TCB Publications - Search
| 10037. Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Journal of Molecular Biology, 393:1129-1142, 2009. |
| 10036. Molecular mechanisms of active transport across the cellular membrane. Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad Tajkhorshid. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes: From Biophysics to Function. Royal Society of Chemistry, 2009. |
| 10035. Structural and functional analysis of SoPIP2;1 mutants add insight into plant aquaporin gating. Maria Nyblom, Anna Frick, Yi Wang, Mikael Ekvall, Karin Hallgren, Kristina Hedfalk, Richard Neutze, Emad Tajkhorshid, and Susanna Törnroth-Horsefield. Journal of Molecular Biology, 387:653-668, 2009. |
| 10034. Dimer opening of the nucleotide binding domains of ABC transporters after atp hydrolysis. P.-C. Wen and E. Tajkhorshid. Biophysical Journal, 95:5100-5110, 2008. |
| 10033. Potential cation and H+ binding sites in acid sensing ion channel-1. S. A. Shaikh and E. Tajkhorshid. Biophysical Journal, 95:5153-5164, 2008. |
| 10027. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 95:2292-2300, 2008. |
| 10026. Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Yi Wang and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 105:9598-9603, 2008. |
| 10025. Resolution enhancement in solid-state NMR spectra of oriented membrane proteins by anisotropic differential linebroadening. T. Vosegaard, K. Bertelsen, J. M. Pedresen, L. Thøgersen, B. Schiøtt, E. Tajkhorshid, T Skrydstrup, and N. Chr. Nielsen. Journal of the American Chemical Society, 130:5028-5029, 2008. |
| 10024. Blood clotting reactions on nanoscale phospholipid bilayers. J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, Y. Z. Ohkubo, and E. Tajkhorshid. Trombosis Research, 122:S23-S26, 2008. |
| 10023. Indirect role of Ca2+ in the assembly of extracelluar matrix proteins. Jiankuai Diao and Emad Tajkhorshid. Biophysical Journal, 95:120-127, 2008. |
| 10022. Gas conduction of lipid bilayers and membrane channels. Y. Wang, Y. Zenmei Ohkubo, and E. Tajkhorshid. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Membrane Bilayers, chapter 60, pp. 343-367. Elsevier, 2008. |
| 10014. Substrate binding and formation of an occluded state in the leucine transporter. L. Celik, B. Schiott, and E. Tajkhorshid. Biophysical Journal, 94:1600-1612, 2008. |
| 10013. Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors. Y. Zenmei Ohkubo and Emad Tajkhorshid. Structure, 16:72-81, 2008. |
| 10012. Molecular mechanisms of conduction and selectivity in aquaporin water channels. Yi Wang and Emad Tajkhorshid. Journal of Nutrition, 137:1509S-1515S, 2007. |
| 10010. Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Journal, 93:496-504, 2007. |
| 10008. Structural mechanism of plant aquaporin gating. S. Törnroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson, E. Tajkhorshid, R. Neutze, and P. Kjellbom. Nature, 439:688-694, 2006. |
| 10007. Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. P. H. Koenig, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, Th. Frauenheim, and Q. Cui. Journal of Physical Chemistry A, 110:548-563, 2006. |
| 10004. Classical force field parameters for the heme prosthetic group of cytochrome c. F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten. Journal of Computational Chemistry, 25:1613-1622, 2004. |
| 10003. Molecular basis of proton blockage in aquaporins. N. Chakrabarti, E. Tajkhorshid, B. Roux, and R. Pomes. Structure, 12:65-74, 2004. |
| 10002. Developing an energy landscape for the novel function of a (b/a)8 barrel: Ammonia conduction through HisF. Rommie Amaro, Emad Tajkhorshid, and Zaida Luthey-Schulten. Proceedings of the National Academy of Sciences, USA, 100:7599-7604, 2003. |
| 495. Molecular dynamics simulations of membrane channels and transporters. Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 19:128-137, 2009. |
| 483. Photochemical reaction dynamics of the primary event of vision studied by a hybrid molecular simulation. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 96:403-416, 2009. |
| 470. 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. |
| 458. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008. |
| 441. 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. |
| 436. 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. |
| 431. Sugar binding and protein conformational changes in lactose permease. Ying Yin, Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 91:3972-3985, 2006. |
| 425. Mechanism of gating and ion conductivity of a possible tetrameric pore in Aquaporin-1. Jin Yu, Andrea J. Yool, Klaus Schulten, and Emad Tajkhorshid. Structure, 14:1411-1423, 2006. |
| 424. Dynamics of K+ ion conduction through Kv1.2. Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 91:L72-L74, 2006. |
| 421. Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. Michael Hoffmann, Marius Wanko, Paul Strodel, Peter H. Koenig, Thomas Frauenheim, Klaus Schulten, Walter Thiel, Emad Tajkhorshid, and Marcus Elstner. Journal of the American Chemical Society, 128:10808-10818, 2006. |
| 400. Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005. |
| 397. Molecular dynamics simulations of proteins in lipid bilayers. James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 15:423-431, 2005. |
| 392. 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. |
| 384. Kinetic theory and simulation of single-channel water transport. Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten. In S. Yip, editor, Handbook of Materials Modeling, Vol. I: Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005. |
| 381. Towards understanding membrane channels. Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor, and Klaus Schulten. In Boris Martinac and Andrzej Kubalski, editors, Bacterial ion channels and their eukaryotic homologues, pp. 153-190. ASM Press, Washington, DC, 2005. |
| 378. Collective diffusion model for water permeation through microscopic channels. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Physical Review Letters, 93:224501, 2004. (4 pages). |
| 375. Role of water in transient cytochrome c2 docking. Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten. Journal of Physical Chemistry B, 108:20376-20387, 2004. |
| 369. Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal mode analysis. Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten. Journal of the American Chemical Society, 126:10516-10517, 2004. |
| 365. Complementarities and convergence of results in bacteriorhodopsin trimer simulations. Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 87:1394-1395, 2004. |
| 355. 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. |
| 350. Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004. |
| 344. Electrostatic tuning of permeation and selectivity in aquaporin water channels. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:2884-2899, 2003. |
| 342. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Journal of Chemical Physics, 119:3559-3566, 2003. |
| 341. Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:1440-1449, 2003. |
| 340. Large scale simulation of protein mechanics and function. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003. |
| 337. 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. |
| 333. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten. Biophysical Journal, 83:3097-3112, 2002. |
| 329. 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. |
| 328. 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. |
| 327. Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002. |
| 325. Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:1281-1297, 2002. |
| 318. The mechanism of glycerol conduction in aquaglyceroporins. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, 9:1083-1093, 2001. |
| 313. 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. |
| 312. Structural determinants of spectral tuning in retinal proteins - bacteriorhodopsin vs sensory rhodopsin II. Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant, Ehud M. Landau, Javier Navarro, and Klaus Schulten. Journal of Physical Chemistry B, 105:10124-10131, 2001. |
| 302. Molecular dynamics study of bacteriorhodopsin and the purple membrane. Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus Schulten. Journal of Physical Chemistry B, 105:905-918, 2001. |
| 285. Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Emad Tajkhorshid, Jerome Baudry, Klaus Schulten, and Sandor Suhai. Biophysical Journal, 78:683-693, 2000. |
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