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Biophysik der Moleküle
kl. Phys. HS Mo 14-16 u. Do 9-10
Vorlesung Rädler WS 2010
Tutorials: Do 10-11 od. Do 11-12 od. Do 18-19 (Fr 9-10)
http://www.softmatter.physik.uni-muenchen.de/tiki-index.php?page=Biophysik_MolekueleWS10
Erich Sackmann &
Rudi Merkel
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Rob PhilipKane KondrevJulie Theriot
Websitehttp://www.garlandscience.com/textbooks/0815341636.asp
- Jonathon Howard
„Mechanics of Motor Proteins and the Cytoskeleton“
Literatur
Bruce Alberts et al.:Molecular Biologyof the Cell (MBoC)
Helmut Pfützner
Roland Glaser
Rodney Cotterill
links : Auf den Folien und auf der Vorlesungsseitewww.softmatter.physik.uni-muenchen.dewww.schwerpunkt-biophysik.physik.lmu.de
5*$6/7"68.%
Rädler/ WS 2010
Inhalt Biophysik der Moleküle
Proteine! Struktur und Dynamik! Funktion als Enzyme! Molekulardynamik Rechnung!
Mechanik der Biomoleküle! Reversible Entfaltung! Bindungen unter Last
Life at low Reynods numbers! Brown‘sche Motoren
Muskel! Molekulare Mechanismen ! ! !
Molekulare Motoren! Turbinen! ! ATP Synthase! ! Flagellenmotor ! Linearmotoren! ! Myosin! ! Kinesin! Cilienmotor
Zellmotilität und Form! Physik der Biopolymere! ! Struktur! ! Dynamik! ! Regulation! Zytoskelett! ! Interm. Filament ! ! Miktotubuli! ! Aktin !
From the living organism down to molecules
movie H.Berg lab
From the living organism down to molecules
cartoon by Goodsell
From the living organism down to molecules
a) Kohlenstoff
b) Zucker
c) ATP
d) Chlorophyll
e) tRNA
f) Antikörper
g) Ribosome
h) Poliovirus
i) Myosin
j) DNA
k) F-actin
l) Enzyme
m) Pyruvat dehydrogenase
Goodsell, 1993
Nucleic
Acids
Proteins
Lipids
Sugars
There are four classes of macromolecules
Macromolecules exhibit a
hierachy of structures
storage of genetic information
cellular
building blocks
& machinery
e.g.
cytoskeleton
enzymes
pores
ECM
Inventory by numbers
Ribosome: Translating Code into Function
MOVIE : „Inner Life“ shows biomolecules at work
http://multimedia.mcb.harvard.edu/media.html
(be aware : animations use artistic freedom)
Speed:
30 na/s
Fidelity:
105
RNA Polymerase II Complex
See Patrick Cramer et al. Genzentrum LMU
_ o=EE
(!
= 4g c
o r !. = 6
ä e3 =
G
ol
- 2 ! 3
E + !5ö f t t ( u--tr
u
_o
WWWWWWWWWWWI o-ls
- f f iäx i r l lum b io log ica l t imesca le ; age o f Ear th , 4 b i l l i on years = l0 l7 s
<- d ivers i f i ca t ion o f metazoans, 600 mi l l ion years = 2 x l0 l6 s
- d ivers i f i ca t ion o f humans and ch impanzees, 6 mi l l ion years = 2 x l0 la s
- sequo ia l i fespan, 3000 years = l0 l I s
<- Calapagos tortoise l i fespan, I 50 years = 5 x l0e s
+ human embryon ic s tem ce l l l i ne doub l ing t ime, 72 h = 3 x l0s s
- mayf ly adu l t l i fespan, I day = 9 x l0a s
<J E. co l i doub l ing t ime, 20 min = I .2 x | 0
j s
\ uns tab le p ro te in ha l f - l i fe , 5 min = 300 s
- lysozyme turnover rate, = 0.5 s-l
- carbonic anhydrase turnover rate, = 600,000 s-'
<- side chain rotat ion, = 500 ps
- H-bond rear rangements in water , = l0 ps
o
G L
_ > : : ,6 0qJ - .,;
o a- Y -
o '
r,,
- coVäl!ht bond vibrat ion in water, = I fs
typical
biological
timescales
See Grubmüller et al. MPI Göttingen
MD Calculation on Water Transport through ecoli Aquaporin
Stochastic Transport!
MD Calculation on Water Transport through ecoli Aquaporin
See Grubmüller et al. MPI Göttingen
See Joe Howard et al. MPI Dresden
Manfred Schliwa et al. LMU
Intracellular Traffic over Long Distances
Axon 10 µm
Kinesin ‘Walking’
S.M. Block, Cell 93, 5 (1998)
Cytoskeleton: a dynamic polymer network
Cell Motility
Fish Keratinicyte
Dis
tance [nm
]
Actin helical
repeat: 36
nm
Force Feedback
Dis
pla
cem
en
t [n
m]
266
228
190
152
114
76
38
0
-38
-76
-114
0.80.60.40.20.0
Time[s]
Single Molecule
Optical Force
Clamp
Matthias Rief et al.
Bead with
MyosinV on Actin
Filament
Where is the physics ?
• measurements
• quantitative models
• concepts
Biophysical models the same object (DNA) depending on the problem/context
use approximations / idealization
212 Chapter 6. Information, entropy, temperature [[Draft March 8, 2002]]
that numerous biological processes like cell division and protein synthesis depend on the abilityof the cell to unfold RNA (as well as to unfold proteins and DNA), and that such unfoldinginvolves mechanical forces, which one might be able to reproduce using biophysical techniques.In the general strategy utilized by cells, an enzyme converts chemical energy (for example, fromATP) into mechanical work, which is then used to restructure the polymer. To investigate howRNA might respond to mechanical forces, we needed to find a way to grab the ends of individualmolecules of RNA, and then to pull on them and watch them buckle, twist and unfold under thee!ect of the applied external force.
We used an optical tweezer apparatus, which allows very small objects, like polystyrene beadswith a diameter of ! 3 µm, to be manipulated using light (Figure 6.10). Though the beads are
actuatorbead
trap bead
laser trap
actuator bead
trap bead
handle
RNAmolecule
actuator
Figure 6.10: (Cartoon.) Optical tweezer apparatus. A piezo-electric actuator controls the position of the bottom
bead. The top bead is captured in an optical trap formed by two opposing lasers, and the force exterted on the
polymer connecting the two beads is measured from the change in momentum of light that exits the dual beam trap.
Molecules are stretched by moving the bottom bead vertically. The end-to-end length of the molecule is obtained as
the di!erence of the position of the bottom bead and the top bead. Inset: The RNA molecule of interest is coupled
to the two beads via molecular handles. The handles end in chemical groups that can be stuck to complementary
groups on the bead. Compared to the diameter of the beads (! 3000 nm), the RNA is tiny (! 20 nm).
transparent, they do bend incoming light rays. This transfers some of the light’s momentum toeach bead, which accordingly experiences a force. A pair of opposed lasers, aimed at a commonfocus, can thus be used to hold the beads in prescribed locations. Since the RNA is too small tobe trapped by itself, we attached it to molecular “handles” made of DNA, which were chemicallymodified to stick to specially prepared polystyrene beads (Figure 6.10, inset). As sketched in theinset, the RNA sequence we studied has the ability to fold back on itself, forming a “hairpin”structure (see Figure 3.19 on page 88).
When we pulled on the RNA via the handles, we saw the force initially increase smoothly withextension (Figure 6.11a, black curve), just as it did when we pulled on the handles alone: The DNAhandles behaved much like a spring (a phenomenon to be discussed in Chapter 9). Then, suddenly,at f = 14.5 pN there was small discontinuity in the force-extension curve (points labeled “a” and“b”). The change in length (! 20 nm) of that event was consistent with the known length of thepart of the RNA that could form a hairpin. When we reduced the force, the hairpin refolded andthe handles contracted.
ExperimentsDown to the single molecule level
the coil - globule transition
light scattering force spectroscopy
Brownian Motor
Concepts
multiple
manifestations
of the simple
harmonic oscillator
in biophysics