Diffusion in nanostructures: Role of interaction potentials Sergey M. Bezrukov Laboratory of Physical and Structural Biology, NICHD National Institutes of Health - PowerPoint PPT Presentation

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Diffusion in nanostructures: Role of interaction potentials Sergey M. Bezrukov Laboratory of Physical and Structural Biology, NICHD National Institutes of Health

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Title: Diffusion in nanostructures: Role of interaction potentials Sergey M. Bezrukov Laboratory of Physical and Structural Biology, NICHD National Institutes of Health


1
Diffusion in nanostructures Role of interaction
potentials Sergey M. BezrukovLaboratory of
Physical and Structural Biology, NICHDNational
Institutes of Health
together with V. Adrian Parsegian, Alexander M.
Berezhkovskii, Philip A. Gurnev, Ekaterina M.
Nestorovich, Amos B. Oppenheim, and Mathias
Winterhalter
2
Sunday, August 26, morning, between 900 and 1000
Alf Honigmann Translocation or not? (A particle
can leave the channel from the side it enters).
Roland Benz Asymmetry? Do you mean
voltage-induced asymmetry?
Boris Shklovskii It is all about linear vs.
non-linear response.
3
Channel asymmetry, Maxwells demons, non-linear
response, and all that
4
A teaser
?
5
Plan of the talk
  • Consider the simplest binding-site model
  • Show experiments on single l-phage docking to
    maltoporin
  • Introduce and explain the benefits of the
    diffusion model (e.g. resolve the teaser)

6
The simplest binding site model of ion channel
7
The simplest binding site model of ion channel
8
The simplest binding site model of ion
channel The flux
9
Consider equilibrium
10
Translocations vs. returns
11
Channel blocked from one side
12
Plan of the talk
  • Consider the simplest binding-site model
  • Show experiments on single l-phage docking to
    maltoporin
  • Introduce and explain the benefits of the
    diffusion model (e.g. resolve the teaser)

13
Constructing a lipid bilayer

60 m Dia. Hole
A
Lipid Monolayer
15 ? Teflon Film
Electrode
Water Tube
KCl
KCl
Teflon Chamber
14
Maltoporin trimeric b-barrel
  • Native Maltoporin is a homotrimer
  • Each subunit is a 421 a.a. 18 stranded b-barrel
  • Loops L4 , L5 and, L6 form a complex near the
    extracellular channel vestibule (amino acid
    residues relevant for phage binding are shown in
    red)

15
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16
Effect of phage on the membrane containing
Maltoporin trimers
  • Current corresponding to 10 Maltoporin trimers is
    reduced by phage at the cis-side addition
  • Phage addition to the trans-side of the membrane
    did not produce any significant changes in the
    current

17
Ion current and maltohexaose transport in single
Maltoporin trimer
10 pA
Maltohexaose molecules bind to a specific site
inside the pore and transiently block ion current
Ion conductance is stable in the absence of
maltohexaose
18
Monitoring the functional properties of the
single Maltoporin trimer embedded into bilayer
cis-
  • In the absence of maltohexaose and l phage
    Maltoporin trimer is permanently open

trans-
/ 150 mV /
0 mV /
19
Monitoring the functional properties of the
single Maltoporin trimer embedded into bilayer
cis-
  • Transmembrane current gets transiently blocked
    when maltohexaose is applied to the cis-side of
    the membrane
  • Phage was added simultaneously to the same (cis)
    side of the membrane

trans-
/ 150 mV /
0 mV /
20
Monitoring the functional properties of the
single Maltoporin trimer embedded into bilayer
cis-
  • Docking of phage decreases ion conductance and
    simultaneously inhibits maltohexaose penetration
    in all the three pores of Maltoporin

trans-
/ 150 mV /
0 mV /
21
Subsequent application of maltohexaose to the
trans-side produces current fluctuations
cis-
trans-
/ 150 mV /
0 mV /
22
Probing the phage-bound state of Maltoporin for
independence of pore blockage Thermodynamics
Binomial distribution probes independence of
blocking events
Pk probability of k (out of 3) blocked pores k
of blocked pores p probability of finding a
single pore blocked p is determined by
equilibrium constant K eq and sugar
(maltohexaose) concentration (C) obtained from
the same current traces
Blocking events are independent
23
Phage docking introduces hierarchy in Maltoporin
conductance
Phage-free Maltoporin trimer D 1 D 2 D 3
Phage-bound Maltoporin trimer D 1 lt D 2 lt D 3
D 1
D 1
D 2
D 2
D 3
D 3
maltohexaose trans-side
24
Phage introduces a new common pathway for ion
fluxes in Maltoporin
Phage-free Maltoporin
Phage-bound Maltoporin
500 pS
Phage introduces a formation of one common
entryway, connecting the extracellular face of
Maltoporin with the outer membrane solution
25
Maltohexaose residence time increases upon phage
binding
Maltohexaose residence time in Maltoporin pore
(at the trans-side sugar application) increases
upon l phage binding This finding suggests that
the phage binding site does not overlap with the
zone of sugar binding
26
Phage introduces a new common pathway for ion
fluxes in Maltoporin
27
Plan of the talk
  • Consider the simplest binding-site model
  • Show experiments on single l-phage docking to
    maltoporin
  • Introduce and explain the benefits of the
    diffusion model (e.g. resolve the teaser)

28
Particle and Channel
29
Particle and Channel
30
Particle and Channel
31
Particle and Channel
32
Analytical Approach
33
Particle Potential in the Channel
34
Computer simulations
L
2a
35
Computer simulations
36
Particle and Channel
37
Free diffusion
Diffusion with 'sticking'
38
2a
L
39
Instead of treating a channel as a featureless
binding site we considered single-particle
dynamics inside its pore
40
Flux
Rectangular potential well of depth U0
occupying the entire channel
41
Dependence of the flux on the depth (bU) and tilt
(bFl/2) of the potential well
42
Which one is more effective?
?
43
Introducing entropic potential
44
Simulations
45
Simulations vs. Theory Entropic Potential
46
References
The phage story J. Molecular Biol., 2006,
3591447-1455. Theory Biophys. J., 2005,
88L7-L19 Phys. Rev. Lett., 2006, 97020601 J.
of Physics Condensed Matter, 2007, 19065148 J.
Chem. Phys., 2007 in press.
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