Publications
2013
S. A. Shaikh, J. Li, G. Enkavi, P.-C. Wen, Z. Huang, and E. Tajkhorshid (2013) Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations. Biochemistry (Current Topic), 52: 569-587.
J. Li, G. Enkavi, P.-C. Wen, S. A. Shaikh, and E. Tajkhorshid (2013) Transient Formation of Water-conducting States in Membrane Transporters. Proceedings of the National Academy of Sciences USA, 110: 7696-7701.
G. Enkavi, J. Li, P. Mahinthichaichan, P.-C. Wen, Z. Huang, S. A. Shaikh, and E. Tajkhorshid (2013) Simulation Studies of the Mechanism of Membrane Transporters. In Editors: Luca Monticelli and Emppu Salonen, “Biomolecular Simulations – Methods and Protocols”, Humana Press. Methods in Molecular Biology, Vol. 924, Part 2, 361-405.
U. K. Eriksson, G. Fischer, R. Friemann, G. Enkavi, E. Tajkhorshid*, and R. Neutze* (2013) Sub-Angstrom resolution x-ray structure details aquaporin-water interactions. Science, in press.
P.-C. Wen, B. Verhalen, S. Wilkens, H. Mchaourab, and E. Tajkhorshid (2013) On the Origin of Large Flexibility of P-glycoprotein in the Inward-Facing State. Journal of Biological Chemistry, in press.
R. R. Geyer, R. Musa-Aziz, G. Enkavi, P. Mahinthichaichan, E. Tajkhorshid, and W. Boron (2013) Movement of NH3 through the Human Urea Transporter B (UT-B): A New Gas Channel. American Journal of Physiology - Renal Physiology, in press.
2012
Y. Z. Ohkubo, T. V. Pogorelov, M. J. Arcario, G. Christensen, and E. Tajkhorshid (2012) Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Biophysical Journal, 102: 2130-2139.(Cover Article)
E. J. Levin, Y. Cao, G. Enkavi, M. Quick, Y Pan, E. Tajkhorshid*, and M. Zhou* (2012) Structure and permeation mechanism of a mammalian urea transporter. Proceedings of the National Academy of Sciences USA, 109: 11194-11199.
N. Noinaj, N. C. Easley, M. Oke, N. Mizuno, J. C. Gumbart, E. Boura, A. N. Steere, O. Zak, P. Aisen, E. Tajkhorshid, R. W. Evans, A. R. Gorringe, A. B. Mason, A. C. Steven, and S. K. Buchanan (2012) Structural basis for iron piracy by pathogenic Neisseria. Nature, 483, 53–58
J. Li and E. Tajkhorshid (2012) A Gate-Free Pathway for Substrate Release from the Inward-Facing State of the Na+-Galactose Transporter. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818: 263-271. NIHMSID: 329267
M. Musgaard, L. Thøgersen, B. Schiøtt, and E. Tajkhorshid (2012) Tracing Cytoplasmic Ca2+ Ion and Water Access Points in the Ca2+-ATPase. Biophysical Journal, 102: 268-277.
T. J. Barnard, J. C. Gumbart, J. H. Peterson, N. Noinaj, N. C. Easley, N. Dautin, A. J. Kuszak, E. Tajkhorshid, H. D. Bernstein, and S. K. Buchanan (2012) Molecular Basis for Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter. Journal of Molecular Biology, 415: 128-142.
F. Khalili-Araghi, E. Tajkhorshid, B. Roux, and K. Schulten (2012) Molecular dynamics investigation of the omega current in the Kv1.2 voltage sensor domains. Biophysical Journal, 102: 258-267.
J. H. Morrissey, E. Tajkhorshid, S. G. Sligar, and C. M. Rienstra (2012) Tissue Factor/Factor VIIa Complex: Role of the Membrane Surface. Thrombosis Research, 129: S8-S10.
2011
P-C Wen and E. Tajkhorshid (2011) Conformational Coupling of the Nucleotide-Binding and the Transmembrane Domains in ABC Transporters. Biophysical Journal, 101: 680-690.
N. Tavoosi, R. L. Davis-Harrison, T. V. Pogorelov, Y. Z. Ohkubo, M. J. Arcario, M. C. Clay, C. M. Rienstra, E. Tajkhorshid, and J. H. Morrissey (2011) Molecular Determinants of Phospholipid Synergy in Blood Clotting. Journal of Biological Chemistry, 286: 23247-23253. (Cover Article)
M. J. Arcario, Y. Z. Ohkubo, and E. Tajkhorshid (2011) Capturing Spontaneous Partitioning of Peripheral Proteins using a Biphasic Membrane-Mimetic Model. Journal of Physical Chemistry B, 115: 7029–7037. PMCID: PMC3102442.
J. Boettcher, R. Davis-Harrison, M. Clay, A. Nieuwkoop, Y. Z. Ohkubo, E. Tajkhorshid, J. H. Morrissey, and C. Rienstra (2011) Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers. Biochemistry, 50: 2264–2273.
Z. Huang, S. A. Shaikh, P.-C. Wen, G. Enkavi, J. Li, and E. Tajkhorshid (2011) Membrane Transporters - Molecular Machines Coupling Cellular Energy to Vectorial Transport Across the Membrane. In Editor: Benoit Roux, "Molecular Machines", Chapter 9: pp. 151–182, World Scientific Publishing, Singapore.
J. H. Morrissey, E. Tajkhorshid, and C. M. Rienstra (2011) Nanoscale studies of protein-membrane interactions in blood clotting. Journal of Thrombosis and Haemostasis, 9 (Suppl. 1):162-167.
2010
Z. Huang and E. Tajkhorshid (2010) Identification of the Third Na+ Site and the Sequence of Extracellular Binding Events in the Glutamate Transporter. Biophysical Journal, 99: 1416-1425.
S. Shaikh and E. Tajkhorshid (2010) Modeling and dynamics of the inward-facing state of a Na+/Cl− dependent neurotransmitter transporter homologue. PLoS Computational Biology, 6(8): e1000905.
Y. Z. Ohkubo, J. H. Morrissey, and E. Tajkhorshid (2010) Dynamical view of human tissue factor, factor VIIa, and their complex in solution and on the surface of anionic membranes. Journal of Thrombosis and Hemostasis, 8: 1044-1053. PMCID: PMC2890040.
Y. Wang, S. A. Shaikh, and E. Tajkhorshid (2010) Exploring transmembrane diffusion pathways with molecular dynamics. Physiology, 25: 142-145.
G. Enkavi and E. Tajkhorshid (2010) Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT. Biochemistry, 49: 1105-1114. PMCID: PMC2829668.
Y. Wang and E. Tajkhorshid (2010) Nitric oxide conduction by the brain aquaporin AQP4. PROTEINS, Structure, Function, and Bioinformatics, 78(3): 661-670. PMCID: PMC2805761.
J. H. Morrissey, R. L. Davis-Harrison, N. Tavoosi, K. Ke, V. Pureza, J. M. Boettcher, M. C. Clay, C. M. Rienstra, Y. Z. Ohkubo, T. V. Pogorelov, and E. Tajkhorshid (2010) Protein-Phospholipid interactions in blood clotting. Thrombosis Research, 125 (Suppl. 1): S23-S25. PMCID: PMC2838931.
A. Kokhan, C. Wraight, and E. Tajkhorshid (2010) The Binding Interface of Cytochrome C and Cytochrome C1 in the BC1 Complex: Rationalizing the Role of Key Residues. Biophysical Journal, 99: 2647-2656.
J. Diao, A. J. Maniotis, R. Follberg, and E. Tajkhorshid (2010) Interplay of mechanical and binding properties of fibronectin type I. Theoretical Chemistry Accounts, 125: 397-405. PMCID: PMC2932639.
F. Khalili-Araghi, V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten (2010) Calculation of the gating charge for the Kv1.2 voltage–activated potassium channel. Biophysical Journal, 98: 2189-2198.
P.-C. Wen, Z. Huang, G. Enkavi, Y. Wang, J. C. Gumbart, and E. Tajkhorshid (2010) Molecular mechanisms of active transport across the cellular membrane. In, Editors: Mark Sansom and Philip Biggin, "Molecular Simulations and Biomembranes: From Biophysics to Function" pp. 248-286. Royal Society of Chemistry, Cambridge, UK.
S. Shaikh, P.-C. Wen, G. Enkavi, Z. Huang, and E. Tajkhorshid (2010) Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation. Journal of Computational and Theoretical Nanosciences, 7;2481-2500.
J. Feng, E. Lucchinetti, G. Enkavi, Y. Wang, P. Gehrig, B. Roschitzki, M. C. Schaub, E. Tajkhorshid, K. Zaugg, and M. Zaugg (2010) Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria. American Journal of Physiology - Cell Physiology, 298: 740-748.
X.-D. Yang, E. Tajkhorshid, and L.-F. Chen (2010) Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-kappaB. Molecular and Cellular Biology, 30: 2170-2180.
H.-C. Siebert, M. Burg-Roderfeld, Th. Eckert, S. Stötzel, U. Kirch, T. Diercks, M. J. Humphries, M. Frank, R. Wechselberger, E. Tajkhorshid, and S. Oesser (2010) Interaction of the alpha2A domain of integrin with small collagen fragments. Protein and Cell, 1:393-405.
2009
J. Li and E. Tajkhorshid (2009) Ion-releasing State of A Secondary Membrane Transporter. Biophysical Journal, 97: L29-L31.
Ch. Law, G. Enkavi, D.-N. Wang, and E. Tajkhorshid (2009)
Structural basis of substrate selectivity in the glycerol-3-phosphate:phosphate antiporter GlpT.
Biophysical Journal, 97: 1346-1353.
PMCID: PMC2749764.
J. C. Gumbart, M. C. Wiener, and E. Tajkhorshid (2009)
Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB.
Journal of Molecular Biology, 393: 1129-1142.
PMCID: PMC2775145.
F. Khalili-Araghi, J. C. Gumbart, P.-C. Wen, M. Sotomayor, E. Tajkhorshid, and K. Schulten (2009) Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19: 128-137.
M. Nyblom, A. Frick, Y. Wang, M. Ekvall, K. Hallgren, K. Hedfalk, R. Neutze, E. Tajkhorshid, and S. Tornroth-Horsefield (2009) Structural and Functional Analysis of SoPIP2;1 Mutants Adds Insight into Plant Aquaporin Gating. Journal of Molecular Biology, 387: 653-668.
S. Hayashi, E. Tajkhorshid, and K. Schulten (2009) Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation. Biophysical Journal, 96: 403-416.
J. Dittmer, L. Thogersen, J. Underhaug, K. Bertelsen, T. Vosegaard, J. M. Pedersen, B. Schiott, E. Tajkhorshid, T. Skrydstrup, and N. C. Nielsen (2009) Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles. Journal of Physical Chemistry B, 113: 6928-6937.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, C. M. Rienstra, A. Z. Kijak, Y. Z. Ohkubo, and E. Tajkhorshid (2009) Protein-membrane interactions: Blood clotting on nanoscale bilayers. Journal of Thrombosis and Haemostasis, 7 (Suppl. 1):169-172.
K. Bertelsen, B. Paaske, L. Thogersen, E. Tajkhorshid, B. Schiott, T. Skrydstrup, N. Chr. Nielsen, and Th. Vosegaard (2009) Residue-Specific Information about the Dynamics of Antimicrobial Peptides from 1H-15N and 2H Solid-State NMR Spectroscopy. Journal of the American Chemical Society, 131: 18335-18342.
2008
Y. Wang and E. Tajkhorshid (2008) Electrostatic funneling of substrate in mitochondrial membrane carriers. Proceedings of the National Academy of Sciences USA, 105: 9598-9603.
Z. Huang and E. Tajkhorshid (2008) Dynamics of the Extracellular Gate and Ion-Substrate Coupling in the Glutamate Transporter. Biophysical Journal, 95: 2292-2300.
Y. Zenmei Ohkubo and E. Tajkhorshid (2008) Distinct Structural and Adhesive Roles of Ca2+ in Membrane Binding of Blood Coagulation Factors. Structure, 16: 72-81.
L. Celik, B. Schiott, and E. Tajkhorshid (2008) Substrate binding and formation of an occluded state in the leucine transporter. Biophysical Journal, 94: 1600-1612.
Y. Wang, Y. Zenmei Ohkubo and E. Tajkhorshid (2008) Gas conduction of lipid bilayers and membrane channels. In Scott Feller, Editor, Computational Modeling of Membrane Bilayers. Elsevier, Oxford, UK. Current Topics in Membranes, 60: 343-367.
J. Diao and E. Tajkhorshid (2008) Indirect role of Ca2+ in the assembly of the extracellular matrix proteins. Biophysical Journal, 95: 120-127.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, Y. Z. Ohkubo, and E. Tajkhorshid (2008) Blood clotting reactions on nanoscale phospholipid bilayers. Thrombosis Research, 122: S23-S26.
L. Thogersen, B. Schiott, T. Vosegaard, N. Chr. Nielsen, and E. Tajkhorshid (2008) Peptide Aggregation and Pore Formation in a Lipid Bilayer - a Combined Coarse Grained and All Atom Molecular Dynamics study. Biophysical Journal, 95: 4337-4347.
S. A. Shaikh and E. Tajkhorshid (2008) Potential cation and H+ binding sites in acid sensing ion channel-1. Biophysical Journal, 95: 5153-5164.
P.-C. Wen and E. Tajkhorshid (2008) Dimer Opening of the Nucleotide Binding Domains of ABC Transporters after ATP hydrolysis. Biophysical Journal, 95: 5100-5110.
B. Isin, K. Schulten, E. Tajkhorshid, and I. Bahar. (2008) Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes. Biophysical Journal, 95: 789-803.
T. Vosegaard, K. Bertelsen, J. M. Pedersen, L. Thogersen, B. Schiott, E. Tajkhorshid, T. Skrydstrup, and N. Chr. Nielsen (2008) Resolution Enhancement in Solid-State NMR Spectra of Oriented Membrane Proteins by Anisotropic Differential Linebroadening. The Journal of the American Chemical Society, 130: 5028-5029.
J. Henin, E. Tajkhorshid, K. Schulten, and C. Chipot (2008) Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophysical Journal, 94: 832-839 (cover article).
2007
J. C. Gumbart, M. C. Wiener, and E. Tajkhorshid (2007)
Mechanics of force propagation in TonB-dependent outer membrane transport.
Biophysical Journal, 93: 496-504 (cover article).
Highlighted in Science Editors' Choice: Science 316: 1099-1101 (2007).
Y. Wang and E. Tajkhorshid (2007) Molecular mechanisms of conduction and selectivity in aquaporin water channels. Journal of Nutrition, 137: 1509S-1515S.
Y. Wang, J. Cohen, W. Boron, K. Schulten, and E. Tajkhorshid (2007) Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. Journal of Structural Biology, 157: 534-544.
M. Jensen, Y. Yin, E. Tajkhorshid, and K. Schulten (2007) Sugar transport across lactose permease probed by steered molecular dynamics. Biophysical Journal, 93: 92-102.
S. Tornroth-Horsefield, K. Hedfalk, M. Karlsson, U. Johanson, Y. Wang, E. Tajkhorshid, R. Horsefield, M. Nyblom, A. Backmark, P. Kjellbom, and R. Neutze (2007) Aquaporin gating. Journal of Biomolecular Structure and Dynamics, 24: 719-721.
2006
S. Tornroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson, E. Tajkhorshid*, R. Neutze*, and P. Kjellbom* (2006) Structural mechanism of plant aquaporin gating. Nature, 439: 688-694.
J. Yu, A. Yool, K. Schulten, and E. Tajkhorshid (2006) Mechanism of Gating and Ion Conductivity of a Possible Tetrameric Pore in Aquaporin-1. Structure, 14: 1411-1423.
F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten (2006) Dynamics of K+ ion conduction through Kv1.2. Biophysical Journal, 91: L72-L74.
P. H. Koenig, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, Th. Frauenheim and Q. Cui (2006) Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. Journal of Physical Chemistry A, 110: 548-563.
H.-C. Siebert, E. Tajkhorshid, J. F. G. Vliegenthart, C.-W. von der Lieth, S. Andre, and H.-J. Gabius (2006) Laser photo CIDNP technique as a versatile tool for structural analysis of inter- and intramolecular protein - carbohydrate interactions. In J. F. G. Vliegenthart, R. Woods (eds.), NMR spectroscopy and computer modeling of carbohydrates. ACS Symposia Series, 930: 81-113.
M. Hoffmann, M. Wanko, P. Strodel, P. H. Koenig, Th. Frauenheim, K. Schulten, W. Thiel, E. Tajkhorshid, and M. Elstner (2006) Color tuning in Rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. Journal of the American Chemical Society, 128: 10808-10818.
Y. Yin, M. Jensen, E. Tajkhorshid, and K. Schulten (2006) Sugar binding and protein conformational changes in lactose permease. Biophysical Journal, 91: 3972-3985.