TCB Publications - Search
303. Targeting lipid-protein interaction for drug development: Development of a novel resistance-proof Syk inhibitor for 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, 2022. In Press.
302. 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, 2022. In Press.
301. 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. In Press.
300. ANARI: A 3D rendering API standard. J. E. Stone, K. Griffin, J. Amstutz, D. DeMarle, W. Sherman, and J. Günther. Computing in Science and Engineering, 2022. In Press.
299. Post-translational 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, 2022. In Press.
298. 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. Chemica Scripta, 13:4150-4169, 2022. Published. (PMC: PMC8985516)
297. 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.
296. 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. Published. (PMC: PMC8970671)
295. 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. Published.
294. 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. Published.
293. 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. Published.
292. 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. Published.
291. 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, 2022. In Press.
290. 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. Published. (PMC: PMC8872756)
289. 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. Published. (PMC: PMC8860876)
288. 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. Published.
287. 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. Published.
286. 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, 2021. Published. (PMC: PMC8903035)
285. 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. Published.
284. ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome. Alexander T. Baker, Ryan J. Boyd, Daipayan Sarkar, John Vant, Alicia Teijeira Crespo, Chloe D. Truong, Emily Bates, Eric Wilson, Chun Kit Chan, Magdalena Lipka-Lloyd, Petra Fromme, Marius Bolni Nagalo, Meike Heurich, Dewight Williams, Po-Lin Chiu, Pierre J. Rizkallah, Alan L. Parker, Abhishek Singharoy, and Mitesh J. Borad. Science Advances, 7:eabl8213, 2021. Published.
283. 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. Published. (PMC: PMC8403832)
282. 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. Published.
281. 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. Published.
280. 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. Published.
279. 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. Published.
278. 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. Published.
277. 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. Published.
276. 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. Published.
275. 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. Published.
274. 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. Published.
273. 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.
272. Use of microscale thermophoresis to measure protein-lipid interactions. Robert P. Sparks, Andreas Becker, Andres S. Arango, Emad Tajkhorshid, and Rutilio A. Fratti. Journal of Visualized Experiments, 2021. In Press.
271. 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. Published. (PMC: PMC8338773)
270. 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.
269. Multilevel summation for periodic electrostatics using B-splines. Hüseyin Kaya, David J. Hardy, and Robert D. Skeel. Journal of Chemical Physics, 154:144105, 2021. (PMC: PMC8036131)
268. 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.
267. 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. Published.
266. 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. (PMC: PMC8009841)
265. 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. (PMC: PMC8762579)
264. 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.
263. 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.
262. Theoretical description of the primary proton-coupled electron transfer reaction in the cytochrome bc1 complex. Angela M. Barragan, Alexander V. Soudackov, Zaida Luthey-Schulten, Sharon Hammes-Schiffer, Klaus Schulten, and Ilia A. Solov'yov. Journal of the American Chemical Society, 143:715-723, 2021.
261. Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz, Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida Luthey-Schulten, and Donna Cox. Parallel Computing, 2021. Published.
260. 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. Published.
259. 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.
258. Scalable analysis of authentic viral envelopes on FRONTERA. Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla, and Juan R. Perilla. Computing in Science and Engineering, 22:11-20, 2020.
256. 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. (PMC: PMC7707832)
255. 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. (PMC: PMC7710758)
254. 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.
253. 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. (PMC: PMC7553777)
252. Benchmarking machine learning workloads in structural bioinformatics applications. Heng Ma, Austin Clyde, Anda Trifan, Venkatram Vishwanath, Arvind Ramanathan, Debsindhu Bhowmik, and Shantenu Jha. First International Workshop on Benchmarking Machine Learning Workloads on Emerging Hardware: CHALLENGE20, 2020.
251. 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. (PMC: PMC7527224)
250. 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.
249. 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. (PMC: PMC7686227)
248. 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.
247. 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. (PMC: PMC7395834)
246. 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. (PMC: PMC7339978)
245. Membrane interactions of Cy3/Cy5 fluorophores and their effects on membrane protein dynamics. Kin Lam and Emad Tajkhorshid. Biophysical Journal, 119:24-34, 2020. (PMC: PMC7335937)
244. 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. (PMC: PMC7296003)
243. 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. (PMC: PMC7433777)
242. 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. (PMC: PMC7731932)
241. 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. (PMC: PMC7094167)
240. 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. (PMC: PMC7075958)
239. 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. (PMC: PMC7098852)
238. 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.
237. In situ conformational changes of the Escherichia coli serine chemoreceptor in different signaling states. Wen Yang, Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten, Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel. Molecular Biology and Physiology, 10:e00973-19, 2019. (PMC: PMC6606802)
236. Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations. C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang. Communications Biology, 3:24, 2020. (PMC: PMC6954272)
235. 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. (PMC: PMC7253180)
234. Streptavidin/biotin: Tethering geometry defines unbinding mechanics. Steffen M. Sedlak, Leonard C. Schendel, Hermann E. Gaub, and Rafael C. Bernardi. Science Advances, 6:eaay5999, 2020.
233. Mechanisms of nanonewton mechanostability in a protein complex revealed by molecular dynamics simulations and single-molecule force spectroscopy. Rafael C. Bernardi, Ellis Durner, Constantin Schoeler, Klara H. Malinowska, Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub, and Michael A. Nash. Journal of the American Chemical Society, 141:14752-14763, 2019. (PMC: PMC6939381)
232. 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. (PMC: PMC6925253)
231. 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. (PMC: PMC6983364)
230. 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.
229. 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. (PMC: PMC6814714)
228. 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.
227. Microscopic characterization of GRP1 PH domain interaction with anionic membranes. Shashank Pant and Emad Tajkhorshid. Journal of Computational Chemistry, 41:489-499, 2020. (PMC: PMC7000246)
226. High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities. Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, and Juan R. Perilla. Journal of Chemical Information and Modeling, 59:4328-4338, 2019. (PMC: PMC6817393)
225. 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.
224. 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. (PMC: PMC7059649)
223. 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. (PMC: PMC7059651)
222. 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. (PMC: PMC7035594)
221. Probing cholesterol binding and translocation in P-glycoprotein. Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1862:183090, 2020. (PMC: PMC6934093)
220. 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. (PMC: PMC6873166)
219. 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. (PMC: PMC7058097)
218. 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. (PMC: PMC7024014)
217. 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. (PMC: PMC6778221)
216. Non-syndromic mitral valve dysplasia mutation changes the force resilience and interaction of human Filamin A. Tatu J.K. Haataja, Rafael C. Bernardi, Simon Lecointe, Romain Capoulade, Jean Merot, and Ulla Pentikäinen. Structure, 27:102-112, 2019.
215. Direction matters: Monovalent streptavidin/biotin complex under load. Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig, Zaida Luthey-Schulten, Hermann E. Gaub, and Rafael C. Bernardi. Nano Letters, 19:3415-3421, 2019. (PMC: PMC6486461)
214. 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. (PMC: PMC6610721)
213. 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. (PMC: PMC6750207)
212. 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. (PMC: PMC6506392)
211. 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. (PMC: PMC7528618)
210. The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells. Sean W Fanning, Rinath Jeselsohn, Venkatasubramanian Dharmarajan, Christopher G Mayne, Mostafa Karimi, Gilles Buchwalter, René Houtman, Weiyi Toy, Colin E Fowler, Ross Han, Muriel Lainé, Kathryn E Carlson, Teresa A Martin, Jason Nowak, Jerome C Nwachukwu, David J Hosfield, Sarat Chandarlapaty, Emad Tajkhorshid, Kendall W Nettles, Patrick R Griffin, Yang Shen, John A Katzenellenbogen, Myles Brown, and Geoffrey L Greene. eLife, 7:e37161, 2018. (PMC: PMC6335054)
209. 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. (PMC: PMC6475452)
208. 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. (PMC: PMC6398130)
207. 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. (PMC: PMC6325563)
206. Scalable molecular dynamics with NAMD on the Summit system. Bilge Acun, David J. Hardy, Laxmikant Kale, Ke Li, James C. Phillips, and John E. Stone. IBM Journal of Research and Development, 62:4:1-4:9, 2018.
205. Best practices in running collaborative GPU hackathons: Advancing scientific applications with a sustained impact. Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin, Matthew Otten, Dirk Pleiter, John E Stone, Juan Lucio-Vega, Michael Zingale, and Fernanda Foertter. Computing in Science and Engineering, 20:95-106, 2018.
204. NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia. Bioinformatics, 35:1241-1243, 2018. (PMC: PMC6449750)
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