|
| |
| |
| 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,
2021.
|
| 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.
ChemRxiv, 2021.
|
| 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, 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, 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.
In Press.
|
| 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, 2020.
In Press.
|
| 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.
|
| 257. Conformational changes of the nucleotide binding domains of
P-glycoprotein induced by ATP hydrolysis.
Sepehr Dehghani-Ghahnaviyeh, Karan Kapoor, and Emad Tajkhorshid.
FEBS Letters, 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.
|
| 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) |
| |
| 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, 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) |
| |
| 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) |
| 203. 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.
(PMC: PMC6265297) |
| 202. 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.
(PMC: PMC6262108) |
| 201. 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.
(PMC: PMC6311388) |
| 200. 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.
(PMC: PMC6175955) |
| 199. 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.
(PMC: PMC6394829) |
| 198. 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.
(PMC: PMC6124899) |
| 197. 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.
(PMC: PMC6130951) |
| 196. Molecular insight into drug exporters within the cellular membrane.
Emad Tajkhorshid.
Pharmacological Research, 133:328, 2018.
|
| 195. 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.
(PMC: PMC6221948) |
| 194. 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.
(PMC: PMC6290684) |
| 193. 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.
(PMC: PMC6094130) |
| 192. 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.
(PMC: PMC6078787) |
| 191. Inchworm movement of two rings switching onto a thread by biased
Brownian diffusion represent a three-body problem.
Christopher R. Benson, Christopher Maffeo, Elisabeth M. Fatila, Yun Liu,
Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, and Amar H. Flood.
Proceedings of the National Academy of Sciences, USA,
115:9391-9396, 2018.
(PMC: PMC6156619) |
| 190. 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.
(PMC: PMC5993042) |
| 189. Structural underpinnings of oestrogen receptor mutations in endocrine
therapy resistance.
John A. Katzenellenbogen, Christopher G. Mayne, Benita S. Katzenellenbogen,
Geoffrey L. Greene, and Sarat Chandarlapaty.
Nature Reviews Cancer, 18:377-388, 2018.
(PMC: PMC6252060) |
| 188. 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.
(PMC: PMC5936630) |
| 187. 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.
(PMC: PMC6004266) |
| 186. In situ structure of neuronal C9orf72 poly-GA
aggregates reveals proteasome recruitment.
Qiang Guo, Carina Lehmer, Antonio Martínez-Sánchez, Till Rudack,
Florian Beck, Hannelore Hartmann, Manuela Pérez-Berlanga,
Frédéric Frottin, Mark S. Hipp, F. Ulrich Hartl, Dieter Edbauer,
Wolfgang Baumeister, and Rubén Fernández-Busnadiego.
Cell, 172:696-705, 2018.
(PMC: PMC6035389) |
| 185. Effects of cytosine modifications on DNA flexibility and nucleosome
mechanical stability.
Thuy TM Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei
Aksimentiev, and Taekjip Ha.
Nature Communications, 7:10813, 2016.
(PMC: PMC4770088) |
| 184. Simulating biological processes: Stochastic physics from whole cells
to colonies.
Tyler Earnest, John Cole, and Zaida Luthey-Schulten.
Reports on Progress in Physics, 81:052601, 2018.
|
| 183. Population FBA predicts metabolic phenotypes in yeast.
Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, and Zaida Luthey-Schulten.
PLoS Computational Biology, 13:e1005728, 2017.
(PMC: PMC5626512) |
| 182. Nanoscale ion pump derived from a biological water channel.
Karl Decker, Martin Page, and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:7899-7906, 2017.
(PMC: PMC5570624) |
| 181. 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.
(PMC: PMC5909925) |
| 180. 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.
(PMC: PMC5800941) |
| 179. 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.
(PMC: PMC5743546) |
| 178. CryoEM structure refinement by integrating NMR chemical shifts
with molecular dynamics simulations.
Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L.
Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang.
Journal of Physical Chemistry B, 121:3853-3863, 2017.
(PMC: PMC5459578) |
| 177. Parametric studies of metabolic cooperativity in escherichia coli
colonies: Strain and geometric confinement effects.
Joseph R. Peterson, John A. Cole, and Zaida Luthey-Schulten.
PLoS One, 12:e0182570, 2017.
(PMC: PMC5562313) |
| 176. Careful accounting of extrinsic noise in protein expression reveals
correlations among its sources.
John A. Cole and Zaida Luthey-Schulten.
Physical Review E, 95:062418, 2017.
(PMC: PMC5669626) |
| 175. Porphyrin-assisted docking of a thermophage portal protein into lipid
bilayers: Nanopore engineering and characterization.
Benjamin Cressiot, Sandra J. Greive, Wei Si, Tomas C. Pascoa, Mehrnaz
Mojtabavi, Maria Chechik, Huw T. Jenkins, Xueguang Lu, Ke Zhang, Aleksei
Aksimentiev, Alfred A. Antson, and Meni Wanunu.
ACS Nano, 11:11931-11945, 2017.
(PMC: PMC5963890) |
| 174. Quantification of membrane protein-detergent complex interactions.
Aaron J. Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack F.
Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei
Aksimentiev, and Liviu Movileanu.
Journal of Physical Chemistry B, 121:10228-10241, 2017.
(PMC: PMC5680101) |
| 173. 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.
(PMC: PMC5539350) |
| 172. Determination of cell doubling times from the return-on-investment
time of photosynthetic vesicles based on atomic detail structural models.
Andrew Hitchcock, C. Neil Hunter, and Melih Sener.
Journal of Physical Chemistry B, 121:3787-3797, 2017.
|
| 171. 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.
(PMC: PMC5558440) |
| 170. 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.
(PMC: PMC4877275) |
| 169. Ribosome biogenesis in replicating cells: integration of experiment
and theory.
Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock,
Thomas E. Kuhlman, and Zaida Luthey-Schulten.
Biopolymers, 105:735-751, 2016.
(PMC: PMC4958520) |
