monomeric pores water, glycerol, …
DESCRIPTION
Tetrameric pore Perhaps ions???. Monomeric pores Water, glycerol, …. Aquaporins of known structure: GlpF – E. coli glycerol channel (aquaglycerolporin) AQP1 – Mammalian aquaporin-1 (pure water channel). Revealing the Functional Role of Reentrant Loops. Single Glycerol per channel. - PowerPoint PPT PresentationTRANSCRIPT
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Monomeric poresWater, glycerol, …
Tetrameric porePerhaps ions???
Aquaporins of known structure:Aquaporins of known structure:GlpF – E. coli glycerol channel (aquaglycerolporin)
AQP1 – Mammalian aquaporin-1 (pure water channel)
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Revealing the Functional Role of Reentrant Loops
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Single Glycerol per channel
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Note that glycerols moved, but not as extensively as earlier!
We need to enforce an entire
conduction event.
initial state
final (1ns) state
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constant velocity (30 Å/ns)
constant force
(250 pN)
Steered Molecular Dynamics
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Free Energy Calculation in SMD
Free energy
displacement
applied force
SMD simulationa non-equilibrium process
One needs to discount irreversible
work
TkWTkG BB ee // Jarzynski, PRL 1997Hummer, PNAS, JCP 2001Liphardt, et al., Science 2002
WG
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4 trajectoriesv = 0.03, 0.015 Å/psk = 150 pN/Å
Constructing the Potential of Mean Force
])([)( 0 vtztzktf
t
0)()( tvftdtW
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zp zc
M
mpcpm zzzzmazG
1
)]()(sin[)(
determined by minimizing the difference between (d) and (e)
Constructing the Potential of Mean Force – cont.
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• Captures major features of the channel• The largest barrier 7.3 kcal/mol; exp.: 9.61.5 kcal/mol
Features of the Potential of Mean Force
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Asymmetry of the Potential of Mean
Force
phosphorylationAsymmetric Profile in the Vestibules
Peri
pla
sm
Cyto
pla
sm
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MaltoporinOmpF GlpF AQP1
Assymetric structure; biological implication?
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Asymmetric structure of maltoporin
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Trajectory of glycerol pulled by constant force
SMD Simulation of Glycerol Passage
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Aquaporins’ Mechanisms of Selectivity
Protons, ions, and charged molecules cannot be transported.
Aquaglyceroporins (GlpF) transport linear sugars in a highly stereo-selective manner
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carbohydrate
440 nm
scattered light
H2O carbohydrate + H2O
lipid vesicles
channel-containing proteoliposomes
shrinking reswelling
100 mM Ribitol
Liposome Swelling Assay
Courtesy of Peter Nollert
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stereoisomers
Stereoselective Transport of Carbohydrates
Some stereoisomers show over tenfold difference in
conductivity.
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GlpF + glycerolGlpF + water
Channel Constriction
HOLE2: O. Smart et al., 1995
red < 2.3 Å 2.3 Å > green > 3.5 Å blue > 3.5 Å
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Selectivity filter
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Evidence for Stereoselectivity of Glycerol
Cannot be verified by experimental measurements.
H
H
HH
H
OH
OH
OHH
HO
HH
H
OH
H
OH
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Complementarityglycerol molecule channel
hydrophobic
acceptor
donor
H
H
HH
H
OH
OH
OH
H
HO
HH
H
OH
H
OH
HO
HO
HOH
H
H
H
H
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RibitolOptimal hydrogen
bonding and hydrophobic matching
Arabitol10 times slower
Evidence for Stereoselectivityby Interactive Molecular Dynamics
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J. Stone, J. Gullingsrud, K. Schulten, and P. Grayson. A System for Interactive Molecular Dynamics Simulation. 2001 ACM Symposium on Interactive 3D Graphics, pp.191-194, ACM SIGGRAPH
Interactive Molecular Dynamics
VMD NAMD• Any PC/Workstation• Supports 3D force-
feedback devices for interaction
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Results of Interactive Simulations
Pathways An interesting position
Ribitol’s C-shaped conformation
Restricted motion filter for both sugars
Dipole reversal for ribitol at NPA
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Glycerol-Free GlpF
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Water permeation through GlpF
7-8 water molecules in each channel
5 nanosecond Simulation
18 water conducted In 4 monomers in 4 ns
1.125 water/monomer/ns
Exp. = ~ 1-2 /ns
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The single file of water molecules is maintained.
Correlated Movement of Water in the Channel
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Diffusion of Water in the channel
Experimental value for AQP1: 0.4-0.8 e-5
One dimensional diffusion: 22 SDt
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Water Bipolar Configuration in Aquaporins
E.T. et al., Science 296, 525 (2002)
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H+H
H
O H
H
O H
H
O
H
H
O H
H
O H
H
OH+H+
H+
H+H+
H+
H+
H+H+H+
H+
H
H
O H
H
O H
H
O
H+
H+H+
Proton transfer through water
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Electrostatic Stabilization of Water Bipolar Arrangement
E.T. et al., Science 296, 525 (2002)
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Proton Blocking by a Global Orientation
Mechanism