A / Q A
G
bound
RC-QA-
RC + QA
 G  0
Q A
Gdissociation
Q / Q
G free
RC + QA-
Linear Interaction Energy (LIE) method
for determination of ligand binding free energies
J. Aqvist and J. Marelius, Combinatorial Chemistry and High Throughput Screening, 2001
This method is based on force field estimations of the receptor-ligand interactions and thermal
conformational sampling. A notable feature is that the binding energetics can be predicted by
considering only the intermolecular interactions between the ligand and receptor.
QA
Q A

G

G
Direct calculation of
dissociation
dissociation and
from MD model and determination of the change of the midpoint redox potential from the
thermodynamic cycle.

Q
Mutant M265IT
A
Wild type
G
dissociation
Acknowledgements.
Thanks to
• László Rinyu – Ph.D. student
• OTKA