Research Topics - Membrane Biophysics

Research Topics - Membrane Biophysics

Exchange of materials and information between a living cell and its environment is mediated and regulated by membrane proteins. These proteins are involved in the regulation of electrical activity of the cell, transport of water and water soluble materials across the membrane, and production of ATP. Membrane receptors are the sites for detection informational signals, such as neurotransmitters and hormones, light, and even mechanical stress. The atomic-resolution structures of a few membrane proteins have been solved, and recent advances in structure determination of membrane proteins promise more structure to be solved soon. Our group studies the mechanism of function of membrane proteins with various computational methodologies. The proteins are simulated in their natural environment, i.e., embedded in fully hydrated patches of lipid bilayers and under constant pressure and temperature conditions. The main objective is to understand how specific structural motifs and/or chemical interactions in a protein play a role in its function.

Spotlight - Photosynthetic Chromatophore
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Chromatophores are the photosynthetic machineries of bacteria. Each chromatophore contains, embedded in a membrane, all the photosynthetic proteins needed to absorb sunlight and turn it into chemical fuel. Chromatophores come in different shapes: while some chromatophores are spherical, others are flat or tubular. It has puzzled scientists how all these different geometries arise, and a hypothesis has developed that it is the photosynthetic proteins that render the shape of chromatophore membrane. In a study reported recently, computational biologists using NAMD took an atomistic look at how the chromatophore proteins bend the membrane. Simulations showed that the most numerous photosynthetic proteins dome the membrane, building arched membrane patches that can then be assembled into a spherical chromatophore. These simulations demonstrated that photosynthetic proteins construct their individual membrane environment, and when many of such proteins come together in the bacterial membrane, they can build functional cellular units with unique geometries. For more details, please see our chromatophore website.

All Spotlights

Papers

The roles of pore ring and plug in the SecY protein-conducting channel. James Gumbart and Klaus Schulten. Journal of General Physiology, 132:709-719, 2008.

A structural mechanism for MscS gating in lipid bilayers. Valeria Vasquez, Marcos Sotomayor, Julio Cordero-Morales, Klaus Schulten, and Eduardo Perozo. Science, 321:1210-1214, 2008.

Four-scale description of membrane sculpting by BAR domains. Anton Arkhipov, Ying Yin, and Klaus Schulten. Biophysical Journal, 95:2806-2821, 2008.

Intrinsic curvature properties of photosynthetic proteins in chromatophores. Danielle Chandler, Jen Hsin, Christopher B. Harrison, James Gumbart, and Klaus Schulten. Biophysical Journal, 95:2822-2836, 2008.

Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Basak Isin, Klaus Schulten, Emad Tajkhorshid, and Ivet Bahar. Biophysical Journal, 95:789-803, 2008.

Three dimensional architecture of membrane-embedded MscS in the closed conformation. Valeria Vasquez, Marcos Sotomayor, D. Marien Cortes, Benoit Roux, Klaus Schulten, and Eduardo Perozo. Journal of Molecular Biology, 378:55-70, 2008.

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008.

Sugar transport across lactose permease probed by steered molecular dynamics. Morten Ø. Jensen, Ying Yin, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 93:92-102, 2007.

Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. Yi Wang, Jordi Cohen, Walter F. Boron, Klaus Schulten, and Emad Tajkhorshid. Journal of Structural Biology, 157:534-544, 2007.

Dynamics of K+ ion conduction through Kv1.2. Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 91:L72-L74, 2006.

Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel. Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. Proceedings of the National Academy of Sciences, USA, 102:12377-12382, 2005.

What makes an aquaporin a glycerol channel: A comparative study of AqpZ and GlpF. Yi Wang, Klaus Schulten, and Emad Tajkhorshid. Structure, 13:1107-1118, 2005.

Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map. Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal, 88:3745-3761, 2005.

Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. Biophysical Journal, 86:1332-1344, 2004.

Lipid bilayer pressure profiles and mechanosensitive channel gating. Justin Gullingsrud and Klaus Schulten. Biophysical Journal, 86:3496-3509, 2004.

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.

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