Publications

2017

Tim1 in its membrane-bound form
G. T. Tietjen*, J. L. Baylon*, D. Kerr, Z. Gong, J. M. Henderson, C. T. R. Heffern, M. Meron, B. Lin, M. L. Schlossman, E. J. Adams, E. Tajkhorshid*, and K. Y. C. Lee* (2017) Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1. Biophysical Journal, 113: 1505-1519.

phospholipid transolcation pathway
T. Jiang, K. Yu, H. C. Hartzell, and E. Tajkhorshid (2017) Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase. eLife, 10.7554/eLife.28671.

S. Chen, Y. Zhao, Y. Wang, M. Shekhar, E. Tajkhorshid, and E. Gouaux (2017) Activation and desensitization mechanism of AMPA receptor-TARP complex by cryo-EM. Cell, 170(6): 1234-1246.

pathway of desflurane binding to GLIC - cover
M. J. Arcario, C. G. Mayne, and E. Tajkhorshid (2017) A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus Ion Channel. J. Biol. Chem., 292(23), 9480-9492. (Cover Article)

Outward-facing state of P-glycoprotein
B. Verhalen, R. Dastvan, S. Thangapandian, Y. Peskova, H. A. Koteiche, R. K. Nakamoto, E. Tajkhorshid, and H. S. Mchaourab (2017) Energy Transduction and Alternating Access of the mammalian ABC Transporter P-glycoprotein. Nature, 543: 738-741.

F. Zeng, Y. Chen, J. Remis, M. S. Shekhar, J. C. Phillips, E. Tajkhorshid, and H. Jin (2017) Structural Basis of Co-translational Quality Control by ArfA and RF2 Binding to Ribosome. Nature, 541, 554-557.

J. V. Vermaas and E. Tajkhorshid (2017) Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed at Atomic Detail. Biochemistry, 56: 281-293.

Psb28 docking on to RC47
D. A. Weisz, H. Liu, H. Zhang, S. Thangapandian, E. Tajkhorshid, M. L. Gross, and H. B. Pakrasi (2017) Structural analysis of Photosystem II: Mass spectrometry-based cross-linking study show that the Psb28 protein binds to cytochrome b559. Proceedings of the National Academy of Sciences USA, 114: 2224-2229.

Klaus Schulten
E. Tajkhorshid and C. Chipot (2017) Tribute to Klaus Schulten. Journal of Physical Chemistry B, Klaus Schulten Memorial Issue, 121: 3203-5.

Search for an in silico solvent
J. V. Vermaas, T. V. Pogorelov, and E. Tajkhorshid (2017) Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents. Journal of Physical Chemistry B, 121: 3764-3776.

A. K. S. Camara, Y. Zhou, P.-C. Wen, E. Tajkhorshid and W.-M. Kwok (2017) Mitochondrial VDAC1: A Key Gatekeeper as Potential Therapeutic Target. Frontiers in Physiology, 8: 640.

X. Yu, G. Yang, C. Yan, J. L. Baylon, J. Jiang, H. Fan, G. Lu, K. Hasegawa, H. Okumura, T. Wang, E. Tajkhorshid, S. Li, and N. Yan (2017) Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters. Cell Research, 27: 1020-1033.

J. H. Leung, P. Mahinthichaichan, E. Tajkhorshid, A. Ishchenko, V. Cherezov, M. Soltis, B. J. Jackson, C. D. Stout, R. B. Gennis, Q. Zhang, and P. S. Padayatti (2017) Critical role of water molecules in proton translocation by the membrane-bound transhydrogenase. Structure, 25(7): 1111-1119.e3.

M. P. Muller, Y. Wang, J. H. Morrissey, and E. Tajkhorshid (2017) Lipid Specificity of the Membrane Binding Domain of Coagulation Factor X. J. Thromb. Haemost., In press.

Giovanni Gonzalez-Gutierrez, Yuhang Wang, Gisela Cymes, Emad Tajkhorshid, and Claudio Grosman (2017) Chasing the open-state structure of pentameric ligand-gated ion channels J. Gen. Physiol., accepted

2016

N. Trebesch, J. V. Vermaas, E. Tajkhorshid (2016) Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. In Editor: Carmen Domene, "Computational Biophysics of Membrane Proteins", Chapter 7: pp. 197-236. Royal Society of Chemistry, Cambridge, UK.

ion permeation through P2X receptor
S. E. Mansoor, W. Lü, W. Oosterheert, M. Shekhar, E. Tajkhorshid, and E. Gouaux (2016) X-ray structures of human P2X3 receptor define complete gating cycle and antagonist action. Nature, 538, 66-71.

T. Jiang, W. Han, M. Maduke, and E. Tajkhorshid (2016) Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl-/H+ Exchanger ClC-ec1. Journal of the American Chemical Society, 138: 3066-3075.

C. M. Khantwal, S. J. Abraham, W. Han, T. Jiang, T. S. Chavan, R. C. Cheng, S. M. Elvington, C. W. Liu, I. I. Mathews, E. Tajkhorshid*, and M. Maduke* (2016) Revealing an outward-facing open conformational state in a CLC Cl/H exchange transporter. eLife, 10.7554/eLife.11189.

J. Vermaas, N. Trebesch, C. G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J. L. Baylon, T. Jiang, Y. Wang, M. P. Muller, E. Shinn, Z. Zhao, P.-C. Wen, and E. Tajkhorshid (2016) Microscopic Characterization of Membrane Transport Function by In Silico Modeling and Simulation. In Gregory A. Voth, editor: Methods in Enzymology, Vol 578: Computational Approaches for Studying Enzyme Mechanism Part B, MIE, UK: Academic Press, 2016, pp. 373-428.

P. Mahinthichaichan, R. Gennis, and E. Tajkhorshid (2016) All the O2 consumed by Thermus thermophilus cytochrome ba3 is delivered to the active site through a long, open hydrophobic tunnel with entrances within the lipid bilayer. Biochemistry, 55(8): 1265-1278..

small molecule - memberane interactions toc
C. G. Mayne, M. J. Arcario, P. Mahinthichaichan, J. L. Baylon, J. V. Vermaas, L. Navidpour, P.-C. Wen, S. Thangapandian, and E. Tajkhorshid (2016) The Cellular Membrane as a Mediator for Small Molecule Interaction with Membrane Proteins. Biochimica et Biophysica Acta - Biomembranes, 1058(10), 2290-2304.

J. L. Baylon, J. V. Vermaas, M. P. Muller, M. J. Arcario, T. V. Pogorelov, and E. Tajkhorshid (2016) Atomic-Level Description of Protein--Lipid Interactions Using an Accelerated Membrane Model. Biochimica et Biophysica Acta - Biomembranes, 1858: 1573-1583.

Cytochrome C2 binding on to BC1 complex
A. Singharoy, A. Barragan, S. Thangapandian, E. Tajkhorshid, and K. Schulten (2016) Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2. Journal of the American Chemical Society, 138: 12077-12089.

K. K. Skeby, O. J. Andersen, T. V. Pogorelov, and E. Tajkhorshid*, and B. Schiøtt* (2016) Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form. Biochemistry, 55: 2031-2042.

W. R. Arnold, J. L. Baylon, E. Tajkhorshid*, and A. Das* (2016) Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55: 6969-6980.

J. Vermaas, D. Hardy, J. Stone, E. Tajkhorshid*, and A. Kohlmeyer* (2016) TopoGromacs: Automated Topology Conversion from CHARMM to Gromacs within VMD. Journal of Chemical Information and Modeling, 56: 1112-1116.

stapled peptides cover
T. E. Speltz, S. W. Fanning*, C. G. Mayne*, C. Fowler, E. Tajkhorshid, G. L. Greene, and T. W. Moore (2016) Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction. Angewandte Chemie International Edition, 55: 4252-4255. ("Hot Paper", Cover Article)

P. Hosseinzadeh, E. Mirts, T. Pfister, Y-G. Gao, C. G. Mayne, H. Robinson, E. Tajkhorshid, and Y. Lu (2016) Enhancing Mn(II)-binding and manganese peroxidase activity in a designed cytochrome c peroxidase through fine-tuning secondary sphere interactions. Biochemistry, 55(10): 1494-1502.

S. W. Fanning*, C. G. Mayne*, V. Dharmarajan*, K. E. Carlson, T. A. Martin, S. J. Novick, W. Toy, B. Green, S. Panchamukhi, B. S. Katzenellenbogen, E. Tajkhorshid, P. R. Griffin, Y. Shen, S. Chandarlapaty, J. A. Katzenellenbogen, and G. L. Greene (2016) Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation. eLife, 10.7554/eLife.12792. (Accompanied by a "Related Insight" Article)

C. Sun, A. T. Taguchi, J. V. Vermaas, N. J. Beal, P. J. O'Malley*, E. Tajkhorshid*, R. B. Gennis*, and S. A. Dikanov* (2016) Q-band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry, 55: 5714-5725.

2015

Transport Cycle Thermodynamics
M. Moradi, G. Enkavi, and E. Tajkhorshid (2015) Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:Phosphate Antiporter. Nature Communications, 6:8393. PMC4598623

J. Li, P.-C. Wen, M. Moradi, and E. Tajkhorshid (2015) Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters Current Opinion in Structural Biology, 31: 96-105. PMC4476910

J. Li, J. Newhall, N. Ishiyama, C. Gottardi, M. Ikura, D. E. Leckband*, and E. Tajkhorshid* (2015) Structural Determinants of the Mechanical Stability of Alpha Catenin. Journal of Biological Chemistry, 290: 18890-18903.

J. L. Baylon and E. Tajkhorshid (2015) Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide. Journal of Physical Chemistry B, 119(25): 7882-7893.

J. V. Vermaas, J. L. Baylon, M. J. Arcario, M. P. Muller, Zh. Wu, T. V. Pogorelov, and E. Tajkhorshid (2015) Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. Journal of Membrane Biology, 248: 563-582. PMC4490090

J. V. Vermaas, A. T. Taguchi, S. A. Dikanov, C. A. Wraight, and E. Tajkhorshid (2015) Redox Potential Tuning Through Differential Quninone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides Biochemistry, 54: 2104-2116.

I. G. Denisov, Y. V. Grinkova, J. L. Baylon, E. Tajkhorshid, and S. G. Sligar (2015) Mechanism of Drug-Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Biochemistry, 54: 2227-2239.

D. R. McDougle*, J. L. Baylon*, D. D. Meling, A. Kambalyal, Y. V. Grinkova, J. Hammernik, E. Tajkhorshid*, and A. Das* (2015) Incorporation of Charged Residues in the CYP2J2 F-G Loop Disrupts CYP2J2-Lipid Bilayer Interactions. Biochimica et Biophysica Acta - Biomembranes, 1848: 2460-2470.

J. Madsen, Y. Z. Ohkubo, G. Peters, J. H. Faber, E. Tajkhorshid*, and O. H. Olsen* (2015) Membrane interaction of the factor VIIIa discoidin domains in atomistic details. Biochemistry, 54: 6123-6131.

Y. Qi, X. Cheng, J. Lee, J. Vermaas, T. V. Pogorelov, E. Tajkhorshid, S. Park, J. B. Klauda, and W. Im (2015) CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical Journal, 109: 2012-22.

2014

M. J. Arcario, C. G. Mayne, and E. Tajkhorshid (2014) Atomistic models of general anesthetics for use in in silico biological studies. Journal of Physical Chemistry B, 118: 12075-12086.

W. Han, R. Chang, M. Maduke, and E. Tajkhorshid (2014) Water Access Points and Hydration Pathways in the ClC-ec1 H+/Cl- Transporters. Proceedings of the National Academy of Sciences USA, 111: 1819-1824. (Cover Article)

lipid insertion cover
J. V. Vermaas and E. Tajkhorshid (2014) A Microscopic View of Phospholipid Insertion into Biological Membranes. Journal of Physical Chemistry B, 118: 1754-1764. (Cover Article)

Amino acid insertion TOC
T. V. Pogorelov, J. V. Vermaas, M. J. Arcario, and E. Tajkhorshid (2014) Partitioning of amino acids into a model membrane: capturing the interface. Journal of Physical Chemistry B, 118: 1481-1492. PMCID: PMC3983343

R. E. Hulse, J. Sachleben, P.-C. Wen, M. Moradi, E. Tajkhorshid, and E. Perozo (2014) Conformational dynamics at the inner gate of KcsA during activation. Biochemistry (Rapid Report), 53: 2557-2559. (live molecular demo sessions of KcsA channel)

S. Mishra, B. Verhalen, R. A. Stein, P.-C. Wen, E. Tajkhorshid, and H. S. Mchaourab (2014) Conformational Dynamics of the Nucleotide Binding Domains and the Power Stroke of a Heterodimeric ABC Transporter. eLife, 3: e02740

M. Moradi and E. Tajkhorshid (2014) Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. Journal of Chemical Theory and Computation, 10: 2866-2880. PMCID: PMC4089915

A. Barati Farimani, N. Aluru, and E. Tajkhorshid (2014) Thermodynamic Insight into Spontaneous Hydration and Rapid Water Permeation in Aquaporins. Applied Physics Letters, 105, 083702.

J. V. Vermaas and E. Tajkhorshid (2014) Conformational Heterogeneity of alpha-synuclein in Membrane. Biophysica Biochemica Acta - Biomembranes, 1838: 3107-3117.

M. J. Arcario and E. Tajkhorshid (2014) Membrane-Induced Structural Rearrangement of Talin Subdomains Providing a Molecular Mechanism for Inside-Out Activation of Integrin. Biophysical Journal, 107: 2059-2069.
Animation highlighted on the Biophysical Journal page

A. E. Blanchard*, M. J. Arcario*, K. Schulten, and E. Tajkhorshid (2014) A Highly Tilted Membrane Configuration For Pre-Fusion State of Synaptobrevin. Biophysical Journal, 107: 2112-2121.
* These authors contributed equally to the paper.

Y. Ahn, P. Mahinthichaichan, H. J. Lee, H. Ouyang, D. Kaluka, S.-R. Yeh, D. Arjona, D. L. Rousseau, E. Tajkhorshid, P. Ädelroth, and R. B. Gennis (2014) Conformational coupling between the active site and residues within the KC-channel of the Vibrio cholerae cbb3-type oxygen reductase. Proceedings of the National Academy of Sciences USA, 111: E4419-E4428.

M.-R. Kalani and E. Tajkhorshid (2014) Molecular Dynamics: The Computational Molecular Microscope. Razavi International Journal of Medicine, 2(3): e20117.

S. N. Smith, Y. Wang, J. L. Baylon, N. Singh, B. Baker, E. Tajkhorshid, and D. M. Kranz (2014) Changing the peptide specificity of a human T cell receptor by directed evolution. Nature Communication, 5:5223.

G. Enkavi, J. Li, P.-C. Wen, S. Thangapandian, M. Moradi, T. Jiang, W. Han, and E. Tajkhorshid (2014) A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. Annual Reports in Computational Chemistry, 10:77-125.

2013

fftk cover
C. G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid*, and J. C. Gumbart* (2013) Rapid parameterization of small molecules using the Force Field Toolkit. Journal of Computational Chemistry, 34: 2757-2770. PMCID: PMC3874408. (Cover Article, Top 10 most-accessed article Sept-Nov 2013, Mar-Apr 2014)

Access the recommendation on F1000Prime
M. Moradi and E. Tajkhorshid (2013) Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proceedings of the National Academy of Sciences USA, 110: 18916-18921.

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. PMCID: PMC3651479

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, 340: 1346-1349.

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. PMCID: PMC3560430

J. L. Baylon, I. Lenov, S. G. Sligar, and E. Tajkhorshid (2013) Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation. Journal of the American Chemical Society, 135: 8542-8551.

M. Moradi and E. Tajkhorshid (2013) Driven Metadynamics: Reconstructing Equilibrium Free Energies From Driven Adaptive-Bias Simulations. Journal of Physical Chemistry Letters, 4: 1882-1887.

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, 288: 19211-19220.

M. R. Kalani, A. Moradi, M. Moradi, and E. Tajkhorshid (2013) Characterizing a Histidine Switch Controlling pH-Dependent Conformational Changes of the Influenza Virus Hemagglutinin. Biophysical Journal, 105: 993-1003.

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.

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, 304: F1447-F1457.

2012

fftk cover
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.

Blood Clotting Cover
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.

O. Kokhan, C. A. 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-κB. 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 α2A 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.
(live molecular demo sessions of MalK dimers)

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.

Aquaglyceroporin Cover
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

TonB-dependent Membrane Transport Cover
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.