| Year |
Citation |
Score |
| 2025 |
Bondar AN, Smith JC. Bacteriorhodopsin proton-pumping mechanism: successes and challenges in computational approaches. Biophysical Journal. PMID 40186354 DOI: 10.1016/j.bpj.2025.03.035 |
0.351 |
|
| 2025 |
Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP. Structural insights into light-gating of potassium-selective channelrhodopsin. Nature Communications. 16: 1283. PMID 39900567 DOI: 10.1038/s41467-025-56491-9 |
0.583 |
|
| 2024 |
Pinto M, Saliminasab M, Harris A, Lazaratos M, Bondar AN, Ladizhansky V, Brown LS. The retinal chromophore environment in an inward light-driven proton pump studied by solid-state NMR and hydrogen-bond network analysis. Physical Chemistry Chemical Physics : Pccp. 26: 24090-24108. PMID 39248601 DOI: 10.1039/d4cp02611j |
0.366 |
|
| 2024 |
Sun L, Hristova K, Bondar AN, Wimley WC. Structural Determinants of Peptide Nanopore Formation. Acs Nano. 18: 15831-15844. PMID 38844421 DOI: 10.1021/acsnano.4c02824 |
0.646 |
|
| 2023 |
Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Computational and Structural Biotechnology Journal. 21: 4370-4384. PMID 37711190 DOI: 10.1016/j.csbj.2023.08.034 |
0.301 |
|
| 2023 |
Saliminasab M, Yamazaki Y, Palmateer A, Harris A, Schubert L, Langner P, Heberle J, Bondar AN, Brown LS. A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins. The Journal of Physical Chemistry. B. 127: 7872-7886. PMID 37694950 DOI: 10.1021/acs.jpcb.3c04032 |
0.347 |
|
| 2023 |
Bertalan É, Bondar AN. Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins. Frontiers in Chemistry. 10: 1075648. PMID 36712989 DOI: 10.3389/fchem.2022.1075648 |
0.333 |
|
| 2022 |
Bondar AN. Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster. Biochimica Et Biophysica Acta. Biomembranes. 184052. PMID 36116514 DOI: 10.1016/j.bbamem.2022.184052 |
0.324 |
|
| 2022 |
Bondar AN. Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics. The Journal of Physical Chemistry. B. 126: 3973-3984. PMID 35639610 DOI: 10.1021/acs.jpcb.2c00200 |
0.308 |
|
| 2022 |
Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. Biochimica Et Biophysica Acta. Biomembranes. 1864: 183896. PMID 35217000 DOI: 10.1016/j.bbamem.2022.183896 |
0.305 |
|
| 2022 |
Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. Advances in Protein Chemistry and Structural Biology. 128: 199-239. PMID 35034719 DOI: 10.1016/bs.apcsb.2021.09.002 |
0.361 |
|
| 2021 |
Bondar AN. Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S. Frontiers in Chemistry. 9: 685761. PMID 34136464 DOI: 10.3389/fchem.2021.685761 |
0.343 |
|
| 2021 |
Kim SY, Bondar AN, Wimley WC, Hristova K. pH-triggered pore-forming peptides with strong composition-dependent membrane selectivity. Biophysical Journal. PMID 33460594 DOI: 10.1016/j.bpj.2021.01.010 |
0.605 |
|
| 2020 |
Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin V, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, et al. Frontiers in Multiscale Modelling of Photoreceptor Proteins. Photochemistry and Photobiology. PMID 33369749 DOI: 10.1111/php.13372 |
0.686 |
|
| 2020 |
Lazaratos M, Karathanou K, Bondar AN. Graphs of dynamic H-bond networks: from model proteins to protein complexes in cell signaling. Current Opinion in Structural Biology. 64: 79-87. PMID 32683247 DOI: 10.1016/j.sbi.2020.06.006 |
0.368 |
|
| 2020 |
Harris A, Lazaratos M, Siemers M, Watt E, Hoang A, Tomida S, Schubert L, Saita M, Heberle J, Furutani Y, Kandori H, Bondar AN, Brown LS. Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. The Journal of Physical Chemistry. B. PMID 32436389 DOI: 10.1021/Acs.Jpcb.0C02767 |
0.316 |
|
| 2019 |
Kemmler L, Ibrahim M, Dobbek H, Zouni A, Bondar AN. Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II. Physical Chemistry Chemical Physics : Pccp. 21: 25449-25466. PMID 31713551 DOI: 10.1039/c9cp03926k |
0.34 |
|
| 2019 |
Siemers M, Lazaratos M, Karathanou K, Guerra F, Brown LS, Bondar AN. Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins. Journal of Chemical Theory and Computation. PMID 31652399 DOI: 10.1021/acs.jctc.9b00697 |
0.342 |
|
| 2019 |
Karathanou K, Bondar AN. Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor. Journal of Chemical Information and Modeling. 59: 1882-1896. PMID 31038944 DOI: 10.1021/acs.jcim.8b00979 |
0.309 |
|
| 2019 |
Bondar AN, Lemieux MJ. Reactions at Biomembrane Interfaces. Chemical Reviews. 119: 6162-6183. PMID 31021080 DOI: 10.1021/acs.chemrev.8b00596 |
0.313 |
|
| 2019 |
Karathanou K, Bondar AN. Dynamic hydrogen-bond networks in bacterial protein secretion. Fems Microbiology Letters. 365. PMID 29905789 DOI: 10.1093/femsle/fny124 |
0.32 |
|
| 2018 |
Adam S, Bondar AN. Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin. Plos One. 13: e0201298. PMID 30086158 DOI: 10.1371/journal.pone.0201298 |
0.735 |
|
| 2018 |
Guerra F, Siemers M, Mielack C, Bondar AN. Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II. The Journal of Physical Chemistry. B. 122: 4625-4641. PMID 29589763 DOI: 10.1021/acs.jpcb.8b00649 |
0.33 |
|
| 2018 |
Karathanou K, Bondar AN. Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol. The Journal of Membrane Biology. 251: 461-473. PMID 29523937 DOI: 10.1007/s00232-018-0023-1 |
0.323 |
|
| 2018 |
Elghobashi-Meinhardt N, Phatak P, Bondar AN, Elstner M, Smith JC. Catalysis of Ground State cis[Formula: see text] trans Isomerization of Bacteriorhodopsin's Retinal Chromophore by a Hydrogen-Bond Network. The Journal of Membrane Biology. PMID 29516110 DOI: 10.1007/S00232-018-0027-X |
0.33 |
|
| 2017 |
Adam S, Knapp-Mohammady M, Yi J, Bondar AN. Revised CHARMM force field parameters for iron-containing cofactors of photosystem II. Journal of Computational Chemistry. PMID 28850168 DOI: 10.1002/jcc.24918 |
0.694 |
|
| 2017 |
Bondar AN, Smith JC. Protonation-state Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. Photochemistry and Photobiology. PMID 28477350 DOI: 10.1111/Php.12790 |
0.402 |
|
| 2016 |
Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, ... ... Bondar AN, et al. A three-dimensional movie of structural changes in bacteriorhodopsin. Science (New York, N.Y.). 354: 1552-1557. PMID 28008064 DOI: 10.1126/Science.Aah3497 |
0.328 |
|
| 2016 |
Bondar AN. Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics. Seminars in Cell & Developmental Biology. PMID 27641824 DOI: 10.1016/j.semcdb.2016.09.006 |
0.317 |
|
| 2015 |
Capponi S, Heyden M, Bondar AN, Tobias DJ, White SH. Anomalous behavior of water inside the SecY translocon. Proceedings of the National Academy of Sciences of the United States of America. 112: 9016-21. PMID 26139523 DOI: 10.1073/Pnas.1424483112 |
0.531 |
|
| 2015 |
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, ... ... Bondar AN, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology. 248: 611-40. PMID 26063070 DOI: 10.1007/S00232-015-9802-0 |
0.313 |
|
| 2015 |
Guerra F, Adam S, Bondar AN. Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. Journal of Molecular Graphics & Modelling. 58: 30-9. PMID 25829096 DOI: 10.1016/j.jmgm.2015.03.001 |
0.705 |
|
| 2015 |
Guerra F, Bondar AN. Dynamics of the Plasma Membrane Proton Pump Journal of Membrane Biology. 248: 443-453. PMID 25274016 DOI: 10.1007/s00232-014-9732-2 |
0.376 |
|
| 2015 |
Wolter T, Elstner M, Fischer S, Smith JC, Bondar AN. Mechanism by which untwisting of retinal leads to productive bacteriorhodopsin photocycle states. The Journal of Physical Chemistry. B. 119: 2229-40. PMID 25196390 DOI: 10.1021/Jp505818R |
0.523 |
|
| 2014 |
Jardón-Valadez E, Bondar AN, Tobias DJ. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin. Biochimica Et Biophysica Acta. 1837: 1964-72. PMID 25256652 DOI: 10.1016/J.Bbabio.2014.09.006 |
0.306 |
|
| 2014 |
del Val C, Bondar L, Bondar AN. Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter. Journal of Structural Biology. 186: 95-111. PMID 24576681 DOI: 10.1016/j.jsb.2014.02.010 |
0.356 |
|
| 2013 |
Del Val C, Royuela-Flor J, Milenkovic S, Bondar AN. Channelrhodopsins: a bioinformatics perspective. Biochimica Et Biophysica Acta. 1837: 643-55. PMID 24252597 DOI: 10.1016/j.bbabio.2013.11.005 |
0.35 |
|
| 2012 |
Andersson M, Bondar AN, Freites JA, Tobias DJ, Kaback HR, White SH. Proton-coupled dynamics in lactose permease. Structure (London, England : 1993). 20: 1893-904. PMID 23000385 DOI: 10.1016/J.Str.2012.08.021 |
0.509 |
|
| 2012 |
Del Val C, White SH, Bondar AN. Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics. The Journal of Membrane Biology. 245: 717-30. PMID 22836667 DOI: 10.1007/S00232-012-9452-4 |
0.574 |
|
| 2012 |
Bondar AN, Dau H. Extended protein/water H-bond networks in photosynthetic water oxidation. Biochimica Et Biophysica Acta. 1817: 1177-90. PMID 22503827 DOI: 10.1016/j.bbabio.2012.03.031 |
0.33 |
|
| 2012 |
Bondar AN, White SH. Hydrogen bond dynamics in membrane protein function. Biochimica Et Biophysica Acta. 1818: 942-50. PMID 22178866 DOI: 10.1016/J.Bbamem.2011.11.035 |
0.568 |
|
| 2011 |
Bondar AN, Fischer S, Smith JC. Water pathways in the bacteriorhodopsin proton pump. The Journal of Membrane Biology. 239: 73-84. PMID 21113780 DOI: 10.1007/S00232-010-9329-3 |
0.548 |
|
| 2010 |
Jardón-Valadez E, Bondar AN, Tobias DJ. Coupling of retinal, protein, and water dynamics in squid rhodopsin. Biophysical Journal. 99: 2200-7. PMID 20923654 DOI: 10.1016/J.Bpj.2010.06.067 |
0.351 |
|
| 2010 |
Bondar AN, del Val C, Freites JA, Tobias DJ, White SH. Dynamics of SecY translocons with translocation-defective mutations. Structure (London, England : 1993). 18: 847-57. PMID 20637421 DOI: 10.1016/J.Str.2010.04.010 |
0.517 |
|
| 2009 |
Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith JC, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. Journal of the American Chemical Society. 131: 7064-78. PMID 19405533 DOI: 10.1021/Ja809767V |
0.376 |
|
| 2009 |
Jardón-Valadez E, Bondar AN, Tobias DJ. Dynamics of the internal water molecules in squid rhodopsin. Biophysical Journal. 96: 2572-6. PMID 19348742 DOI: 10.1016/J.Bpj.2008.12.3927 |
0.353 |
|
| 2009 |
Bondar AN, del Val C, White SH. Rhomboid protease dynamics and lipid interactions. Structure (London, England : 1993). 17: 395-405. PMID 19278654 DOI: 10.1016/J.Str.2008.12.017 |
0.534 |
|
| 2008 |
Bondar AN, Baudry J, Suhai S, Fischer S, Smith JC. Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions. The Journal of Physical Chemistry. B. 112: 14729-41. PMID 18973373 DOI: 10.1021/Jp801916F |
0.563 |
|
| 2006 |
Bondar AN, Suhai S, Fischer S, Smith JC, Elstner M. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. Journal of Structural Biology. 157: 454-69. PMID 17189704 DOI: 10.1016/J.Jsb.2006.10.007 |
0.574 |
|
| 2006 |
Bondar AN, Smith JC, Fischer S. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 5: 547-52. PMID 16761083 DOI: 10.1039/B516451F |
0.539 |
|
| 2005 |
Bondar AN, Fischer S, Suhai S, Smith JC. Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps. The Journal of Physical Chemistry. B. 109: 14786-8. PMID 16852870 DOI: 10.1021/Jp0531255 |
0.52 |
|
| 2005 |
Gruia AD, Bondar AN, Smith JC, Fischer S. Mechanism of a molecular valve in the halorhodopsin chloride pump. Structure (London, England : 1993). 13: 617-27. PMID 15837200 DOI: 10.1016/J.Str.2005.01.021 |
0.519 |
|
| 2005 |
Bondar AN, Elstner M, Suhai S, Smith JC, Fischer S. Mechanism of primary proton transfer in bacteriorhodopsin. Structure (London, England : 1993). 12: 1281-8. PMID 15242604 DOI: 10.1016/J.Str.2004.04.016 |
0.515 |
|
| 2004 |
Bondar AN, Fischer S, Smith JC, Elstner M, Suhai S. Key role of electrostatic interactions in bacteriorhodopsin proton transfer. Journal of the American Chemical Society. 126: 14668-77. PMID 15521787 DOI: 10.1021/Ja047982I |
0.567 |
|
| 2004 |
Smith JC, Merzel F, Bondar AN, Tournier A, Fischer S, Kornyshev A, Daniel RM, Halle B, Wilson K. Structure, dynamics and reactions of protein hydration water Philosophical Transactions of the Royal Society B: Biological Sciences. 359: 1181-1190. PMID 15306375 DOI: 10.1098/Rstb.2004.1497 |
0.541 |
|
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