The group's papers have been cited so far over 56,000 times (ISI, August 2015), and according to Google Scholar over 160,000 times (as of July 2017). See highly cited publications. Our group's papers have made a few journal covers.

  Recent Publications

S. Pant, Z. Smith, Y. Wang, E. Tajkhorshid, and P. Tiwary (2020) Confronting pitfalls of AI-augmented molecular dynamics using statistical physics. J. Chem. Phys., 153: 234118. (Featured Article)

R. Jia, C. Martens, M. Shekhar, S. Pant, G. A. Pellowe, A. M. Lau, H. E. Findlay, N. J. Harrisa, E. Tajkhorshid, P. J. Booth, and A. Politis (2020) Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. Nat. Commun., 11:6162.

C. Thomas, S. G. Aller, K. Beis, E. P. Carpenter, G. Chang, L. Chen, E. Dassa, M. Dean, F. D. V. Hoa, D. Ekiert, R. Ford, R. Gaudet, X. Gong, I. B. Holland, Y. Huang, D. K. Kahne, H. Kato, V. Koronakis, C. M. Koth, Y. Lee, O. Lewinson, R. Lill, E. Martinoia, S. Murakami, H. W. Pinkett, B. Poolman, D. Rosenbaum, B. Sarkadi, L. Schmitt, E. Schneider, Y. Shi, S. L. Shyng, D. J. Slotboom, E. Tajkhorshid, D. P. Tieleman, K. Ueda, A. Váradi, P. C. Wen, N. Yan, P. Zhang, H. Zheng, J. Zimmer, and R. Tampé Structural and functional diversity calls for a new classification of ABC transporters. FEBS Lett., 594:3767-75.

H. Chen, J. Maia, B. Radak, D. Hardy, W. Cai, C. Chipot, and E. Tajkhorshid (2020) Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. J. Chem. Inf. Model., 60(11):5301-5307.

F. González-Arias, T. Reddy, J. E. Stone, J. A. Hadden-Perilla, and J. R. Perilla (2020) Scalable analysis of authentic viral envelopes on FRONTERA. Comput. Sci. Eng., 22:11-20.

S. K. Bharathkar, B. W. Parker, A. G. Malyutin, N. Haloi, K. E. Huey-Tubman, E. Tajkhorshid, B. Stadtmueller (2020) The structures of Secretory and dimeric Immunoglobulin A. eLife, 9:e56098.

Y. T. Pang, A. Pavlova, E. Tajkhorshid, and J. C. Gumbart (2020) Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing and comparison. J. Chem. Phys., 153: 164104.

J. Phillips, D. Hardy, J. Maia, J.Stone, J. Ribeiro, R. Bernardi, R. Buch, G. Fiorin, J. Henin, W. Jiang, R. McGreevy, M. C. R. Melo, B. Radak, R. Skeel, A. Singharoy, Y. Wang, B. Roux, A. Aksimentiev, Z. L. Schulten, L. Kale, K. Schulten, C. Chipot, and E. Tajkhorshid (2020) Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys., 153:044130.

D. B. Sauer, N. Trebesch, J. J. Marden, N. Cocco, J. Song, A. Koide, S. Koide, E. Tajkhorshid, and D.-N. Wang (2020) Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife, 9: e61350.

O. Soubias*, S. Pant*, F. Heinrich, Y. Zhang, N. S. Roy, J. Li, X. Jian, M. E Yohe, P. A. Randazzo, M. Lösche*, E. Tajkhorshid*, and R. A. Byrd* (2020) Membrane Surface Recognition by the ASAP1 PH Domain and Consequences for Interactions with the small GTPase Arf1. Sci. Adv., 6 : eabd1882.

H. Ma, A. Clyde, A. Trifan, V. Vishwanath, A. Ramanathan, D. Bhowmik, S. Jha (2020) Benchmarking Machine Learning Workloads in Structural Bioinformatics Applications. CHALLENGE ,20, 3.

M. Yang, J. Sun, D. F. Stowe, E. Tajkhorshid, W.-M. Kwok, and A. K. S. Camara (2020) Knockout of VDAC1 in H9c2 Cells Promotes Oxidative Stress-induced Cell Apoptosis Through Decreased Mitochondrial Hexokinase II Binding and Enhanced Glycolytic Stress. Cell. Physiol. Biochem., 54(5):853-874.

K. Lam, and E. Tajkhorshid (2020) Membrane Interactions of Cy3/Cy5 Fluorophores and Their Effects on Membrane Protein Dynamics. Biophys. J., 119: 24-34.

G. Licari, K. Strakova, S. Matile, E. Tajkhorshid (2020) Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. Chem. Sci., 11:5637-49.

S. Ciudad, E. Puig, T. Botzanowski, M. Meigooni, A. S. Arango, J. Do, M. Mayzel, M. Bayoumi, S. Chaignepain, G. Maglia, S. Cianferani, V. Orekhov, E. Tajkhorshid, B. Bardiaux, and N. Carulla (2020) Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Nat. Commun., 11(1):3014.

F. J. Moss, P. Mahinthichaichan, D. Lodowski, T. Kowatz, E. Tajkhorshid, A. Engel, W. F. Boron, and A. Vahedi-Faridi (2020) Aquaporin-7: A Dynamic Aquaglyceroporin with Greater Water and Glycerol Permeability than its Bacterial Homolog GlpF. Front. Physiol., 11, 728.

T. S. Chavan, R. C. Cheng, T. Jiang, I. I. Mathews, R. A. Stein, A. Koehl, H. S. Mchaourab, E. Tajkhorshid*, and M. Maduke* (2020) A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the Cl-/H+ transport cycle. eLife, 9:e53479.

S. M. Sedlak, L. C. Schendel, H. E. Gaub, and R. C. Bernardi (2020) Streptavidin/Biotin: Tethering Geometry Defines Unbinding Mechanics. Sci. Adv., 6:(13)eaay5999.

A. K. Yadav, C. J. Reinhardt, A. S. Arango, H. C. Huff, L. Dong, M. G. Malkowski, A. Das, E. Tajkhorshid, and J. Chan (2020) An activity-based sensing approach for the detection of Cyclooxygenase-2 in live cells. Angew. Chem., 132:3333-3340

P. Kumar, Y. Wang, Z. Zhang, Z. Zhao, G. D. Cymes, E. Tajkhorshid, and C. Grosman (2020) Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayers. Proc. Natl. Acad. Sci. USA, 117:1788-1798.

S. Pant and E. Tajkhorshid (2020) Microscopic Characterization of GRP1 PH Domain Interaction With Anionic Membranes. J. Comput. Chem, 41:489-499.

S. Thangapandian, K. Kapoor, and E. Tajkhorshid (2020) Probing cholesterol binding and translocation in P-glycoprotein. Biochim. Biophys. Acta Biomembr., 1862: 183090.

R. Shahoei, and E. Tajkhorshid (2020) Menthol binding to the human α4β2 nicotinic acetylcholine receptor, facilitated by its strong partitioning in membrane. J. Phys. Chem. B, 124:1866-1880.

T. Jiang, P.C. Wen, N. Trebesch, Z. Zhao, S. Pant, K. Kapoor, M. Shekhar, E. Tajkhorshid (2020) Computational Dissection of Membrane Transport at a Microscopic Level. Trends Biochem. Sci., 45: 202-216.

J. W. Smith, X. Jiang, H. An, A. M. Barclay, G. Licari, E. Tajkhorshid, E. Moore, C. M. Rienstra, J. S. Moore and Q. Chen (2020) Polymer-peptide conjugates induce uniform fragmentation and bundling of amyloid fibrils into ordered nanostructures. ACS Appl. Nano Mater., 2: 937-945.

J. Zhang, E. C. Kim, C. Chen, E. Procko, S. Pant, K. Lam, J. Patel, R. Choi, M. Hong, D. Joshi, E. Bolton, E. Tajkhorshid, and H.-J. Chung (2020) Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy. Sci. Rep., 10, 4756.

M. Mahdavi, A. Fattahi, E. Tajkhorshid, and S. Nouranian (2020) Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers. ACS Appl. Bio Mater., 3, 1354-1363.

C. Misra, S. Bangru, F. Lin, K. Lam, S. N. Koenig, E. R. Lubbers, J. Hedhli, N. P. Murphy, D. J. Parker, L. W. Dobrucki, T. A. Cooper, E. Tajkhorshid, P. J. Mohler, and A. Kalsotra (2020) Aberrant expression of a non-muscle RBFOX2 isoform triggers cardiac conduction defects in myotonic dystrophy. Dev. Cell, 52: 748-763.

A. Singharoy*, C. Maffeo, K.H. Delgado-Magnero, D. J. K. Swainsbury, M.Sener, U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. W. Vant, J. E. Stone, J. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, P. Tieleman, C. N. Hunter, E. Tajkhorshid*, A. Aksimentiev*, and K. Schulten (2019) Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell,179:1098-1111.

R. C. Bernardi*, E. Durner, C. Schoeler, K. H. Malinowska, B. G. Carvalho, E. A. Bayer, Z. Luthey-Schulten, H. E. Gaub, and M. A. Nash* (2019) Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. J. Am. Chem. Soc.,141(37):14752-14763.

K. Yu*, T. Jiang*, Y. Cui, E. Tajkhorshid*, and H. C. Hartzell* (2019) A Network of Phosphatidylinositol 4,5-bisphosphate Binding Sites Regulate Gating of the Ca2+-activated Cl- Channel ANO1 (TMEM16A). Proc. Natl. Acad. Sci. USA ,116:19952-19962.

M. P. Muller*, T. Jiang*, C. Sun, M. Lihan, S. Pant, P. Mahinthichaichan, A. Trifan, and E. Tajkhorshid (2019) Characterization of Lipid-Protein Interactionsand Lipid-mediated Modulation of MembraneProtein Function Through Molecular Simulation. Chem. Rev., 119:6086-6161.

J. A. Coleman, D. Yang, Z. Zhao, P. C. Wen, C. Yoshioka , E. Tajkhorshid, and E. Gouaux (2019) Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. Nature, 569:141-145.

A. M. Barragan, A. V. Soudackov, Z. Luthey-Schulten, S. Hammes-Schiffer, K. Schulten, and I. A. Solov'yov (2021) Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex. J. Am. Chem. Soc., In press.

I. Chen, S. Pant, Q. Wu, R. Cater, M. Sobti, R. Vandenberg, A. G. Stewart, E. Tajkhorshid, J. Font, and R. Ryan (2021) Glutamate transporters have a chloride channel with two hydrophobic gates. Nature, In press.

M. Michenkova, S. Taki, M. C. Blosser, H. J. Hwang, T. Kowatz, F. J. Moss, R. Occhipinti, X. Qin, S. Sen, E. Shinn, D. Wang, B. S. Zeise, P. Zhao, N. Malmstadt, A. Vahedi-Faridi, E. Tajkhorshid, and W. F. Boron (2021) Carbon dioxide transport across membranes. Interface Focus, In press.

W. R. Arnold, L. N. Carnevale, Z. Xie, J. L. Baylon, E. Tajkhorshid, H. Hu, and A. Das (2020) Anti-inflammatory dopamine- and serotonin-based endocannabinoid epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel. Nat. Commun., In press.

S. Dehghani-Ghahnaviyeh, K. Kapoor, and E. Tajkhorshid (2020) Conformational changes of the nucleotide binding domains of P-glycoprotein induced by ATP hydrolysis. FEBS Lett., In press.

R. P. Sparks, A. S. Arango, E. Tajkhorshid, and R. A. Fratti (2020) Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions. J. Visual. Exp. (JoVE), In press.

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