|
| 9352. Distinct interactions of cannabinol and its cytochrome
P450-generated metabolites with receptors and sensory neurons.
Debanjan Kundu, Luca Franchini, Hale Hasdemir, Elliot Lloyd, Jonathan Maturano,
Katalin Rabl, Anna Denissiouk, Mark Schumacher, David Sarlah, Judith Hellman,
Emad Tajkhorshid, Cesare Orlandi, and Aditi Das.
Journal of Medicinal Chemistry, 2025.
|
| 9351. Cholesterol-targeting Wnt-β-catenin signaling inhibitors for
colorectal cancer.
Ashutosh Sharma, Julian Zalejski, Shruti Vijay Bendre, Simona Kavrokova,
Hale S. Hasdemir, Defne Gorgun Ozgulbas, Jiachen Sun, Koralege C. Pathmasiri,
Ruicheng Shi, Ahmed Aloulou, Kyli Berkley, Charles F. Delisle, Young Wang,
Erin Weisser, Pawanthi Buweneka, Dominick Pierre-Jacques, Sayandeb Mukherjee,
Diana A. Abbasi, Daesung Lee, Bo Wang, Vladimir Gevorgyan, Stephanie M.
Cologna, Emad Tajkhorshid, Erik R. Nelson, and Wonhwa Cho.
Nature Chemical Biology, 2025.
|
| 9350. Dissecting large-scale structural transitions in membrane
transporters using advanced simulation technologies.
Shashank Pant, Sepehr Dehghani-Ghahnaviyeh, Noah Trebesch, Ali Rasouli, Tianle
Chen, Karan Kapoor, Po-Chao Wen, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 129:3703-3719, 2025.
|
| 9349. Characterization of membrane binding and protein-lipid interactions
at atomic level with accelerated HMMM model.
Hale S. Hasdemir, Yupeng Li, Payam Kelich, Po-Chao Wen, and Emad Tajkhorshid.
Methods in Molecular Biology, 2025.
|
| 9348. Modeling diffusive motion of ferredoxin and plastocyanin on the PSI
domain of Procholorococcus marinus MIT931.
Aaron Chan, Emad Tajkhorshid, Zaida Luthey-Schulten, and Melih Sener.
Journal of Physical Chemistry B, 129:52-70, 2025.
|
| 9347. Membrane-bound model of the ternary complex between factor
VIIa/tissue factor and factor X.
Melanie P. Muller, Alex Mortenson, Josepha C. Sedzro, Po-Chao Wen, James H
Morrissey, and Emad Tajkhorshid.
Blood Advances, 2024.
|
| 9346. Atomistic characterization of β2-glycoprotein I domain V
interaction with anionic membranes.
Hale S. Hasdemir, Nicola Pozzi, and Emad Tajkhorshid.
Journal of Thrombosis and Haemostasis, 22:3277-3289, 2024.
|
| 9345. Modulation of ABCG2 transporter activity by Ko143 derivatives.
Qin Yu, Sepehr Dehghani-Ghahnaviyeh, Ali Rasouli, Anna Sadurni, Julia Kowal,
Rose Bang-Soerensen, Po-Chao Wen, Melanie Tinzl-Zechner, Rossitza N.
Irobalieva, Dongchun Ni, Henning Stahlberg, Karl-Heinz Altmann, Emad
Tajkhorshid, and Kaspar P. Locher.
ACS Chemical Biology, 19:2304-2313, 2024.
(PMC: PMC11574751) |
| 9344. The role of protein-lipid interactions in priming the bacterial
translocon.
Matt Sinclair and Emad Tajkhorshid.
Membranes, 14, 2024.
(PMC: PMC11677795) |
| 9343. Structure of the human dopamine transporter and mechanisms of
inhibition.
Dushyant Kumar Srivastava, Vikas Navratna, Dilip K. Tosh, Audrey Chinn,
Md Fulbabu Sk, Emad Tajkhorshid, Kenneth A. Jacobson, and Eric Gouaux.
Nature, 632, 2024.
(PMC: PMC11324517) |
| 9342. Secondary structure determines electron transport in peptides.
Rajarshi Samajdar, Moeen Meigooni, Hao Yang, Jialing Li, Xiaolin Liu,
Nicholas E. Jackson, Martín A. Mosquera, Emad Tajkhorshid, and Charles M.
Schroeder.
Proceedings of the National Academy of Sciences, USA,
121:e2403324121, 2024.
Published.
|
| 9341. GOLEM: Automated and robust cryo-EM-guided ligand docking with
explicit water molecules.
Zhiyu Zhao and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 2024.
In Press.
|
| 9340. Topological learning approach to characterizing biological membranes.
Andres S. Arango, Hyun Park, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 64:5242-5252,
2024.
Published.
|
| 9339. Improved highly mobile membrane mimetic model for investigating
protein-cholesterol interactions.
Muyun Lihan and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 64:4822-4834,
2024.
Published.
|
| 9338. Broadening access to small-molecule parameterization with the force
field toolkit.
Yunlin Zeng, Anna Pavlova, Philip M. Nelson, Zachary L. Glick, Lan Yang,
Yui Tik Pang, Mariano Spivak, Giuseppe Licari, Emad Tajkhorshid, C. David
Sherrill, and James C. Gumbart.
Journal of Chemical Physics, 160:242501, 2024.
Published.
|
| 9337. 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, 87:639-651, 2024.
Published.
(PMC: PMC11061835) |
| |
| 9335. 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.
|
| 9334. A Gram-negative-selective antibiotic spares the gut microbiome and
prevents Clostridioides Difficile infection.
K. A. Muñoz, 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, 630:429-436, 2024.
Published.
|
| 9333. 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.
(PMC: PMC11012027) |
| 9332. 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, 52:4969-4984, 2024.
Published.
(PMC: PMC11109945) |
| 9331. 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.
(PMC: PMC11009415) |
| 9330. 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.
(PMC: PMC11137617) |
| 9329. 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.
|
| 9328. 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.
(PMC: PMC10849595) |
| 9327. 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, 15, 2024.
Published.
(PMC: PMC10980826) |
| 9326. 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.
(PMC: PMC10847778) |
| 9325. APACE: AlphaFold2 and advanced computing as a service for
accelerated discovery in biophysics.
Hyun Park, Parth Patel, Roland Haas, and E. A. Huerta.
Proceedings of the National Academy of Sciences, USA,
121:e2311888121, 2024.
Published.
|
| 9324. 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.
(PMC: PMC11145395) |
| 9323. 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.
(PMC: PMC10695947) |
| 9322. 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.
(PMC: PMC10632425) |
| 9321. Tuning sterol extraction kinetics yields a renal-sparing polyene
antifungal.
Arun Maji, Corinne P. Soutar, Jiabao Zhang, Agnieszka Lewandowska, Brice E.
Uno, Su Yan, Yogesh Shelke, Ganesh Murhade, Evgeny Nimerovsky, Collin G.
Borcik, Andres S. Arango, Justin D. Lange, Jonnathan P. Marin-Toledo,
Yinghuan Lyu, Keith L. Bailey, Patrick J. Roady, Jordan T. Holler, Anuj
Khandelwal, Anna M. SantaMaria, Hiram Sanchez, Praveen R. Juvvadi, Gina
Johns, Michael J. Hageman, Joanna Krise, Teclegiorgis Gebremariam, Eman G.
Youssef, Ken Bartizal, Kieren A. Marr, William J. Steinbach, Ashraf S.
Ibrahim, Thomas F. Patterson, Nathan P. Wiederhold, David R. Andes, Taras V.
Pogorelov, Charles D. Schwieters, Timothy M. Fan, Chad M. Rienstra, and
Martin D. Burke.
Nature, 623:1079-1085, 2023.
Published.
(PMC: PMC10883201) |
| 9320. 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.
(PMC: PMC10663523) |
| 9319. 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.
|
| 9318. 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.
|
| 9317. Application experiences on a gpu-accelerated arm-based hpc testbed.
Wael Elwasif, William Godoy, Nick Hagerty, J. Austin Harris, Oscar Hernandez,
Balint Joo, Paul Kent, Damien Lebrun-Grandie, Elijah Maccarthy,
Veronica Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei
Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan,
Rene Widera, Spencer Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey
Young, Sunita Chandrasekaran, Florina Ciorba, Osman Simsek, Kate Clark,
Filippo Spiga, Jeff Hammond, John Stone, David Hardy, Sebastian Keller,
Jean-Guillaume Piccinali, and Christian Trott.
In Proceedings of the HPC Asia 2023 Workshops, HPC Asia '23
Workshops, pp. 35-49, New York, NY, USA, 2023. Association for Computing
Machinery.
|
| 9316. 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.
|
| 9315. 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.
|
| 9314. 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.
(PMC: PMC10257117) |
| 9313. 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.
(PMC: PMC9813137) |
| 9312. #COVIDisAirborne: AI-enabled multiscale computational microscopy
of delta SARS-CoV-2 in a respiratory aerosol.
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer,
Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda
Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra
Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa
Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith,
Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick Manby, Anima
Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David
Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher
Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard
Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas
Miller, Shantenu Jha, Arvind Ramanathan, Lillian Chong, and Rommie Amaro.
The International Journal of High Performance Computing
Applications, 37:10943420221128233, 2022.
(PMC: PMC8609898) |
| 9311. 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.
(PMC: PMC8455456) |
| 9310. 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.
(PMC: PMC9726985) |
| 9309. 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.
(PMC: PMC9890230) |
| 9308. 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.
(PMC: PMC9910490) |
| 9307. 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.
(PMC: PMC9653410) |
| 9306. 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.
|
| 9305. 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.
(PMC: PMC9605866) |
| 9304. 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.
|
| 9303. 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.
(PMC: PMC9898191) |
| 9302. 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.
|
| 9301. 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.
|
| 9300. ANARI: A 3-D rendering API standard.
J. E. Stone, K. Griffin, J. Amstutz, D. DeMarle, W. Sherman, and
J. Günther.
Computing in Science and Engineering, 24:7-18, 2022.
|
| 9299. 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.
(PMC: PMC9282386) |
| 9298. 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.
(PMC: PMC8985516) |
| 9297. 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.
|
| 9296. 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.
(PMC: PMC8970671) |
| 9295. 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.
|
| 9294. 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.
|
| 9293. 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.
(PMC: PMC8892158) |
| 9292. 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.
|
| 9291. 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.
|
| 9290. 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.
(PMC: PMC8872756) |
| 9289. 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.
(PMC: PMC8860876) |
| 9288. 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.
|
| 9287. 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.
|
| 9286. 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.
(PMC: PMC8903035) |
| 9285. 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.
|
| 9284. 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.
|
| 9283. 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.
(PMC: PMC8403832) |
| 9282. 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.
|
| 9281. 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.
|
| 9280. 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.
|
| 9279. 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.
|
| 9278. 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.
|
| 9277. 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.
|
| 9276. 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.
|
| 9275. 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.
|
| 9274. 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.
|
| 9273. 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.
|
| |
| 9271. 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.
(PMC: PMC8338773) |
| 9270. 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.
|
| 9269. 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) |
| 9268. 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.
|
| 9267. 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.
|
| 9266. 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) |
| 9265. 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) |
| 9264. 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.
|
| 9263. 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.
|
| 9262. 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.
|
| 9261. 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, 102:102698, 2021.
|
| 9260. 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.
|
| 9259. 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.
|
| 9258. 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.
|
| |
| 9256. 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) |
| 9255. 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) |
| 9254. 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.
|
| 9253. 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) |
