TCB Publications - Search
10337. Elucidating the mechanism of metabolism of cannabichromene by human cytochrome P450s. Pritam Roy, Jonathan Maturano, Hale Hasdemir, Angel Lopez, Fengyun Xu, Judith Hellman, Emad Tajkhorshid, David Sarlah, and Aditi Das. Journal of Natural Products, 2024. In Press.
10335. IHMCIF: An extension of the PDBx/mmCIF data standard for integrative structure determination methods. Brinda Vallat, Benjamin M Webb, John D Westbrook, Thomas D Goddard, Christian A Hanke, Andrea Graziadei, Ezra Peisach, Arthur Zalevsky, Jared Sagendorf, Hongsuda Tangmunarunkit, Serban Voinea, Monica Sekharan, Jian Yu, Alexander A M J J Bonvin, Frank DiMaio, Gerhard Hummer, Jens Meiler, Emad Tajkhorshid, Thomas E Ferrin, Catherine L Lawson, Alexander Leitner, Juri Rappsilber, Claus A M Seidel, Cy M Jeffries, Stephen K Burley, Jeffrey C Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar, Torsten Schwede, Jill Trewhella, Carl Kesselman, Helen M Berman, and Andrej Sali. Journal of Molecular Biology, pp. 168546, 2024. In Press.
10334. A Gram-negative-selective antibiotic spares the gut microbiome and prevents Clostridioides difficile infection. K. A. Mu noz, Archit K. Vasan, Matt Sinclair, P.-C. Wen, J. R. Holmes, R. J. Ulrich, H. Y. Lee, C.-C. Hung, C. J. Fields, Emad Tajkhorshid, G. W. Lau, and P. J. Hergenrother. Nature. In Press.
10333. Generating concentration gradients across membranes for molecular dynamics simulations of periodic systems. Eric J. Shinn and Emad Tajkhorshid. International Journal of Molecular Sciences, 25:3616, 2024. Published.
10332. WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination. Jie Zhang, Yuanyuan Yu, Xiuqun Zou, Yaning Du, Qiankun Liang, Mengyao Gong, Yurong He, Junqi Luo, Dandan Wu, Xiaoli Jiang, Matt Sinclair, Emad Tajkhorshid, Hong-Zhuan Chen, Zhaoyuan Hou, Yuejuan Zheng, Lin-Feng Chen, and Xiao-Dong Yang. Nucleic Acids Research, pp. gkae161, 2024. Published.
10331. Beyond nothingness in the formation and functional relevance of voids in polymer films. Falon C. Kalutantirige, Jinlong He, Lehan Yao, Stephen Cotty, Shan Zhou, John W. Smith, Emad Tajkhorshid, Charles M. Schroeder, Jeffrey S. Moore, Hyosung An, Xiao Su, Ying Li, and Qian Chen. Nature Communications, 15:2852, 2024. Published.
10330. Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. Tomoka Gose, Ali Rasouli, Sepehr Dehghani-Ghahnaviyeh, Po-Chao Wen, Yao Wang, John Lynch, Yu Fukuda, Talha Shafi, Robert C. Ford, Emad Tajkhorshid, and John D. Schuetz. Drug Resistance Updates, 73:101066, 2024. Published.
10329. A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture. Hyun Park, Xiaoli Yan, Ruijie Zhu, Eliu A Huerta, Santanu Chaudhuri, Donny Cooper, Ian Foster, and Emad Tajkhorshid. Communications Chemistry, 7:21, 2024. Published.
10328. Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model. Matt Sinclair, Richard A. Stein, Jonathan H. Sheehan, Emily M. Hawes, Richard M. O'Brien, Emad Tajkhorshid, and Derek P. Claxton. PNAS Nexus, 3:pgae036, 2024. Published.
10327. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. D. D. Dhavale, A. M. Barclay, C. G. Borcik, K. Basore, D. A. Berthold, I. R. Gordon, J. Liu, M. H. Milchberg, J. Y. O'Shea, M. J. Rau, Z. Smith, Soumyo Sen, B. Summers, J. Smith, O. A. Warmuth, Q. Chen, J. A. J. Fitzpatrick, C. D. Schwieters, Emad Tajkhorshid, C. M. Rienstra, and P. T. Kotzbauer. Nature Communications, 2023. In Press.
10326. The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. Christopher D. Radka, Christy R. Grace, Hale S. Hasdemir, Yupeng Li, Carlos C. Rodriguez, Patrick Rodrigues, Michael L. Oldham, M. Zuhaib Qayyum, Aaron Pitre, William J. MacCain, Ravi C. Kalathur, Emad Tajkhorshid, and Charles O. Rock. Journal of Biological Chemistry, 300:105627, 2024. Published.
10324. A rigorous framework for calculating protein-protein binding affinities in membranes. Marharyta Blazhynska, James C. Gumbart, Haochuan Chen, Emad Tajkhorshid, Benoît Roux, and Christophe Chipot. Journal of Chemical Theory and Computation, 19:9077-9092, 2023. Published.
10323. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions. Zhaleh Ghaemi, Oluwadara Nafiu, Emad Tajkhorshid, Martin Gruebele, and Jianming Hu. Scientific Reports, 13:21392, 2023. Published.
10322. Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Qingyu Tang, Matt Sinclair, Hale S. Hasdemir, Richard A. Stein, Erkan Karakas, Emad Tajkhorshid, and Hassane S. Mchaourab. Nature Communications, 14:7183, 2023. Published.
10320. Myr-Arf1 conformational flexibility at the membrane surface: insights for ArfGAP ASAP1 interactions. Y. Zhang, O. Soubias, Shashank Pant, F. Heinrich, A. Vogel, J. Li, Y. Li, L. A. Clifton, S. Daum, K. Bacia, D. Huster, P. A. Randazzo, M. Lösche, Emad Tajkhorshid, and R. A. Byrd. Nature Communications, 14:7570, 2023. Published.
10319. VMD as a platform for interactive small molecule preparation and visualization in quantum and classical simulations. Mariano Spivak, John E. Stone, Jo ao Ribeiro, Jan Saam, Peter L. Freddolino, Rafael C. Bernardi, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 63:4664-4678, 2023. Published.
10318. Quinoline thiourea-based zinc ionophores with antibacterial activity. Subhasis Dey, Anjali Patel, Nandan Haloi, Soumya Srimayee, Suman Paul, Ganesh Kumar Barik, Nasim Akhtar, Dipanjan Shaw, Gunanka Hazarika, Biswa Mohan Prusty, Mohit Kumar, Manas Kumar Santra, Emad Tajkhorshid, Surajit Bhattacharjee, and Debasis Manna. Journal of Medicinal Chemistry, 66:11078-11093, 2023. Published.
10316. Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Dongxue Yang, Zhiyu Zhao, Emad Tajkhorshid, and Eric Gouaux. Proceedings of the National Academy of Sciences, USA, 120:e2304602120, 2023. Published.
10315. End-to-end AI framework for interpretable prediction of molecular and crystal properties. Hyun Park, Ruijie Zhu, E. A. Huerta, Santanu Chaudhuri, Emad Tajkhorshid, and Donny Cooper. Machine Learning: Science and Technology, 4:025036, 2023. Published.
10314. Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3. Yupeng Li, Atanu Acharya, Lixinhao Yang, Jinchan Liu, Emad Tajkhorshid, Helen I. Zgurskaya, Mary Jackson, and James C. Gumbart. Biophysical Journal, 122:2342-2352, 2023. Published.
10313. Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Grace D. Galles, Daniel T. Infield, Colin J. Clark, Marcus L. Hemshorn, Shivani Manikandan, Frederico Fazan, Ali Rasouli, Emad Tajkhorshid, Jason D. Galpin, Richard B. Cooley, Ryan A. Mehl, and Christopher A. Ahern. Nature Communications, 14, 2023. Published.
10311. Differential interactions of selected phytocannabinoids with human CYP2D6 polymorphisms. Hannah C. Huff, Archit Vasan, Pritam Roy, Aayush Kaul, Emad Tajkhorshid, and Aditi Das. Biochemistry, 60:2749-2760, 2021.
10310. Backbone amides are key determinants of Cl selectivity in CLC ion channels. Lilia Leisle, Kin Lam, Sepehr Dehghani-Ghahnaviyeh, Eva Fortea, Jason Galpin, Christopher A. Ahern, Emad Tajkhorshid, and Alessio Accardi. Nature Communications, 13, 2022. Published.
10309. Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. Le Thi My Le, James R. Thompson, Sepehr Dehghani-Ghahnaviyeh, Shashank Pant, Phuoc X. Dang, Takahisa Kanikeyo, Emad Tajkhorshid, and Amer Alam. EMBO Journal, 42:e111065, 2023.
10308. Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Ali Rasouli, Qin Yu, Sepehr Dehghani-Ghahnaviyeh, Po-Chao Wen, Julia Kowal, Kaspar Lochar, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 120:e2213437120, 2022. Published.
10307. Lipid-mediated prestin organization in outer hair cell membranes and its implications in sound amplification. Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, and Emad Tajkhorshid. Nature Communications, 13, 2022.
10306. Molecular view into preferential binding of the factor VII gla domain to phosphatidic acid. Melanie P. Muller, James H. Morrissey, and Emad Tajkhorshid. Biochemistry, 61:1694-1703, 2022.
10305. Structures of the TMC-1 complex illuminate mechanosensory transduction. H. Jeong, S. Clark, A. Goehring, Sepehr Dehghani-Ghahnaviyeh, Ali Rasouli, Emad Tajkhorshid, and Eric Gouaux. Nature, 610:796-803, 2022.
10304. Proton-driven alternating access in a spinster lipid transporter. Reza Dastvan, Ali Rasouli, Sepehr Dehghani-Ghahnaviyeh, Samantha Gies, and Emad Tajkhorshid. Nature Communications, 13, 2022.
10303. Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia. I. Singaram, A. Sharma, S. Pant, M. Lihan, M.-J. Park, P. Buwaneka, Y. Hu, N. Mahmud, Y.-M. Kim, V. Gevorgyan, I. Khan, Emad Tajkhorshid, and W. Cho. Nature Chemical Biology, 19:239-250, 2023. Published.
10302. py-MCMD: Python software for performing hybrid monte carlo/molecular dynamics simulations with GOMC and NAMD. Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy, John E. Stone, Loren Schwiebert, Jeffrey Potoff, and Emad Tajkhorshid. Journal of Chemical Theory and Computation, 18:4983-4994, 2022.
10301. Phthalate monoesters act through peroxisome proliferator-activated receptors in the mouse ovary. Daryl D. Meling, Kathy M. De La Torre, Andres S. Arango, Andressa Gonsioroski, Ashley R. K. Deviney, Alison M. Neff, Mary J. Laws, Genoa R. Warner, Emad Tajkhorshid, and Jodi A. Flaws. Reproductive Toxicology, 110:113-123, 2022.
10299. Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. Karan Kapoor, Tianle Chen, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 119:e2119761119, 2022.
10298. Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Karan Kapoor, Sundar Thangapandian, and Emad Tajkhorshid. Chemical Science, 13:4150-4169, 2022.
10297. Experiences porting NAMD to the Data Parallel C++ programming model. David J. Hardy, Jaemin Choi, Wei Jiang, and Emad Tajkhorshid. In International Workshop on OpenCL, IWOCL'22, New York, NY, USA, 2022. Association for Computing Machinery.
10296. Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. Qianyi Wu, Azman Akhter, Shashank Pant, Eunjoo Cho, Jin Xin Zhu, Alastair R Garner, Tomoko Ohyama, Emad Tajkhorshid, Donald J van Meyel, and Renae M Ryan. Journal of Clinical Investigation, 132:e154891, 2022.
10295. Use of microscale thermophoresis to measure protein-lipid interactions. Robert P. Sparks, William Lawless, Andres S. Arango, Emad Tajkhorshid, and Rutilio A. Fratti. Journal of Visualized Experiments, 180, 2022.
10294. Microscopic characterization of the chloride permeation pathway in the human excitatory amino acid transporter 1 (EAAT1). Shashank Pant, Qianyi Wu, Renae Ryan, and Emad Tajkhorshid. ACS Chemical Neuroscience, 13:776-785, 2022.
10293. Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. Jessica M. Gullett, Maxime G. Cuypers, Christy R. Grace, Shashank Pant, Chitra Subramanian, Emad Tajkhorshid, Charles O. Rock, and Stephen W. White. Journal of Biological Chemistry, 298:101676, 2022.
10292. A companion guide to the string method with swarms of trajectories: Characterization, performance, and pitfalls. Haochuan Chen, Dylan Ogden, Shashank Pant, Wensheng Cai, Emad Tajkhorshid, Mahmoud Moradi, Benoit Roux, and Christophe Chipot. Journal of Chemical Theory and Computation, 18:1406-1422, 2022.
10291. Intelligent resolution: Integrating cryo-EM with AI-driven multi-resolution simulations to observe the SARS-CoV-2 replication-transcription machinery in action. Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei Huang, John McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Thomas Gibbs, James Phillips, S. Chakra Chennubhotla, Ian Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, and Arvind Ramanathan. The International Journal of High Performance Computing Applications, 36:603-623, 2022.
10290. Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf, Po-Chao Wen, William W. Metcalf, Paul J. Hergenrother, Diwakar Shukla, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 119:e2117009119, 2022.
10289. Anthracycline derivatives inhibit cardiac CYP2J2. Justin S. Kim, Andres S. Arango, Swapnil Shah, William R Arnold, Emad Tajkhorshid, and Aditi Das. Journal of Inorganic Biochemistry, 229:111722, 2022.
10288. Anionic lipids confine cytochrome c2 to the surface of bioenergetic membranes without compromising its interaction with redox partners. Chun Kit Chan, Abhishek Singharoy, and Emad Tajkhorshid. Biochemistry, 61:385-397, 2022.
10287. Membrane Mixer: A toolkit for efficient shuffling of lipids in heterogeneous biological membranes. Giuseppe Licari, Sepehr Dehghani-Ghahnaviyeh, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 62:986-996, 2022.
10286. Assembly and analysis of cell-scale membrane envelopes. Josh Vermaas, Chris Mayne, Eric Shinn, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 62:602-617, 2022.
10285. Lessons learned from responsive molecular dynamics studies of the COVID-19 virus. David J. Hardy, John E. Stone, Barry Isralewitz, and Emad Tajkhorshid. IEEE/ACM HPC for Urgent Decision Making 2021, pp. 1-10, 2021.
10283. Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Jiao Li, Long Han, Francesca Vallese, Ziqiao Ding, Sylvia K. Choi, Sangjin Hong, Yanmei Luo, Bin Liu, Chun Kit Chan, Emad Tajkhorshid, Jiapeng Zhu, Oliver Clarke, Kai Zhang, and Robert Gennis. Proceedings of the National Academy of Sciences, USA, 118:e2106750118, 2021.
10282. PIP2-dependent coupling of voltage sensor and pore domains in Kv7.2. Shashank Pant, Jiaren Zhang, Eung Kim, Kin Lam, Hee Jung Chung, and Emad Tajkhorshid. Communications Biology, 4, 2021.
10281. Rationalizing generation of broad spectrum antibiotics with the addition of a positive charge. Nandan Haloi, Archit Kumar Vasan, Emily Jane Geddes, Arjun Prasanna, Po-Chao Wen, William W. Metcalf, Paul J Hergenrother, and Emad Tajkhorshid. Chemical Science, 12:15028-15044, 2021.
10280. Molecular mechanism of capsid disassembly in hepatitis B virus. Zhaleh Ghaemi, Martin Gruebele, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 118:e2102530118, 2021.
10279. Molecular mechanism of prestin electromotive signal amplification. Jingpeng Ge, Johannes Elferich, Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, Marc Meadows, Henrique von Gersdorff, Emad Tajkhorshid, and Eric Gouaux. Cell, 184:4669-4679, 2021.
10278. CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps. M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, J. Nguyn, N. J. Sisco, A. Mondal, J. Vant, P. Fromme, W. D. Van Horn, Emad Tajkhorshid, D. Kihara, K. Dill, A. Perez, and A. Singharoy. Matter, 4:3195-3216, 2021.
10277. Editorial: Mitochondrial exchangers and transporters in cell survival and death. Amadou K. S. Camara Wai-Meng Kwok, Emad Tajkhorshid. Frontiers in Physiology, 12:1415, 2021.
10276. Defining the energetic basis for a conformational switch mediating ligand-independent activation of mutant estrogen receptors in breast cancer. Chris Mayne, W. Toy, K. Carlson, T. Bhatt, S. W. Fanning, G. L. Greene, B. S. Katzenellenbogen, S. Chandarlapaty, J. A. Katzenellenbogen, and Emad Tajkhorshid. Molecular Cancer Research, 19:1559-1570, 2021.
10275. Structural basis of complex formation between mitochondrial anion channel VDAC1 and hexokinase-II. Nandan Haloi, Po-Chao Wen, Qunli Cheng, Meiying Yang, Gayathri Natarajan, Amadou KS Camara, Wai-Meng Kwok, and Emad Tajkhorshid. Communications Biology, 4:667, 2021.
10274. Calmodulin complexes with brain and muscle creatine kinase peptides. Janina Sprenger, Anda Trifan, Neal Patel, Ashley Vanderbeck, Jenny Bredtfelt, Emad Tajkhorshid, Roger Rowlett, Leila Lo Leggio, Karin S. Åkerfeldt, and Sara Linse. Current Research in Structural Biology, 3:121-132, 2021.
10273. Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein. Karan Kapoor, Shashank Pant, and Emad Tajkhorshid. Chemical Science, 12:6293-6306, 2021.
10271. Cation-π interactions and their functional roles in membrane proteins. Daniel T. Infield, Ali Rasouli, Grace G. Galles, Christophe Chipot, Emad Tajkhorshid, and Christopher A. Ahern. Journal of Molecular Biology, 433:167035, 2021.
10270. Structural insights into photosystem II assembly. Jure Zabret, Stefan Bohn, Sandra K. Schuller, Oliver Arnolds, Madeline Möller, Jakob Meier-Credo, Pasqual Liauw, Aaron Chan, Emad Tajkhorshid, Julian D. Langer, Raphael Stoll, Anja Krieger-Liszkay, Benjamin D. Engel, Till Rudack, Jan M. Schuller, and Marc M. Nowaczyk. Nature Plants, 7:524-538, 2021.
10268. Classical molecular dynamics. Charles L. Brooks III, David A. Case, Steve Plimpton, Benoit Roux, David van der Spoel, and Emad Tajkhorshid. Journal of Chemical Physics, 154:10041, 2021.
10267. Binding mode of SARS-CoV2 fusion peptide to human cellular membrane. Defne Gorgun, Muyun Lihan, Karan Kapoor, and Emad Tajkhorshid. Biophysical Journal, 120:191a, 2021.
10266. Mechanical properties of ester- and ether-DPhPC bilayers: a molecular dynamics study. Ali Rasouli, Yousef Jamali, Emad Tajkhorshid, Omid Bavi, and Hossein Nejat Pishkenari. Journal of the Mechanical Behavior of Biomedical Materials, 117:104386, 2021.
10265. Amphiphilic distyrylbenzene derivatives as potential therapeutic and imaging agents for the soluble amyloid-β oligomers in alzheimer's disease. Liang Sun, Hong-Jun Cho, Soumyo Sen, Andres S. Arango, Truc T. Huynh, Yiran Huang, Nilantha Bandara, Buck E. Rogers, Emad Tajkhorshid, and Liviu M. Mirica. Journal of the American Chemical Society, 143:10462-10476, 2021.
10264. Glutamate transporters have a chloride channel with two hydrophobic gates. Ichia Chen, Shashank Pant, Qianyi Wu, Rosemary Cater, Meghna Sobti, Robert Vandenberg, Alastair G. Stewart, Emad Tajkhorshid, Josep Font, and Renae Ryan. Nature, 591:327-331, 2021.
10263. Carbon dioxide transport across membranes. Marie Michenkova, Sara Taki, Matthew C. Blosser, Hyea J. Hwang, Thomas Kowatz, Fraser J. Moss, Rossana Occhipinti, Xue Qin, Soumyo Sen, Eric Shinn, Dengke Wang, Brian S. Zeise, Pan Zhao, Noah Malmstadt, Ardeschir Vahedi-Faridi, Emad Tajkhorshid, and Walter F. Boron. Interface Focus, 11:20200090, 2021.
10260. Anti-inflammatory dopamine- and serotonin-based endocannabinoid epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel. William R. Arnold, Lauren N. Carnevale, Zili Xie, Javier L. Baylon, Emad Tajkhorshid, Hongzhen Hu, and Aditi Das. Nature Communications, 12, 2021.
10259. Confronting pitfalls of AI-augmented molecular dynamics using statistical physics. Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, and Pratyush Tiwary. Journal of Chemical Physics, 153, 2020.
10256. The structures of secretory and dimeric immunoglobulin A. Sonya Kumar Bharathkar, Benjamin W Parker, Andrey G Malyutin, Nandan Haloi, Kathryn E Huey-Tubman, Emad Tajkhorshid, and Beth Stadtmueller. eLife, 9:e56098, 2020.
10255. Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. Ruyu Jia, Chloe Martens, Mrinal Shekhar, Shashank Pant, Grant Pellowe, Andy Lau, Heather Findlay, Nicola Harris, Emad Tajkhorshid, Paula Booth, and Argyris Politis. Nature Communications, 11, 2020.
10254. Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison. Yui Tik Pang, Anna Pavlova, Emad Tajkhorshid, and James C. Gumbart. Journal of Chemical Physics, 153:164104, 2020.
10253. Structural basis for the reaction cycle of DASS dicarboxylate transporters. David B Sauer, Noah Trebesch, Jennifer J Marden, Nicolette Cocco, Jinmei Song, Akiko Koide, Shohei Koide, Emad Tajkhorshid, and Da-Neng Wang. eLife, 9:e61350, 2020.
10251. Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. O. Soubias, Shashank Pant, F. Heinrich, N. S. Roy Y. Zhang, J. Li, X. Jian, M. E Yohe, P. A. Randazzo, M. Lösche, Emad Tajkhorshid, and R. A. Byrd. Science Advances, 6, 2020.
10250. Structural and functional diversity calls for a new classification of ABC transporters. Christoph Thomas, Stephen G. Aller, Konstantinos Beis, Elisabeth P. Carpenter, Geoffrey Chang, Lei Chen, Elie Dassa, Michel Dean, Franck Duong Van Hoa, Damian Ekiert, Robert Ford, Rachelle Gaudet, Xin Gong, I. Barry Holland, Yihua, Vassilis Koronakis, Christopher M. Koth, Youngsook Lee, Oded Lewinson, Roland Lill, Enrico Martinoia, Satoshi Murakami, Heather W. Pinket, Bert Poolman, Daniel Rosenbaum, Balazs Sarkadi, Lutz Schmitt, Erwin Schneider, Yigong Shi, Show-Ling Shyng, Dirk J. Slotboom, Emad Tajkhorshid, Kazumitsu Ueda D. Peter Tieleman, Andras Varadi, Po-Chao Wen, Nieng Yan, Peng Zhang, Hongjin Zheng, Jochen Zimmer, and Robert Tampe. FEBS Letters, 594:3767-3775, 2020.
10249. Boosting free-energy perturbation calculations with GPU-accelerated NAMD. Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai, Christophe Chipot, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 60:5301-5307, 2020.
10248. Knockout of VDAC1 in H9c2 cells promotes oxidative stress-induced cell apoptosis through decreased mitochondrial hexokinase II binding and enhanced glycolytic stress. Meiying Yang, Jie Sun, David F Stowe, Emad Tajkhorshid, Wai-Meng Kwok, and Amadou KS Camara. Cellular Physiology & Biochemistry, 54:853-874, 2020. Published.
10247. Scalable molecular dynamics on CPU and GPU architectures with NAMD. James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Journal of Chemical Physics, 153:044130, 2020.
10246. Aquaporin-7: A dynamic aquaglyceroporin with higher water and glycerol transport capacity than its bacterial homolog GlpF. Fraser J Moss, Paween Mahinthichaichan, David T Lodowski, Thomas Kowatz, Emad Tajkhorshid, Andreas Engel, Walter F Boron, and Ardeshir Vahedi-Faridi. Frontiers in Physiology, 11, 2020. Published.
10245. Membrane interactions of Cy3/Cy5 fluorophores and their effects on membrane protein dynamics. Kin Lam and Emad Tajkhorshid. Biophysical Journal, 119:24-34, 2020.
10244. Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Sonia Ciudad, Eduard Puig, Thomas Botzanowski, Moeen Meigooni, Andres S. Arango, Jimmy Do, Maxim Mayzel, Mariam Bayoumi, Stéphane Chaignepain, Giovanni Maglia, Sarah Cianferani, Vladislav Orekhov, Emad Tajkhorshid, Benjamin Bardiaux, and Natàlia Carulla. Nature Communications, 11, 2020.
10243. Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. Giuseppe Licari, Karolina Strakova, Stefan Matile, and Emad Tajkhorshid. Chemical Science, 11:5637-5649, 2020.
10242. Molecular insights into the loading and dynamics of doxorubicin on PEGylated graphene oxide nanocarriers. Mina Mahdavi, Ali Fattahi, Emad Tajkhorshid, and Sasan Nouranian. ACS Applied Bio Materials, 3:1354-1363, 2020.
10241. Menthol binding to the human α4β2 nicotinic acetylcholine receptor, facilitated by its strong partitioning in membrane. Rezvan Shahoei and Emad Tajkhorshid. Journal of Physical Chemistry B, 124:1866-1880, 2020.
10240. Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy. Jiaren Zhang, Eung Chang Kim, Congcong Chen, Erik Procko, Shashank Pant, Kin Lam, Jaimin Patel, Rebecca Choi, Mary Hong, Dhruv Joshi, Eric Bolton, Emad Tajkhorshid, and Hee Jung Chung. Scientific Reports, 10:4756, 2020.
10239. Aberrant expression of a non-muscle RBFOX2 isoform triggers cardiac conduction defects in myotonic dystrophy. Chaitali Misra, Sushant Bangru, Feikai Lin, Kin Lam, Sara N. Koenig, Ellen R. Lubbers, Jamila Hedhli, Nathaniel P. Murphy, Darren J. Parker, Lawrence W. Dobrucki, Thomas A. Cooper, Emad Tajkhorshid, Peter J. Mohler, and Auinash Kalsotra. Developmental Cell, 52:748-763, 2020.
10238. An activity-based sensing approach for the detection of cyclooxygenase-2 in live cells. Anuj K. Yadav, Christopher J. Reinhardt, Andres S. Arango, Hannah C. Huff, Liang Dong, Michael G. Malkowski, Aditi Das, Emad Tajkhorshid, and Jefferson Chan. Angewandte Chemie - International Edition in English, 132:2-10, 2019.
10235. A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the Cl-/H+ transport cycle. Tanmay S. Chavan, Ricky C. Cheng, Tao Jiang, Irimpan I. Mathews, Richard A. Stein, Antoine Koehl, Hassane S. Mchaourab, Emad Tajkhorshid, and Merritt Maduke. eLife, 9:e53479, 2020.
10232. Locking two rigid-body bundles in an outward-facing conformation: A general ion-coupling mechanism in LeuT-fold transporters. Jing Li, Zhiyu Zhao, and Emad Tajkhorshid. Scientific Reports, 9:19479, 2019.
10231. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Pramod Kumar, Yuhang Wang, Zhening Zhang, Zhiyu Zhao, Gisela D. Cymes, Emad Tajkhorshid, and Claudio Grosman. Proceedings of the National Academy of Sciences, USA, 117:1788-1798, 2020.
10230. Atoms to phenotypes: Molecular design principles of cellular energy metabolism. A. Singharoy, C. Maffeo, K. Delgardo, D. J. K. Swainsbury, M. Sener, U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. Stone, J. Phillips, T. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, P. Tieleman, C. N. Hunter, Emad Tajkhorshid, A. Aksimentiev, and K. Schulten. Cell, 179:1098-1111, 2019.
10229. Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling. Ksenia Terekhova, Sabine Pokutta, Yee S. Kee, Jing Li, Emad Tajkhorshid, Gerald Fuller, Alexander R. Dunn, and William I. Weis. Scientific Reports, 9:15375, 2019.
10228. Federating structural models and data: Outcomes from a workshop on archiving integrative structures. Helen M. Berman, Paul D. Adams, Alexandre A. Bonvin, Stephen K. Burley, Bridget Carragher, Wah Chiu, Frank DiMaio, Thomas E. Ferrin, Margaret J. Gabanyi, Thomas D. Goddard, Patrick R. Griffin, Juergen Haas, Christian A. Hanke, Jeffrey C. Hoch, Gerhard Hummer, Genji Kurisu, Catherine L. Lawson, Alexander Leitner, John L. Markley, Jens Meiler, Gaetano T. Montelione, George N. Phillips Jr., Thomas Prisner, Juri Rappsilber, David C. Schriemer, Torsten Schwede, Claus A.M. Seidel, Timothy S. Strutzenberg, Dmitri I. Svergun, Emad Tajkhorshid, Jill Trewhella, Brinda Vallat, Sameer Velankar, Geerten W. Vuister, Benjamin Webb, John D. Westbrook, Kate L. White, and Andrej Sali. Structure, 27:1745-1759, 2019.
10227. Microscopic characterization of GRP1 PH domain interaction with anionic membranes. Shashank Pant and Emad Tajkhorshid. Journal of Computational Chemistry, 41:489-499, 2020.
10225. Tuning symmetry breaking charge separation in perylene bichromophores by conformational control. Alexander Aster, Giuseppe Licari, Francesco Zinna, Elodie Brun, Tatu Kumpulainen, Emad Tajkhorshid, Jerome Lacour, and Eric Vauthey. Chemical Science, 10:10629-10639, 2019.
10224. Multivalent polymer-peptide conjugates: A general platform for inhibiting amyloid beta peptide aggregation. Xing Jiang, Abigail J. Halmes, Giuseppe Licari, John W. Smith, Yang Song, Edwin G. Moore, Qian Chen, Emad Tajkhorshid, Chad M. Rienstra, and Jeffrey S. Moore. ACS Macro Letters, 8:1365-1371, 2019.
10223. Polymer-peptide conjugates convert amyloid into protein nanobundles through fragmentation and lateral association. John W. Smith, Xing Jiang, Hyosung An, Alexander M. Barclay, Giuseppe Licari, Emad Tajkhorshid, Edwin G. Moore, Chad M. Rienstra, Jeffrey S. Moore, and Qian Shen. ACS Applied Materials and Interfaces, 3:937-945, 2020.
10222. A chalcogen-bonding cascade switch for planarizable push-pull probes. Mariano Macchione, Antoine Goujon, Karolina Strakova, Heorhii V. Humeniuk, Giuseppe Licari, Emad Tajkhorshid, Naomi Sakai, and Stefan Matile. Angewandte Chemie - International Edition in English, 58:15752-15756, 2019.
10221. Probing cholesterol binding and translocation in P-glycoprotein. Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1862:183090, 2020.
10220. A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion. Robert P. Sparks, Andres S. Arango, Matthew L. Starr, Zachary L. Aboff, Logan R. Hurst, David A. Rivera-Kohr, Chi Zhang, Kevin A. Harden, Jermaine L. Jenkins, Wayne C. Guida, Emad Tajkhorshid, and Rutilio A. Fratti. Journal of Biological Chemistry, 294:17168-17185, 2019.
10219. Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. Chloe Martens, Mrinal Shekhar, Andy M. Lau, Emad Tajkhorshid, and Argyris Politis. Nature Protocols, 14:3183-3204, 2019. Published.
10218. Computational dissection of membrane transport at a microscopic level. Tao Jiang, Po-Chao Wen, Noah Trebesch, Zhiyu Zhao, Shashank Pant, Karan Kapoor, Mrinal Shekhar, and Emad Tajkhorshid. Trends in Biochemical Sciences, 45:202-216, 2020.
10217. A network of phosphatidylinositol 4,5-bisphosphate binding sites regulate gating of the Ca2+-activated Cl channel ANO1 (TMEM16A). Kuai Yu, Tao Jiang, Yuanyuan Cui, Emad Tajkhorshid, and H Criss Hartzell. Proceedings of the National Academy of Sciences, USA, 116:19952-19962, 2019.
10214. Structural insights into the lipid A transport pathway in MsbA. Pius S. Padayatti, Sung Chang Lee, Robyn L. Stanfield, Po-Chao Wen, Emad Tajkhorshid, Ian A. Wilson, and Qinghai Zhang. Structure, 27:1114-1123, 2019.
10213. Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. Jonathan A. Coleman, Dongxue Yang, Zhiyu Zhao, Po-Chao Wen, Craig Yoshioka, Emad Tajkhorshid, and Eric Gouaux. Nature, 569:141-145, 2019.
10212. Characterization of lipid-protein interactions and lipid-mediated modulation of membrane protein function through molecular simulations. Melanie P. Muller, Tao Jiang, Chang Sun, Muyun Lihan, Shashank Pant, Paween Mahinthichaichan, Anda Trifan, and Emad Tajkhorshid. Chemical Reviews, 119:6086-6161, 2019.
10211. Allosteric interactions in human cytochrome P450 CYP3A4: The role of phenylalanine 213. Ilia G. Denisov, Yelena V. Grinkova, Prithviraj Nandigrami, Mrinal S. Shekhar, Emad Tajkhorshid, and Stephen G. Sligar. Biochemistry, 58:1411-1422, 2019.
10209. Calcium-induced lipid nanocluster structures: Sculpturing of the plasma membrane. Michael J. Hallock, Alexander I. Greenwood, Yan Wang, James H. Morrissey, Emad Tajkhorshid, Chad M. Rienstra, and Taras V. Pogorelov. Biochemistry, 57:6897-6905, 2018.
10208. Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming. Matthew L Starr, Robert P Sparks, Andres S Arango, Logan R Hurst, Zhiyu Zhao, Muyun Lihan, Jermaine L Jenkins, Emad Tajkhorshid, and Rutilio A Fratti. Journal of Biological Chemistry, 294:3100-3116, 2019.
10207. Menthol stereoisomers exhibit different effects on α4β2 nAChR upregulation and dopamine neuron spontaneous firing. Brandon J. Henderson, Stephen Grant, Betty W. Chu, Rezvan Shahoei, Stephanie M. Huard, Shyam S. M. Saladi, Emad Tajkhorshid, Dennis A. Dougherty, and Henry A. Lester. eNeuro, 5:ENEURO.0465-18.2018, 2018.
10203. Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor. Daniel T. Infield, Kimberly Matulef, Jason D. Galpin, Kin Lam, Emad Tajkhorshid, Christopher A. Ahern, and Francis I. Valiyaveetil. Nature Communications, 9:5055, 2018.
10202. Endocannabinoid virodhamine is an endogenous inhibitor of human cardiovascular CYP2J2 epoxygenase. Lauren Carnevale, Andres Arango, William R. Arnold, Emad Tajkhorshid, and Aditi Das. Biochemistry, 57:6489-6499, 2018.
10201. Selective permeability of carboxysome shell pores to anionic molecules. Paween Mahinthichaichan, Dylan M. Morris, Yi Wang, Grant J. Jensen, and Emad Tajkhorshid. Journal of Physical Chemistry B, 122:9110-9118, 2018.
10200. Direct protein-lipid interactions shape the conformational landscape of secondary transporters. C. Martens, M. Shekhar, A. Borysik, A. Lau, E. Reading, E. Tajkhorshid, P. J. Booth, and A. Politis. Nature Communications, 9:4151, 2018.
10199. Constructing atomic structural models into cryo-EM densities using molecular dynamics - pros and cons. Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J Williams, Ryan Mcgreevy, Jane Richardson, Abhishek Singharoy, and Emad Tajkhorshid. Journal of Structural Biology, 204:319-328, 2018.
10198. Probing key elements of teixobactin-lipid II interactions in membrane. Po-Chao Wen, Juan M Vanegas, Susan B Rempe, and Emad Tajkhorshid. Chemical Science, 9:6997-7008, 2018.
10197. Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin. Arpita Chakravarti, Kiruthika Selvadurai, Rezvan Shahoei, Hugo Lee, Shirin Fatma, Emad Tajkhorshid, and Raven H. Huang. Journal of Biological Chemistry, 293:14122-14133, 2018.
10196. Molecular insight into drug exporters within the cellular membrane. Emad Tajkhorshid. Pharmacological Research, 133:328, 2018.
10195. Microscopic view of lipids and their diverse biological functions. Po-Chao Wen, Paween Mahinthichaichan, Noah Trebesch, Tao Jiang, Zhiyu Zhao, Eric Shinn, Mrinal Shekhar Yuhang Wang, Karan Kapoor, Chun Kit Chan, and Emad Tajkhorshid. Current Opinion in Structural Biology, 51:177-186, 2018.
10194. Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins. Daniel Kerr, Gregory T Tietjen, Zhiliang Gong, Emad Tajkhorshid, Erin J Adams, and Ka Yee C. Lee. Biochimica et Biophysica Acta - Biomembranes, 1860:2126-2133, 2018.
10193. Electrostatic lock in the transport cycle of the multi-drug resistance transporter EmrE. Josh V Vermaas, Susan B. Rempe, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 115:E7502-E7511, 2018.
10192. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Bioenergetics, 1859:712-724, 2018.
10190. A "cross-stitched" peptide with improved helicity and proteolytic stability. Thomas E. Speltz, Christopher G. Mayne, Sean W. Fanning, Zamia Siddiqui, Emad Tajkhorshid, Geoffrey L Greene, and Terry W. Moore. Organic & Biomolecular Chemistry, 16:3702-3706, 2018.
10188. Cytochrome aa3 oxygen reductase utilizes the tunnel observed in the crystal structures to deliver O2 for catalysis. Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid. Biochemistry, 57:2150-2161, 2018.
10187. Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Chang Sun, Samir Benlekbir, Padmaja Venkatakrishnan, Yuhang Wang, Emad Tajkhorshid, John L. Rubinstein, and Robert B. Gennis. Nature, 557:123-126, 2018.
10181. Salt bridges gate α-catenin activation at intercellular junctions. Samantha Barrick, Jing Li, Xinyu Kong, Alokananda Ray, Emad Tajkhorshid, and Deborah Leckband. Molecular Biology of the Cell, 29:111-122, 2018.
10180. Drug-drug interactions between atorvastatin and dronedarone mediated by monomeric CYP3A4. Ilia G. Denisov, Javier L. Baylon, Yelena V. Grinkova, Emad Tajkhorshid, and Stephen G. Sligar. Biochemistry, 57:805-816, 2017.
10179. Arachidonic acid metabolism by human cardiovascular CYP2J2 is modulated by doxorubicin. William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das. Biochemistry, 56:6700-6712, 2017.
10173. Dimeric structure of the uracil: proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters. Xinzhe Yu, Guanghui Yang, Chuangye Yan, Javier L Baylon, Jing Jiang, He Fan, Guifeng Lu, Kazuya Hasegawa, Hideo Okumura, Tingliang Wang, Emad Tajkhorshid, Shuo Li, and Nieng Yan. Cell Research, 27:1020-1033, 2017.
10171. Q-band electron-nuclear double resonance reveals out-of-plane hydrogen bonds stabilize an anionic ubisemiquinone in cytochrome bo3 from Escherichia coli. Chang Sun, Alexander T. Taguchi, Josh V. Vermaas, Nathan J. Beal, Patrick J. O'Malley, Emad Tajkhorshid, Robert B. Gennis, and Sergei A. Dikanov. Biochemistry, 55:5714-5725, 2016.
10170. Atomic-level description of protein-lipid interactions using an accelerated membrane model. Javier L. Baylon, Josh V. Vermaas, Melanie P. Muller, Mark J. Arcario, Taras V. Pogorelov, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1858:1573-1583, 2016.
10168. Conformational dynamics of the human islet amyloid polypeptide in a membrane environment: Toward the aggregation prone form. Katrine Kirkeby Skeby, Ole Juul Andersen, Taras V. Pogorelov, Emad Tajkhorshid, and Birgit Schiott. Biochemistry, 55:2031-2042, 2016.
10167. TopoGromacs: Automated topology conversion from CHARMM to GROMACS within VMD. Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel Kohlmeyer. Journal of Chemical Information and Modeling, 56:1112-1116, 2016.
10165. Mitochondrial VDAC1: A key gatekeeper as potential therapeutic target. Amadou K.S. Camara, Yi Fan Zhou, Po Chao Wen, Emad Tajkhorshid, and Wai Meng Kwok. Frontiers in Physiology, 8:640, 2017.
10164. Activation and desensitization mechanism of AMPA receptor-tarp complex by cryo-EM. Shanshuang Chen, Yan Zhao, Yuhang Wang, Mrinal Shekhar, Emad Tajkhorshid, and Eric Gouaux. Cell, 170:1234-1246, 2017.
10163. Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase. Tao Jiang, Kuai Yu, H. Criss Hartzell, and Emad Tajkhorshid. eLife, 6:e28671, 2017.
10162. Chasing the open-state structure of pentameric ligand-gated ion channels. Giovanni Gonzalez-Gutierrez, Yuhang Wang, Gisela Cymes, Emad Tajkhorshid, and Claudio Grosman. Journal of General Physiology, 149:1119-1138, 2017.
10160. Coupling X-ray reflectivity and in silico binding to yield dynamics of membrane recognition by Tim1. Gregory T. Tietjen, Javier L. Baylon, Daniel Kerr, Zhiliang Gong, J. Michael Henderson, Charles T. R. Heffern, Mati Meron, Binhua Lin, Mark L. Schlossman, Erin J. Adams, Emad Tajkhorshid, and Ka Yee C. Lee. Biophysical Journal, 113:1505-1519, 2017.
10159. X-ray structures define human P2X3 receptor gating cycle and antagonist action. Steven E. Mansoor, Wei Lü, Wout Oosterheert, Mrinal Shekhar, Emad Tajkhorshid, and Eric Gouaux. Nature, 538:66-71, 2016.
10158. Lipid specificity of the membrane binding domain of coagulation factor X. Melanie P. Muller, Yan Wang, James H. Morrissey, and Emad Tajkhorshid. Journal of Thrombosis and Haemostasis, 15:2005-2016, 2017.
10157. Critical role of water molecules in proton translocation by the membrane-bound transhydrogenase. Pius S. Padayatti, Josephine H. Leung, Paween Mahinthichaichan, Emad Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S. Michael Soltis, J. Baz Jackson, C. David Stout, Robert B. Gennis, and Qinghai Zhang. Structure, 25:1111-1119, 2017.
10156. Computational characterization of molecular mechanisms of membrane transporter function. Noah Trebesch, Josh V. Vermaas, and Emad Tajkhorshid. In Carmen Domene, editor, Computational Biophysics of Membrane Proteins, chapter 7, pp. 197-236. Royal Society of Chemistry, Cambridge, UK, 2017.
10154. Extension of the highly mobile membrane mimetic to transmembrane systems through customized in Silico solvents. Josh V. Vermaas, Taras V. Pogorelov, and Emad Tajkhorshid. Journal of Physical Chemistry B, 121:3764-3776, 2017.
10152. Tribute to Klaus Schulten. Emad Tajkhorshid and Christophe Chipot. Journal of Physical Chemistry B, 121:3203-3205, 2017.
10151. A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel. Mark J Arcario, Christopher G Mayne, and Emad Tajkhorshid. Journal of Biological Chemistry, 9:9480-9492, 2017.
10150. Energy transduction and alternating access of the mammalian ABC transporter P-glycoprotein. Brandy Verhalen, Reza Dastvan, Sundarapandian Thangapandian, Yelena Peskova, Hanane A. Koteiche, Robert K. Nakamoto, Emad Tajkhorshid, and Hassane S. Mchaourab. Nature, 543:738-741, 2017.
10149. Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II. Daniel A. Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad Tajkhorshid, Michael L. Gross, and Himadri B. Pakrasi. Proceedings of the National Academy of Sciences, USA, 114:2224-2229, 2017.
10148. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C. Phillips, Emad Tajkhorshid, and Hong Jin. Nature, 541:554-557, 2017.
10147. Differential membrane binding mechanics of synaptotagmin isoforms observed at atomic detail. Josh V. Vermaas and Emad Tajkhorshid. Biochemistry, 56:281-293, 2017.
10144. Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das. Biochemistry, 55:6969-6980, 2016.
10134. Computational characterization of structural dynamics underlying function in active membrane transporters. Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid. Current Opinion in Structural Biology, 31:96-105, 2015.
10119. Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. Mahmoud Moradi and Emad Tajkhorshid. Journal of Chemical Theory and Computation, 10:2866-2880, 2014.
10118. Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate transporter. Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid. Nature Communications, 6:8393, 2015.
10117. Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2-lipid bilayer interactions. Daniel R McDougle, Javier L Baylon, Daryl D Meling, Amogh Kambalyal, Yelena V Grinkova, Jared Hammernik, Emad Tajkhorshid, and Aditi Das. Biochimica et Biophysica Acta - Biomembranes, 1848:2460-2470, 2015.
10116. Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer. Ilia G. Denisov, Yelena V. Grinkova, Javier L. Baylon, Emad Tajkhorshid, and Stephen G. Sligar. Biochemistry, 54:2227-2239, 2015.
10115. The cellular membrane as a mediator for small molecule interaction with membrane proteins. Christopher G. Mayne, Mark J. Arcario, Paween Mahinthichaichan, Javier L. Baylon, Josh V. Vermaas, Latifeh Navidpour, Po-Chao Wen, Sundarapandian Thangapandian, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1858:2290-2304, 2016.
10114. Enhancing Mn(II)-binding and manganese peroxidase activity in a designed cytochrome c peroxidase through fine-tuning secondary-sphere interactions. Parisa Hosseinzadeh, Evan N. Mirts, Thomas D. Pfister, Yi-Gui Gao, Christopher Mayne, Howard Robinson, Emad Tajkhorshid, and Yi Lu. Biochemistry, 55:1494-1502, 2016.
10113. Stapled peptides with γ-methylated hydrocarbon chains for the estrogen receptor/coactivator interaction. Thomas E. Speltz, Sean W. Fanning, Christopher G. Mayne, Colin Fowler, Emad Tajkhorshid, Geoffrey L. Greene, and Terry W. Moore. Angewandte Chemie - International Edition in English, 55:4252-4255, 2016.
10112. Molecular basis for differential anion binding and proton coupling in the Cl/H+ exchanger ClC-ec1. Tao Jiang, Wei Han, Merritt Maduke, and Emad Tajkhorshid. Journal of the American Chemical Society, 138:3066-3075, 2016.
10111. 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. Paween Mahinthichaichan, Robert Gennis, and Emad Tajkhorshid. Biochemistry, 55:1265-1278, 2016.
10110. Revealing an outward-facing open conformational state in a CLC Cl/H exchange transporter. Chandra M Khantwal, Sherwin J Abraham, Wei Han, Tao Jiang, Tanmay S Chavan, Ricky C Cheng, Shelley M Elvington, Corey W Liu, Irimpan I Mathews, Richard A Stein, Hassane S Mchaourab, Emad Tajkhorshid, and Merritt Maduke. eLife, 5:e11189, 2016.
10109. Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation. Sean W Fanning, Christopher G Mayne, Venkatasubramanjan Dharmarajan, Kathryn E Carlson, Teresa A Martin, Scott J Novick, Weiyi Toy, Bradley Green, Srinivas Panchamukhi, Benita S Katzenellenbogen, Emad Tajkhorshid, Patrick R Griffin, Yang Shen, Sarat Chandarlapaty, John A Katzenellenbogen, and Geoffrey L Greene. eLife, pp. e12792, 2016.
10107. Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Josh V. Vermaas, Alexander T. Taguchi, Sergel A. Dikanov, Colin A. Wraight, and Emad Tajkhorshid. Biochemistry, 54:2104-2116, 2015.
10106. Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter. Smriti Mishra, Brandy Verhalen, Richard A Stein, Po-Chao Wen, Emad Tajkhorshid, and Hassane S Mchaourab. eLife, 3:e02740, 2014.
10105. Changing the peptide specificity of a human T-cell receptor by directed evolution. Sheena N. Smith, Yuhang Wang, Javier L. Baylon, Nishant K. Singh, Brian M. Baker, Emad Tajkhorshid, and David M. Kranz. Nature Communications, 5:5223, 2014. (13 pages).
10104. Membrane-induced structural rearrangement and identification of a novel membrane anchor in Talin F2F3. Mark J. Arcario and Emad Tajkhorshid. Biophysical Journal, 107:2059-2069, 2014.
10103. Conformational heterogeneity of α-synuclein in membrane. Josh V. Vermaas and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1838:3107-3117, 2014.
10102. Conformational dynamics at the inner gate of KcsA during activation. Raymond E Hulse, Joseph R Sachleben, Po-Chao Wen, Mahmoud Moradi, Emad Tajkhorshid, and Eduardo Perozo. Biochemistry, 53:2557-2559, 2014.
10101. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Mahmoud Moradi and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 110:18916-18921, 2013.
10100. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Mohamad R. Kalani, Abdulvahab Moradi, Mahmoud Moradi, and Emad Tajkhorshid. Biophysical Journal, 105:993-1003, 2013.
10099. On the origin of large flexibility of P-glycoprotein in the inward-facing state. Po-Chao Wen, Brandy Verhalen, Stephan Wilkens, Hassane S. Mchaourab, and Emad Tajkhorshid. Journal of Biological Chemistry, 288:19211-19220, 2013.
10098. Movement of NH3 through the human urea transporter B: a new gas channel. R. Ryan Geyer, Raif Musa-Aziz, Giray Enkavi, Paween Mahinthichaichan, Emad Tajkhorshid, and Walter F. Boron. American Journal of Physiology - Renal Physiology, 304:F1447-F1457, 2013.
10097. Subangstrom resolution X-ray structure details aquaporin-water interactions. Urszula Kosinska Eriksson, Gerhard Fischer, Rosmarie Friemann, Giray Enkavi, Emad Tajkhorshid, and Richard Neutze. Science, 340:1346-1349, 2013.
10096. Characterizing the membrane-bound state of cytochrome P450 3A4: Structure, depth of insertion, and orientation. Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar, and Emad Tajkhorshid. Journal of the American Chemical Society, 135:8542-8551, 2013.
10095. Driven metadynamics: Reconstructing equilibrium free energies from driven adaptive-bias simulations. Mahmoud Moradi and Emad Tajkhorshid. Journal of Physical Chemistry Letters, 4:1882-1887, 2013.
10094. Transient formation of water-conducting states in membrane transporters. Jing Li, Saher A. Shaikh, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 110:7696-7701, 2013.
10093. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Saher A. Shaikh, Jing Li, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad Tajkhorshid. Biochemistry, 52:569-587, 2013.
10092. Simulation studies of the mechanism of membrane transporters. Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh, and Emad Tajkhorshid. In Luca Monticelli and Emppu Salonen, editors, Biomolecular Simulations, volume 924 of Methods in Molecular Biology, pp. 361-405. Humana Press, 2013.
10091. Structure and permeation mechanism of a mammalian urea transporter. Elena J Levin, Yu Cao, Giray Enkavi, Matthias Quick, Yaping Pan, Emad Tajkhorshid, and Ming Zhou. Proceedings of the National Academy of Sciences, USA, 109:11194-11199, 2012.
10090. Tissue factor/factor VIIa complex: Role of the membrane surface. James H. Morrissey, Emad Tajkhorshid, Stephen G. Sligar, and Chad M. Rienstra. Thrombosis Research, 129:S8-S10, 2012.
10089. Structural basis for iron piracy by pathogenic neisseria. Nicholas Noinaj, Nicole C. Easley, Muse Oke, Naoko Mizuno, James Gumbart, Evzen Boura, Ashley N. Steere, Olga Zak, Philip Aisen, Emad Tajkhorshid, Robert W. Evans, Andrew R. Gorringe, Anne B. Mason, Alasdair C. Steven, and Susan K. Buchanan. Nature, 483:53-58, 2012.
10088. Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Travis J. Barnard, James Gumbart, Janine H. Peterson, Nicholas Noinaj, Nicole C. Easley, Nathalie Dautin, Adam J. Kuszak, Emad Tajkhorshid, Harris D. Bernstein, and Susan K. Buchanan. Journal of Molecular Biology, 415:128-142, 2012.
10086. Water access points and hydration pathways in CLC H+/Cl transporters. Wei Han, Ricky C. Cheng, Merritt C. Maduke, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 111:1819-1824, 2014.
10080. A microscopic view of phospholipid insertion into biological membranes. Josh V. Vermaas and Emad Tajkhorshid. Journal of Physical Chemistry B, 118:1754-1764, 2014.
10079. Partitioning of amino acids into a model membrane: Capturing the interface. Taras V. Pogorelov, Josh V. Vermaas, Mark J. Arcario, and Emad Tajkhorshid. Journal of Physical Chemistry B, 118:1481-1492, 2014.
10075. Functional interplay between acetylation and methylation of the RelA subunit of NF-κB. X.-D. Yang, E. Tajkhorshid, and L.-F. Chen. Molecular and Cellular Biology, 30:2170-2180, 2010.
10074. The binding interface of cytochrome c and cytochrome c1 in the bc1 complex: rationalizing the role of key residues. O. Kokhan, C. Wraight, and E. Tajkhorshid. Biophysical Journal, 99:2647-2656, 2010.
10070. Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Y. Zenmei Ohkubo, Taras V. Pogorelov, Mark J. Arcario, Geoff A. Christensen, and Emad Tajkhorshid. Biophysical Journal, 102:2130-2139, 2012.
10065. A gate-free pathway for substrate release from the inward-facing state of the Na+-galactose transporter. Jing Li and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1818:263-271, 2012.
10064. Membrane transporters: Molecular machines coupling cellular energy to vectorial transport across the membrane. Zhijian Huang, Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Jing Li, and Emad Tajkhorshid. In Benoit Roux, editor, Molecular Machines, chapter 9, pp. 151-182. World Scientific Publishing, Singapore, 2011.
10063. Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model. Mark J. Arcario, Y. Zenmei Ohkubo, and Emad Tajkhorshid. Journal of Physical Chemistry B, 115:7029-7037, 2011.
10062. Nanoscale studies of protein-membrane interactions in blood clotting. James H. Morrissey, Emad Tajkhorshid, and Chad M. Rienstra. Journal of Thrombosis and Haemostasis, 9 (Suppl. 1):167-167, 2011.
10061. Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers. John M. Boettcher, Rebecca L. Davis-Harrison, Mary C. Clay, Andrew J. Nieuwkoop, Y. Zenmei Ohkubo, Emad Tajkhorshid, James H. Morrissey, and Chad M. Rienstra. Biochemistry, 50:2264-2273, 2011.
10060. Molecular determinants of phospholipid synergy in blood clotting. Narjes Tavoosi, Rebecca L. Davis-Harrison, Taras V. Pogorelov, Y. Zenmei Ohkubo, Mark J. Arcario, Mary C. Clay, Chad M. Rienstra, Emad Tajkhorshid, and James H. Morrissey. Journal of Biological Chemistry, 286:23247-23253, 2011.
10052. Modeling and dynamics of the inward-facing state of a Na+/Cl dependent neurotransmitter transporter homologue. Saher Afshan Shaikh and Emad Tajkhorshid. PLoS Computational Biology, 6:e1000905, 2010.
10051. Protein membrane interactions: blood clotting on nanoscale bilayer. J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, C. M. Rienstra, A. Z. Kijac, Y. Z. Ohkubo, and E. Tajkhorshid. Journal of Thrombosis and Haemostasis, 7:169-172, 2009.
10050. Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria. Jianhua Feng, Eliana Lucchinetti, Giray Enkavi, Yi Wang, Peter Gehrig, Bernd Roschitzki, Marcus C. Schaub, Emad Tajkhorshid, Kathrin Zaugg, and Michael Zaugg. American Journal of Physiology, 298:C740-748, 2010.
10049. Structural basis of substrate selectivity in the glycerol-3-phosphate:phosphate antiporter GlpT. Christopher J. Law, Giray Enkavi, Da-Neng Wang, and Emad Tajkhorshid. Biophysical Journal, 97:1346-1353, 2009.
10048. Identification of the third Na+ site and the sequence of extracellular binding events in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 99:1416-1425, 2010.
10046. Capturing functional motions of membrane channels and transporters with molecular dynamics simulation. Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, and Emad Tajkhorshid. Journal of Computational and Theoretical Nanosciences, 7:2481-2500, 2010.
10045. Exploring transmembrane diffusion pathways with molecular dynamics. Yi Wang, Saher A. Shaikh, and Emad Tajkhorshid. Physiology, 25:142-154, 2010.
10044. Ion-releasing state of a secondary membrane transporter. Jing Li and Emad Tajkhorshid. Biophysical Journal, 97:L29-L31, 2009.
10043. Nitric oxide conduction by the brain aquaporin AQP4. Yi Wang and Emad Tajkhorshid. PROTEINS: Structure, Function, and Bioinformatics, 78:661-670, 2010.
10042. Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor. Y. Zenmei Ohkubo, James H. Morrissey, and Emad Tajkhorshid. Journal of Thrombosis and Haemostasis, 8:1044-1053, 2010.
10041. Interplay of mechanical and binding properties of Fibronectin type I. Jiankuai Diao, Andrew J. Maniotis, Robert Folberg, and Emad Tajkhorshid. Theoretica Chimica Acta, 125:397-405, 2010.
10040. Protein-phospholipid interactions in blood clotting. James H. Morrissey, Rebecca L. Davis-Harrison, Narjes Tavoosi, Ke Ke, Vincent Pureza, John M. Boettcher, Mary C. Clay, Chad M. Rienstra, Y. Zenmei Ohkubo, Taras V. Pogorelov, and Emad Tajkhorshid. Thrombosis Research, 125(Suppl. 1):S23-S25, 2010.
10038. Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT. Giray Enkavi and Emad Tajkhorshid. Biochemistry, 49:1105-1114, 2010.
10037. Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Journal of Molecular Biology, 393:1129-1142, 2009.
10036. Molecular mechanisms of active transport across the cellular membrane, chapter 10, pp. 248-286. Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad Tajkhorshid. Royal Society of Chemistry, 2010.
10035. Structural and functional analysis of SoPIP2;1 mutants add insight into plant aquaporin gating. Maria Nyblom, Anna Frick, Yi Wang, Mikael Ekvall, Karin Hallgren, Kristina Hedfalk, Richard Neutze, Emad Tajkhorshid, and Susanna Törnroth-Horsefield. Journal of Molecular Biology, 387:653-668, 2009.
10034. Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis. P.-C. Wen and E. Tajkhorshid. Biophysical Journal, 95:5100-5110, 2008.
10033. Potential cation and H+ binding sites in acid sensing ion channel-1. S. A. Shaikh and E. Tajkhorshid. Biophysical Journal, 95:5153-5164, 2008.
10027. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 95:2292-2300, 2008.
10026. 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.
10025. 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.
10024. 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.
10023. Indirect role of Ca2+ in the assembly of extracelluar matrix proteins. Jiankuai Diao and Emad Tajkhorshid. Biophysical Journal, 95:120-127, 2008.
10022. 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.
10014. 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.
10013. 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.
10012. Molecular mechanisms of conduction and selectivity in aquaporin water channels. Yi Wang and Emad Tajkhorshid. Journal of Nutrition, 137:1509S-1515S, 2007.
10010. Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Journal, 93:496-504, 2007.
10008. 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.
10007. 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.
10004. 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.
10003. Molecular basis of proton blockage in aquaporins. Nilmadhab Chakrabarti, Emad Tajkhorshid, Benoît Roux, and Régis Pomès. Structure, 12:65-74, 2004.
724. Pro-nifuroxazide self-assembly leads to triggerable nanomedicine for anti-cancer therapy. Santosh Misra, Zhe Wu, Fatemeh Ostadhossein, Mao Ye, Kingsley Boateng, Klaus Schulten, Emad Tajkhorshid, and Dipanjan Pan. ACS Applied Materials and Interfaces, 11:18074-18089, 2019.
719. PyContact: Rapid, customizable and visual analysis of non-covalent interactions in MD simulations. M. Scheurer, P. Rodenkirch, M. Siggel, R. C. Bernardi, K. Schulten, E. Tajkhorshid, and T. Rudack. Biophysical Journal, 114:577-583, 2018.
698. Binding site recognition and docking dynamics of a single electron transport protein: Cytochrome c2. Abhishek Singharoy, Angela M. Barragan, Sundarapandian Thangapandian, Emad Tajkhorshid, and Klaus Schulten. Journal of the American Chemical Society, 138:12077-12089, 2016.
643. A highly tilted membrane configuration for the pre-fusion state of synaptobrevin. Andrew E. Blanchard, Mark J. Arcario, Klaus Schulten, and Emad Tajkhorshid. Biophysical Journal, 107:2112-2121, 2014.
613. Rapid parameterization of small molecules using the Force Field Toolkit. Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, and James C. Gumbart. Journal of Computational Chemistry, 34:2757-2770, 2013.
575. Molecular dynamics investigation of the ω current in the Kv1.2 voltage sensor domains. Fatemeh Khalili-Araghi, Emad Tajkhorshid, Benoit Roux, and Klaus Schulten. Biophysical Journal, 102:258-267, 2012.
521. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Fatemeh Khalili-Araghi, Vishwanath Jogini, Vladimir Yarov-Yarovoy, Emad Tajkhorshid, Benoit Roux, and Klaus Schulten. Biophysical Journal, 98:2189-2198, 2010.
495. Molecular dynamics simulations of membrane channels and transporters. Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 19:128-137, 2009.
483. 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.
470. 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.
458. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008.
441. 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.
436. 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.
431. 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.
425. 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.
424. Dynamics of K+ ion conduction through Kv1.2. Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 91:L72-L74, 2006.
421. 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.
400. 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.
397. 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.
392. 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.
384. 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.
381. 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.
378. Collective diffusion model for water permeation through microscopic channels. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Physical Review Letters, 93:224501, 2004. (4 pages).
375. 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.
369. 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.
365. Complementarities and convergence of results in bacteriorhodopsin trimer simulations. Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 87:1394-1395, 2004.
355. 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.
350. Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004.
344. Electrostatic tuning of permeation and selectivity in aquaporin water channels. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:2884-2899, 2003.
342. 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.
341. 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.
340. 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.
337. 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.
333. 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.
329. 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.
328. 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.
327. Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002.
325. 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.
318. The mechanism of glycerol conduction in aquaglyceroporins. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, 9:1083-1093, 2001.
313. 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.
312. 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.
302. 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.
285. 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.