Emad Tajkhorshid's Publication List

return to Emad's home page

Full List of Publications:

2009

Publications Database 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.

2008

Publications Database 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. 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. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 95:2292-2300, 2008. 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. Indirect role of Ca2+ in the assembly of extracelluar matrix proteins. Jiankuai Diao and Emad Tajkhorshid. Biophysical Journal, 95:120-127, 2008. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008. 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, volume 60, chapter 12, pp. 343-367. Elsevier, 2008. 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. Thrombosis Research, 122:S23-S26, 2008. 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. 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.

2007

Publications Database Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Journal, 93:496-504, 2007. Molecular mechanisms of conduction and selectivity in aquaporin water channels. Yi Wang and Emad Tajkhorshid. Journal of Nutrition, 137:1509S-1515S, 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. 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.

2006

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

2005

Publications Database 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. 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. 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. 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. 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.
Determination of structural and functional overlap/divergence of five proto-type galectins by analysis of the growth-regulatory interaction with ganglioside GM1 in silico and in vitro human neuroblastoma cells. S. Andre, H. Kaltner, M. Lensch, R. Russwurm, H.-C. Siebert, Emad Tajkhorshid, A. J. R. Heck, M. von Knebel-Doeberitz, H.-J. Gabius, and J. Kopitz. Int. J. Cancer, 114:46-57, 2005.

2004

Publications Database Molecular basis of proton blockage in aquaporins. Nilmadhab Chakrabarti, Emad Tajkhorshid, Benoît Roux, and Régis Pomès. Structure, 12:65-74, 2004. 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. 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. 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. Complementarities and convergence of results in bacteriorhodopsin trimer simulations. Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 87:1394-1395, 2004. Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004. 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.

2003 and earlier

Publications Database Developing an energy landscape for the novel function of a (β/α)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. 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. 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. 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. 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. Electrostatic tuning of permeation and selectivity in aquaporin water channels. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:2884-2899, 2003.
Unique Conformer Selection of the Human Growth-regulatory Lectin Galectin-1 for Ganglioside GM1 Versus Bacterial Toxins. H.-C. Siebert, S. Andre, S.-Y. Lu, M. Frank, H. Kaltner, J. A. van Kuik, E. Y. Korchagina, N. Bovin, . Tajkhorshid, R. Kaptein, J. F. G. Vliegenhart, C.-W. von der Lieth, J. Jimenez-Barbero, J. Kopitz, and H.-J. Gabius. Biochemistry, 42:14762-14773, 2003.
Publications Database Control of the selectivity of the aquaporin water channel family by global orientational tuning. Emad Tajkhorshid, Peter Nollert, Morten O. 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 O. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:6731-6736, 2002.
Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules. Hongyi Zhou, Emad Tajkhorshid, Thomas Frauenheim, Sandor Suhai, and M. Elstner. Chemical Physics, 277:91-103, 2002.

Structure and spectral tuning mechanism of photo-sensory protein sRII (pR). Shigehiko Hayashi, Emad Tajkhorshid, and K. Schulten. Biophysics (Seibutsu-Butsuri), 42:127-130, 2002.
Publications Database Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002. 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. 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.
Publications Database The mechanism of glycerol conduction in aquaglyceroporins. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, 9:1083-1093, 2001. 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. 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. 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.
Comparison of aqueous solvent models used in the calculation of the Raman and ROA spectra of L-alanine. K. J. Jalkanen, R. M. Nieminen, K. Frimand, J. Bohr, H. Bohr, R. Wade, E. Tajkhorshid, and S. Suhai. Chem. Phys., 265:125-151, 2001.

Barriers to rotation around the Csp2-Csp2 bond of the ketoaldehyde enol ether MeC(O)=CH-OEt as determined by 13C NMR and ab initio calculation. H. C. Siebert, E. Tajkhorshid, and J. Dabrowski. J. Phys. Chem. A, 105:8488-8494, 2001.
Publications Database 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.
The dielectric effects of the environment on the the pKa of the retinal Schiff Base and on the stabilization of the ion pair in bacteriorhodopsin. Emad Tajkhorshid and S. Suhai. THEOCHEM J. Mol. Structure, 501-502:297-313, 2000.

Emad Tajkhorshid, Bela Paizs, and Sandor Suhai. Role of isomerization barriers in the pKa control of the retinal Schiff base: a density functional study. J. Phys. Chem. B, 103(21):4518-4527, 1999.

Wenge Han, Emad Tajkhorshid and Sandor Suhai (1999) QM/MM study of the active site of free papain and NMA-papain complex. J. Biomolecular Structure and Dynamics, 16(5), 1019-1032.

E. Tajkhorshid and S. Suhai (1999) Dielectric effects due to the protein environment on the structure and proton affinity of the retinal Schiff base. Chem. Phys. Lett., 299:457-464.

E. Tajkhorshid and S. Suhai (1999) Influence of the methyl groups on the structure, charge distribution, and proton affinity of the retinal Schiff base. J. Phys. Chem. B, 103(26): 5581-5590.

E. Tajkhorshid and S. Suhai (1999) The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in Bacteriorhodopsin. Theoret. Chem. Accounts (Theoret. Chim. Acta), 101/1-3:180-185.

B. Paizs, E. Tajkhorshid, and S. Suhai (1999) Electronic effects on the ground state rotational barrier of the chromophore in bacteriorhodopsin: a molecular orbital study. J. Phys. Chem. B, 103(25), 5388-5395.

E. Tajkhorshid, K. J. Jalkanen and S. Suhai (1998) A density functional study of the structures and vibrational spectra of the zwitterion L-alanine in the presence of explicit water molecules. J. Phys. Chem. B, 102 (30), 5899-5913.

C.-W. von der Lieth, H.-C. Siebert, T. Kozar, M. Burchert, M. Frank, M. Gilleron, H. Kaltner, G. Kayser, E. Tajkhorshid, N. V. Bovin, J. F. G. Vliegenthart and H.-J. Gabius (1998) Lectin ligands: New insights into their conformations and their dynamic behaviour and the discovery of conformer selection by lectins. Acta Anatomica, 161, 91-109.

E. Tajkhorshid, B. Paizs and S. Suhai (1997) Conformational effects on the proton affinity of the Schiff Base in bacteriorhodopsin: a density functional study. J. Phys. Chem. B, 101 (40), 8021-8028.

H.-C. Siebert, R. Adar, R. Arango, M. Burchert, H. Kaltner, G. Kayser, E. Tajkhorshid, C.-W. von der Lieth, R. Kaptein, N. Sharon, J. F. G. Vliegenthart and H.-J. Gabius (1997) Involvement of laser photo CIDNP-reactive amino acid side chains in ligand binding by galctoside-specific lectins in solution. Similarities in the role of tryptophan/tyrosine residues for ligand binding between a plant agglutinin and mammalian/avian galectins and the detection of an influence of single-site mutagenesis on surface presentation of spatially separated residues. Eur. J. Biochem., 249, 27-38.

E. Tajkhorshid, H.-C. Siebert, M. Burchert, H. Kaltner, G. Kayser, C.-W. von der Lieth, R. Kaptein, J. F. G. Vliegenthart and H.-J. Gabius (1997) A combined molecular modelling and CIDNP study of similarities in the pattern of ligand binding in mammalian and avian galectins. J. Mol. Model., 3 (8), 325-331.

I. Yavari, E. Tajkhorshid, D. Nourishargh and S. Balalaie (1997) Semiempirical SCF-MO study of bowl-to-bowl inversion in corannulene and smaller circulenes. THEOCHEM J. Mol. Structure, 393, 163-166.

H.-C. Siebert, E. Tajkhorshid, C.-W. v.d. Lieth, R. Kleineidam, S. Kruse, R. Schauer, R. Kaptein, H.-J. Gabius and J. F. G. Vliegenthart (1996) Knowledge-based homology modelling and experimental determination of amino acid side chain accessibility by the laser photo CIDNP (chemically induced dynamic nuclear polarization) approach in solution: lessons from the small sialidase of Clostridium perfringens. J. Mol. Model., 2, 446-455.

N. Radjaee-Behbahani, A. R. Dehpour, E. Tajkhorshid and K. Kheirollahi (1996) Clonidine-induced rhythmic activity in rabbit annococcygeus muscle. Gen. Pharmacol., 27 (3) , 525-528.

A. R. Dehpour, E. Tajkhorshid, A. Alimian and N. Radjaee-Behbahani (1995) Different calcium dependencies of contractile activity of prostatic and epididymal portions of rat vas deferens. Gen. Pharmacol., 26 (3), 633-639.

A. R. Dehpour, E. Tajkhorshid and N. Radjaee-Behbahani (1994) The role of calcium and alpha-adrenoceptors in contractile response of chick expansor secundariorum muscle to field stimulation. Gen. Pharmacol., 25 (2), 317-323.

A. R. Dehpour, E. Tajkhorshid, N. Radjaee-Behbahani and K. Kheirollahi (1993) Methoxamine-induced rhythmic activity in rabbit annococcygeus muscle. Gen. Pharmacol., 24 (4), 841-845.

E. Tajkhorshid and P. Rashidi-Ranjbar, (1992) Successes of computer-aided molecular design. Iran. J. Chem. Chem. Engineering , 11 (1), 86-100.