Theoretical and Computational Biophysics Group
Structure, Dynamics, and Function of Aquaporins
NIH Resource for Macromolecular Modeling and Bioinformatics

Our water permeation movie and the 2003 Nobel prize for Chemistry

Aquaporins are membrane water channels that play critical roles in controlling the water contents of cells. These channels are widely distributed in all kingdoms of life, including bacteria, plants, and mammals. More than ten different aquaporins have been found in human body, and several diseases, such as congenital cataracts and nephrogenic diabetes insipidus, are connected to the impaired function of these channels. They form tetramers in the cell membrane, and 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 transported readily through water molecules. The results of our simulations have now provided new insight into the mechanism underlying this fascinating property. Water molecules passing the channel are forced, by the protein's electrostatic forces, to flip at the center of the channel (see the animation), thereby breaking the alternative donor-acceptor arrangement that is necessary for proton translocation (read the complete story in our Science paper).

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Download a larger movie of water permeation through aquaporins with more structural details (13MB)

The group's recent studies have revealed several structural and functional features of aquaporins. Our first set of molecular dynamics (MD) simulations was performed on a fully hydrated model of aquaporin-1 (AQP1) in a membrane which was based on the electron microscopy structures. The calculations described the formation of a water single file inside the channel and revealed the critical role of the NPA motifs in the stability and function of the channel (Zhu, et al., FEBS Lett., 2001). The simulations clearly showed the sensitivity of the results to a proper description of hydrogen bonds between the asparagine residues in the NPA motifs and the necessity for a higher resolution structure.

In the year 2000, Stroud's lab in UCSF succeeded in solving the first high resolution structure of an aquaporin by x-ray crystallography. The studied structure was the one of the E. coli glycerol uptake facilitator (GlpF), which is an aquaglyceroporin, i.e., the channel is also permeable to small linear sugar molecules such as glycerol. Nanosecond MD simulations of tetrameric GlpF in a hydrated patch of POPE lipid bilayer characterized the complete pathway of substrate conduction in the channel. Analysis of hydrogen bond interactions of the substrate with the interior of the channel also explained for the first time why these channels incorporate in their architecture two characteristic loops, including energetically unfavorable secondary structure elements, which are conserved in the whole aquaporin family (Jensen et al., Structure, 2001).

Structure cover page

GlpF Tetramer

Then, we explored the energetics of the transport event to understand what barriers a substrate needs to overcome during its passage through the channel. In order to describe the free energy profile, we calculated the potential of mean force for the complete conduction event from the trajectories in which the movement of the substrate along through the channel was accelerated by applying external forces. This technique, known as steered molecular dynamics (SMD), allows the researchers to observe events within the accessible time scale of the simulations. However, due to the non-equilibrium nature of the trajectories, in analyzing results one faces the problem of irreversible work that has to be discounted. Using the recently discovered equality between the free energy and work in non-equilibrium systems, Jarzinsky's identity, we could completely describe the energetics of substrate transport through the channel. The potential of mean force captures major binding sites and barriers in the channel is close agreement with the results of MD simulations and the positions found in the crystal structure. Moreover, it displays a pronounced asymmetry in its shape, suggesting that the asymmetric structure of the protein may be functionally important for an efficient uptake of nutrient molecules from the environment. (Jensen, et al., PNAS, 2002).

Potential of Mean Force SMD

Can we simulate the conduction the same way as in experiments? In order to directly compare the results of MD simulations with biochemical measurements of the conductivity of membrane water channels, in which osmotic pressure gradients are used to induce the flow of water across the membrane, we developed a new methodology for MD simulations. By applying small forces on water molecules in the bulk region (see figure), a hydrostatic pressure gradient is generated across the membrane. The pressure gradient induces conduction rates that can be studied with MD simulations, which are usually limited to a few nanoseconds. The method has been applied in the simulation of water permeation through the GlpF, and has resulted in a linear correlation between the applied pressure and the flux (Zhu et al., Biophys. J., 2002).

Pressure Gradient in MD

Aquaporin research in the news:

Aquaporin team:


Molecular Basis of Proton Blockage in Aquaporins. Nilmadhab Chakrabarti, Emad Tajkhorshid, Benoît Roux, and Régis Pomès. Structure, 12: 65-74, 2004.

The mechanism of proton exclusion in aquaporin channels. Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, and Gregory A. Voth. PROTEINS: Structure, Function, and Bioinformatics, 55:223-228, 2004.

Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004.

Electrostatic tuning of permeation and selectivity in aquaporin water channels. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:2884-2899, 2003.

Water and proton conduction through carbon nanotubes as models for biological channels. Fangqiang Zhu and Klaus Schulten. Biophysical Journal, 85:236-244, 2003.

Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Deyu Lu, Paul Grayson, and Klaus Schulten. Biophysical Journal, 85:2977-2987, 2003.

Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Paul Grayson, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:36-48, 2003.

Control of the selectivity of the aquaporin water channel family by global orientational tuning. Emad Tajkhorshid, Peter Nollert, Morten Ø. Jensen, Larry J. W. Miercke, Joseph O'Connell, Robert M. Stroud, and Klaus Schulten. Science, 296:525-530, 2002.

Energetics of glycerol conduction through aquaglyceroporin GlpF. Morten Ø. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:6731-6736, 2002.

Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002.

The mechanism of glycerol conduction in aquaglyceroporins. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, 9:1083-1093, 2001.

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. FEBS Letters, 504:212-218, 2001.

Last updated: Dec 29, 2003 by Emad Tajkhorshid

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