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, J. Zhang, E. C. Kim, K. Lam, H. J. Chung, and E. Tajkhorshid (2021) PIP2-dependent coupling of voltage sensor and pore domains in Kv7.2 channel. Commun. Biol., 4: 1189.

M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, J. Nguyn, N. J. Sisco, A. Mondal, J. Vant, P. Fromme, W. D. Van Horn, E. Tajkhorshid, D. Kihara, K. Dill, A. Perez, and A. Singharoy (2021) CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps. Matter, 4: 3195-3216.

J. Ge, J. Elferich, S. Dehghani-Ghahnaviyeh, Z. Zhao, M. Medows, H. von Gersdorff, E. Tajkhorshid, and E. Gouaux (2021) Molecular mechanism of prestin electromotive signal amplification. Cell, 184: 4669-4679.e13.

Z. Ghaemi, M. Gruebele, and E. Tajkhorshid (2021) Molecular Mechanism of Capsid Disassembly in Hepatitis B Virus. Proc. Natl. Acad. Sci. USA, 118, e2102530118.

J. Li, L. Han, F. Vallese, Z. Ding, S. K. Choi, S. Hong, Y. Luo, B. Liu, C. K. Chan, E. Tajkhorshid, J. Zhu. O. Clarke, K. Zhang, and R. Gennis (2021) Cryo-EM structures of E. coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Proc. Natl. Acad. Sci. USA, 118, e2106750118.

C. Mayne, W. Toy, K. Carlson, T. Bhatt, S. W. Fanning, G. L. Greene, B. S. Katzenellenbogen, S. Chandarlapaty, J. A. Katzenellenbogen, and E. Tajkhorshid (2021) Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer. Mol. Cancer Res., 19: 1559-s1570.

L. Sun, H. J. Cho, S. Sen, A. S. Arango, T. T. Huynh, Y. Huang, N. Bandara, B. E. Rogers, E. Tajkhorshid, and L. M. Mirica (2021) Amphiphilic Distyrylbenzene Derivatives as Potential Therapeutic and Imaging Agents for Soluble and Insoluble Amyloid β Aggregates in Alzheimer's Disease. J. Am. Chem. Soc., 143: 10462-10476.

D. T. Infield, A. Rasouli, G. D. Galles, C. Chipot, E. Tajkhorshid, and C. Ahern (2021) Cation-π interactions and their functional roles in membrane proteins. J. Mol. Biol., 433: 167035.

H. Kaya, D. J. Hardy, and R. D. Skeel (2021) Multilevel summation for periodic electrostatics using B-splines. J. Chem. Phys., 154, 144105.

J. Sprenger, A. Trifan, N. Patel, A. Vanderbeck, J. Bredfelt, E. Tajkhorshid, R. Rowlett, L. L. Leggio, K. Åkerfeldt, and S. Linse (2021) Calmodulin complexes with brain and muscle creatine kinase peptides. Current Research in Structural Biology, 3: 121-132.

D. Gorgun, M. Lihan, K. Kapoor, and E. Tajkhorshid (2021) Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane. Biophys. J., 120:2914-2926.

N. Haloi, P. C. Wen, Q. Cheng, M. Yang, G. Natarajan, A. K. S. Camara, W. M. Kwok, and E. Tajkhorshid (2021) Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II. Commun. Biol., 4:667.

K. Kapoor*, S. Pant*, and E. Tajkhorshid (2021) Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein. Chem. Sci., 12:6293-6306.

A. Rasouli, Y. Jamali, E. Tajkhorshid, O. Bavi, and H. N. Pishkenari (2021) Mechanical properties of Ester- and Ether-DPhPC bilayers: a molecular dynamics study. J. Mech. Behav. Biomed. Mater., 117, 104386.

J. Zabret, S. Bohn, S. K. Schuller, O. Arnolds, M. Möller, J. Meier-Credo, P. Liauw, A. Chan, E. Tajkhorshid, J. D. Langer, R. Stoll, A. Krieger-Liszkay, B. D. Engel, T. Rudack, J. M. Schuller, and M. M. Nowaczyk (2021) How to build a water-splitting machine: structural insights into photosystem II assembly. Nat. Plants, 7:524-538.

W. R. Arnold, L. N. Carnevale, Z. Xie, J. L. Baylon, E. Tajkhorshid, H. Hu, and A. Das (2021) Anti-inflammatory dopamine- and serotonin-based endocannabinoid epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel. Nat. Commun., 12:926.

S. Dehghani-Ghahnaviyeh, K. Kapoor, and E. Tajkhorshid (2021) Conformational changes of the nucleotide binding domains of P-glycoprotein induced by ATP hydrolysis. FEBS Lett., 595:735-749.

M. Sener, S. Levy, J. E.Stone, A.J. Christensen, B. Isralewitz, R. Patterson, K. Borkiewicz, J. Carpenter, N. Hunter, Z. L. Schulten, and D. Cox (2021) Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. Parallel Comput., 102:102698.

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, 591:327-331.

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. Vah edi-Faridi, E. Tajkhorshid, and W. F. Boron (2021) Carbon dioxide transport across membranes. Interface Focus, 11:20200090.

C. L. Brooks, D. A. Case, S. Plimpton, B. Roux, D. van der Spoel, and E. Tajkhorshid (2021) Classical Molecular Dynamics. Editorial Introduction to the JCP Special Topic on Classical Molecular Dynamics (MD) Simulations: Codes, Algorithms, Force Fields, and Applications. J. Chem. Phys., 154:10041.

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., 143(2):715-723.

N. Haloi, A. K. Vasan, E. Geddes, A. Prasanna, P.C. Wen, W. W. Metcalf, P. Hergenrother, and E. Tajkhorshid (2021) Rationalizing generation of broad spectrum antibiotics with the addition of a positive charge. Chemical Science, In press.

H. C. Huff, A. Vasan, A. Kaul, E. Tajkhorshid, and Aditi Das (2021) Differential Interactions of Selected Phytocannabinoids with Human CYP2D6 Polymorphisms. Biochemistry, In press.

R. P. Sparks, A. Becker, A. S. Arango, E. Tajkhorshid, R. A. Fratti (2021) Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions. JoVE , In press.

S. Pant, Z. Smith, Y. Wang, E. Tajkhorshid, and P. Tiwary (2020) Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions. 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.

Z. Liu, H. Liu, A. M. Vera, R. C. Bernardi, P. Tinnefeld, M. A. Nash (2020) High force catch bond mechanism of bacterial adhesion in the human gut. Nat. Commun., 11(1):4321

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.

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