TCB Publications - Search
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, 2018. In Press.
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, 2018. In Press.
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, 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, 2018. In Press.
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 a-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 g-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, pp. 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. (19 pages).
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, November 2014.
10103. Conformational heterogeneity of a-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-kB. 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.
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 w 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.