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Faculty Publications

BCMB Faculty published more than 70 papers in academic year 2019-2020.

  1. Agarwal R, Shrestha UR, Chu X-Q, Petridis L, Smith JC. (2020) Mesophilic enzyme function at high temperature: molecular dynamics of hyperthermophilic and mesophilic pyrophosphatases. Biophysical Journal 119 (1): 142-150.
  2. Agarwal R., Smith JC, Smith MD. (2020) Capturing deuteration effects in classical molecular dynamics simulations: The case of fully deuterated tetrahydrofuran. Journal of Chemical Theory and Computation. 16 (4): 2529-2540.
  3. Ancín M, Larraya L, Fernández-San Millán A, Veramendi J, Burch-Smith T, Farran I. (2019) NTRC and Thioredoxin f Overexpression Differentially Induces Starch Accumulation in Tobacco Leaves. Plants (Basel). 8(12):543. doi: 10.3390/plants8120543.
  4. Aranh MP, Spooner C, Demerdash ON, Czejdo B, Smith JC, Mitchell J. (2020) Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets. Biochimica et Biophysica Acta – General Subjects. 1864 (4): 129535.
  5. Bañó-Polo M, Martínez-Gil L, Barrera FN, Mingarro I. (2020) Insertion of Bacteriorhodopsin Helix C Variants into Biological Membranes. ACS Omega. 5(1):556-560. doi: 10.1021/acsomega.9b03126.
  6. Binder BM. (2020) Ethylene signaling in plants. Journal of Biological Chemistry 295: 7710-7725. doi: 10.1074/jbc.REV120.010854.
  7. Brady N, Qian S, Bruce BD. (2019) Analysis of Styrene Maleic Acid Alternating Copolymer Supramolecular Assemblies in Solution by Small Angle X-Ray Scattering. Eur. Polymer J. 111: 178-184. doi: 10.1016/j.eurpolymj.2018.11.034.
  8. Brady NG, Li M, Ma Y, Gumbart JC, Bruce BD. (2019) Non-detergent Isolation of a Cyanobacterial Photosystem I using Styrene Maleic Acid Alternating Copolymers. RSC: Advances, 9(54): 31781-31796. doi: 10.1039/c9ra04619d.
  9. Carlew TS, Allen CJ, Binder BM. (2019) Ethylene Receptors in Nonplant Species. Small Methods doi: 10:1002/smtd.201900266.
  10. Chen T, Wagner AS, Tams RN, Eyer JE, Kauffman SJ, Gann ER, Fernandez EJ, Reynolds TB. (2019) Lrg1 Regulates β (1,3)-Glucan Masking in Candida albicans through the Cek1 MAP Kinase Pathway. mBio 10(5): e01767-19. doi: 10.1128/mBio.01767-19.
  11. Chen Y, Almasaud RA, Carrie E, Desbrosses G, Binder BM, Chervin C. (2020) Ethanol, at physiological concentrations, affects ethylene sensing in tomato germinating seeds and seedlings. Plant Science 291: 110368 doi: 10.1016/j.plantsci.2019.110368.
  12. Chen Y, Hu G, Rodriguez C, Liu M, Binder BM, Chervin C. (2020) Characterization SlETR7, a new tomato ethylene receptor. Horticultural Research 7: 17. doi: 10.1038/s41438-020-0239-y.
  13. Chen Y, Rofidal V, Hem S, Gil J, Nosarzewska J, Berger N, Demolombe V, Bouzayen M, Azhar BJ, Shakeel SN, Schaller GE, Binder BM, Santoni V, Chervin C. (2019) Targeted proteomics allow quantification of ethylene receptors and reveal SlETR3 accumulation in Never-Ripe tomatoes. Frontiers in Plant Science 10: doi: 10.3389/fpls.2019.01054
  14. Cherepanov DA, Brady NG, Shelaev IV, Nguyen J, Gostev FE, Mamedov MD, Nadtochenko VA, Bruce BD. (2020) PSI-SMALP, A Detergent-free Form of Cyanobacteial Photosystem I Reveals Faster Femtosecond Photochemistry. Biophysical Journal, 118: 337-351. doi: 10.1016/j.bpj.2019.11.3391).
  15. Close DM, Cooper SJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener (2019) Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Molecular Microbiology. 112 (6): 1784-1797.
  16. Das P, Golloshi R, McCord RP, Shen T. (2020). Using contact statistics to characterize structure transformation of biopolymer ensembles. Physical review. E 101(1-1):, 012419. doi: 10.1103/PhysRevE.101.012419
  17. Ganusova EE, Reagan BC, Fernandez JC, Azim MF, Sankoh AF, Freeman KM, McCray TN, Patterson K, Kim C, Burch-Smith TM. (2020) Chloroplast-to-nucleus retrograde signalling controls intercellular trafficking via plasmodesmata formation. Philos Trans R Soc Lond B Biol Sci. 375(1801):20190408. doi: 10.1098/rstb.2019.0408.
  18. Gisriel G, Coe J, Romain Letrun R, Luna-Chavez C, Stander NE, Lisova S, Yefanov ON, Mariani V, Kuhn M, Grant TD, Dörner K, Sato T, Echelmeier A, Villarreal JC, Hunter MS, Wiedorn MO, Knoska J, Mazalova V, Roy-Chowdhury S, Yang J-H, Jones A, Bean R, Bielecki J, Kim Y, Mills G, Weinhausen B, Meza JD, Al-Qudami N, Bajt S, Brehm G, Botha S, Boukelef D, Brockhauser S, Bruce BD, Coleman MA, Danilevski C, Discianno E, Dobson Z, Fangohr H, Martin-Garcia YM, Gevorkov Y, Hauf S, Giewekemeyer K, Hosseinizadeh A, Januschek F, Ketawala GK, Kupitz C, Maia L, Manetti M, Messerschmidt M, Michelat T, Mondal J, Oberthür, D, Ourmazd A, Previtali G, Sarrou I, Schön S, Schwander P, Shelby ML, Sikorski M, Silenzi A, Sztuk-Dambietz J, Szuba J, Turcato M, White TA, Wrona K, Xu C, Abdellatif MH, Zook JD, Spence J, Chapman H, Barty A, Kirian K, Frank M, Ros A, Schmidt M, Fromme R, Mancuso A, Fromme P, Zatsepin N. (2019) Membrane Protein Megahertz Crystallography at the European XFEL. Nature Communications, 10(1): 1-11. doi: 10.1038/s41467-019-12955-3.
  19. Green AT, Moniruzzaman M, Cooper CJ, Walker JK, Smith JC, Parks JM, Zgurskay ZI. (2020) Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold. BBA Gen Subjects. 1864 (6): 129546.
  20. Guo L, Painter SL, Brooks SC, Parks JM, Smith JC. (2019) A probabilistic perspective on thermodynamic parameter uncertainties: Understanding aqueous speciation of mercury. Geochimica et Cosmochimica Acta. 263: 108-121.
  21. Hazel A, Abdalin N, Leus I, Parks JM, Smith JC, Zgurskaya J, Gumbart JC. (2019) Conformational dynamics of AcrA govern multidrug efflux pump assembly. ACS Infectious Diseases. 5 (11): 1926-1935.
  22. Hercyk B, Das M. (2019) Rho Family GTPases in Fission Yeast Cytokinesis. Commun Integr Biol. 12(1):171-180. doi: 10.1080/19420889.2019.1678453.
  23. Hercyk BS, Das ME. (2019) F-BAR Cdc15 Promotes Cdc42 Activation During Cytokinesis and Cell Polarization in Schizosaccharomyces pombe. Genetics. 213(4): 1341-1356. doi: 10.1534/genetics.119.302649.
  24. Hercyk BS, Onwubiko UN, Das ME. (2019) Coordinating septum formation and the actomyosin ring during cytokinesis in Schizosaccharomyces pombe. Mol Microbiol. 112(6): 1645-1657. doi: 10.1111/mmi.14387.
  25. Hercyk BS, Rich-Robinson J, Mitoubsi AS, Harrell MA, Das ME. (2019) A novel interplay between GEFs orchestrates Cdc42 activity during cell polarity and cytokinesis in fission yeast. J Cell Sci. 132(23):jcs236018. doi: 10.1242/jcs.236018.
  26. Hu X, Smith MD, Humphreys BM, Green AT, Parks JM, Baudry JY, Smith JC. (2019) Ligand-Dependent Sodium Ion Dynamics Within the A2A-Adenosine Receptor: A Molecular Dynamics Study. Journal of Physical Chemistry B, 123 (38): 7947-7954.
  27. Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. (2019) A minimal membrane metal transport system: dynamics and energetics of Mer proteins. Journal of Computational Chemistry. 41 (6): 528-537.
  28. Kathare PK, Dharmasiri S, Vincill ED, Routray P, Ahmad I, Roberts DM, Dharmasiri N. (2020) Arabidopsis PIC30 encodes a major facilitator superfamily transporter responsible for the uptake of picolinate herbicides. Plant J. 102(1):18-33. doi:10.1111/tpj.14608.
  29. Korotych O, Mondal J, Gattas-Asfura K, Hendricks J, Bruce BD. (2019) Evaluation of commercially available styrene-co-maleic acid polymers in extraction of membrane proteins from chloroplast thylakoids. Eur. Polymer J. 114: 485-500. doi: 10.1016/j.eurpolymj.2018.10.035.
  30. Lamichhane R, Liu JJ, White KL, Katritch V, Stevens RC, Wüthrich K, Millar DP. (2020) Biased Signaling of the G-Protein-Coupled Receptor β2AR Is Governed by Conformational Exchange Kinetics. Structure. 28(3):371-377.e3. doi: 10.1016/j.str.2020.01.001.
  31. Lau BYB, Layo DE, Emery B, Everett M, Kumar A, Stevenson P, Reynolds KG, Cherosky A, Bowyer S-A H, Roth S, Fisher DG, McCord RP, Krishnan K.(2020) Lateralized Expression of Cortical Perineuronal Nets during Maternal Experience is Dependent on MECP2. eNeuro. 7(3):ENEURO.0500-19.2020. doi:10.1523/ENEURO.0500-19.2020
  32. Li, M, Calteau A, Semchonok DA, Witt TA, Nguyen J, Sassoon N, Boekema EJ, Whitelegge J, Gugger M, Bruce BD. (2019) Tetrameric Photosystem I in Cyanobacteria: Implications in Physiology and Evolution. Nature Plants 5:1309-1319. doi: 10.1038/s41477-019-0566-x.
  33. Lian P, Guo L, Devarajan D, Parks JM, Painter SL, Brooks SC, Smith JC. (2019) The AQUA-MER Databases and Aqueous Speciation Server: A Web Resource for Multiscale Modeling of Mercury Speciation. Journal of Computational Chemistry. 41(2): 147-155.
  34. Lim GH, Liu H, Yu K, Liu R, Shine MB, Fernandez J, Burch-Smith T, Mobley JK, McLetchie N, Kachroo A, Kachroo P. (2020) The plant cuticle regulates apoplastic transport of salicylic acid during systemic acquired resistance. Sci Adv. 6(19):eaaz0478. doi: 10.1126/sciadv.aaz0478. eCollection.
  35. Lokdarshi A, Guan J, Urquidi Camacho RA, Cho SK, Morgan P, Leonard M, Shimono M, Day B, von Arnim AG. (2020) Light activates the translational regulatory GCN2 kinase via reactive oxygen species emanating from the chloroplast. Plant Cell 32:1161-1178. doi: 10.1105/tpc.19.00751.
  36. Lokdarshi A, Morgan PW, Franks M, Emert Z, Emanuel C, von Arnim AG. (2020). Light dependent activation of the GCN2 kinase under cold and salt stress is mediated by the photosynthetic status of the chloroplast. Frontiers in Plant Science 11:431. doi: 10.3389/fpls.2020.00431.
  37. Lokdarshi A, Papdi C, Pettkó-Szandtner A, Dorokhov S, Scheres B, Magyar Z, von Arnim, AG, Bogre L, Horvath BM. (2019) The ErbB-3 BINDING PROTEIN 1, EBP1 Regulates the Capacity for Protein Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem. Plant Physiology 182:919-932. doi:10.1104/pp.19.00805.
  38. McCord RP, Kaplan N, Giorgetti L. (2020) Chromosome Conformation Capture and Beyond: Toward an Integrative view of Chromosome Structure and Function. Molecular Cell 77: 688-708. doi: 10.1016/j.molcel.2019.12.021.
  39. McCord RP, Prosser R. Potential Gene Therapy to Combat Cocaine Addiction. The Conversation. January 2020.
  40. Mostofian B, Johnson Q, Smith JC, Cheng X. (2020) Carotenoids Promote Lateral Packing and Condensation of Lipid Membranes. Physical Chemistry Chemical Physics. 22: 12281-12293.
  41. Nair S, Bahn J, Lee G, Yoo S, Park JH. (2020) A homeobox transcription factor Scarecrow (SCRO) negatively regulates Pdf neuropeptide expression through binding to an identified cis-acting element in Drosophila melanogaster. Mol. Neurobiol. 57: 2115-2130. doi: 10.1007/s12035-020-01874-w.
  42. Nebenführ A. (2020) Tracking organelle movements in plant cells. Methods in Cell Biology. In press. doi: 10.1016/bs.mcb.2020.03.003.
  43. Nguyen VP, Dixson AC, Barrera FN. (2019) The Effect of Phosphatidylserine on a pH-Responsive Peptide Is Defined by Its Noninserting End. Biophys J. 117(4):659-667. doi: 10.1016/j.bpj.2019.07.023.
  44. Niyikiza D, Piya S, Routray P, Miao L, Kim WS, Burch-Smith T, Gill T, Sams C, Arelli PR, Pantalone V, Krishnan HB, Hewezi T. (2020) Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. Plant Journal. in press. doi: 10.1111/tpj.14861.
  45. O’Banion B, O’Neal L, Alexandre G, and Lebeis S. (2019) Bridging the gap between single-strain and community-level plant-microbe chemical interactions. Mol. Plant-Microbe Interact. 33: 124-134. doi: 10.1094/mpmi-04-19-0115-cr.
  46. O’Neal L, Gullett J, Aksenova A, Hubler A, Briegel A, Ortega D, Kjaer A, Jensen G, Alexandre G. (2019) Distinct chemotaxis protein paralogs assemble into chemoreceptor signaling arrays to coordinate signaling output. mBio 10:e01757-19, doi: 0.1128/mBio.01757-19.
  47. O’Neal L, Vo L, Alexandre G. (2020) Specific root exudates compounds sensed by dedicated chemoreceptors shape A. brasilense chemotaxis in the rhizosphere. Appl. Environ. Microbiol. doi: 10.1128/AEM.01026-20. In press
  48. Onwubiko UN, Rich-Robinson J, Mustaf RA, Das ME. (2020) Cdc42 promotes Bgs1 recruitment for septum synthesis and glucanase localization for cell separation during cytokinesis in fission yeast. Small GTPases. 22: 1-8. doi: 10.1080/21541248.2020.1743926.
  49. Ossyra JR, Sedova A, Baker, MB, Smith JC. (2019) Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions. Lecture Notes in Computer Science High Performance Computing.ISC Proceedings 2019: 514–527.
  50. Ossyra JR, Sedova A, Tharrington A, Noé F, Clementi, C, Smith, JC. (2019) Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer. Lecture Notes in Computer Science High Performance Computing.ISC Proceedings 2019: 397–417.
  51. Palanikumar L, Al-Hosani S, Kalmouni M, Nguyen VP, Ali L, Pasricha R, Barrera FN, Magzoub M. (2020) pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics. Commun Biol 3(1):95. doi: 10.1038/s42003-020-0817-4.
  52. Panchy N, Azeredo-Tseng C, Luo M, Randall N, Hong T. (2020) Integrative transcriptomic analysis reveals a multiphasic epithelial–mesenchymal spectrum in cancer and non-tumorigenic cells. Frontiers in Oncology 9:1479. doi: 10.3389/fonc.2019.01479.
  53. Parks JM, Smith JC. (2020) How to discover antiviral compounds quickly. New England Journal of Medicine. 382: 2261-226.
  54. Päslack C, Smith JC, Heyden M, Schaefer LV. (2019) Hydration-Mediated Stiffening of Collective Membrane Dynamics by Cholesterol. Physical Chemistry Chemical Physics. 21(20): 10370-10376.
  55. Pattarawat P, Hong T, Wallace S, Hu Y, Donnell R, Wang TH, Tsai CL, Wang J, Wang HC. (2020) Compensatory combination of romidepsin with gemcitabine and cisplatin to effectively and safely control urothelial carcinoma. British Journal of Cancer. 11:1-4. doi: 10.1038/s41416-020-0877-8.
  56. Pham B, Arons AB, Vincent JG, Fernandez EJ, Shen T. (2019) Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions. J Chem Inf Model. 59(12):5174-5182. doi:10.1021/acs.jcim.9b00695.
  57. Phan M, Korotych O, Brady NG, Davis M, Akner J, Bruce BD. (2020) X-ray and neutron reflectivity studies of styrene-maleic acid copolymer interactions with galactolipid-containing monolayers. Langmuir 36: 3970-3980. doi: 10.1021/acs.langmuir.9b03817.
  58. Pingali SV, Smith MD, Liu S-H, Rawal TB, Pu Y, Shah R, Evans B, Urban V, Davidson BH, Cai CM, Ragauskas AJ, O’Neill HM, Smith JC, Petridis L. (2020) Deconstruction of biomass enabled by local de-mixing of cosolvents at cellulose and lignin surfaces. Proceedings of the National Academy of Sciences 117: 16776-16781.
  59. Piya S, Liu J, Burch-Smith T, Baum TJ, Hewezi T. (2020) A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism. J Exp Bot. 71(4):1402-1417. doi: 10.1093/jxb/erz502.
  60. Ponnusamy P, He Y, Hwang D-J, Thiyagarajan T, Houtman R, Bocharova V, Sumpter BG, Fernandez E, Johnson D, Du Z, Pfeffer LM, Getzenberg RH, McEwan IJ, Miller DD, Narayanan R. (2019) Orally Bioavailable Androgen Receptor Degrader, Potential Next-Generation Therapeutic for Enzalutamide-Resistant Prostate Cancer. Clin. Cancer Res. 25(22): 6764-6780. doi: 10.1158/1078-0432.CCR-19-1458.
  61. Reagan BC, Burch-Smith TM. (2020) Viruses Reveal the Secrets of Plasmodesmal Cell Biology. Mol Plant Microbe Interact. 33(1):26-39. doi: 10.1094/MPMI-07-19-0212-FI.
  62. Saleheen A, Campbell WM, Prosser RA, Baker C. (2020) Estimation of available epinephrine dose in expired and discolored autoinjectors via quantitative smartphone imaging. Anal Bioanal Chem 412:2785-2793. doi: 10.1007/s00216-020-02505-y.
  63. Shrestha UR, Junejab P, Zhangb Q, Gurumoorthy V. Borreguero JM, Urban V, Cheng X, Pingali SV, Smith JC, O’Neill HM, Petridis L. (2019) Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proceedings of the National Academy of Sciences (USA). 116 (41): 20446-20452.
  64. Smith JC. (2019) Foreword in Data Processing Handbook for Complex Biological Data Sources. Ed. Misra. Academic press p.11.
  65. Smith JC. (2020) Four countries for Science. Biochimica et Biophysica Acta – General Subjects. 1864: 4. doi: 10.1016/j.bbagen.2020.129518.
  66. Svoronos AA, Bahal R, Pereira MC, Barrera FN, Deacon JC, Bosenberg M, DiMaio D, Glazer PM, Engelman DM. (2020) Tumor-Targeted, Cytoplasmic Delivery of Large, Polar Molecules Using a pH-Low Insertion Peptide. Mol Pharm. 17(2):461-471. doi: 10.1021/acs.molpharmaceut.9b00883.
  67. Teodor AH, Bruce BD. (2020) Putting Photosystem I to Work: Strategies and Challenges to Make a Green Solar Cell. Trends in Biotechnology. doi: 10.1016/j.tibtech.2020.04.004 In press
  68. Urquidi Camacho RA, Lokdarshi A, von Arnim, AG. (2020). Translational Gene Regulation in Plants: A Green New Deal. WIRES RNA May 4:e1597. doi: 10.1002/wrna.1597.
  69. Voloshin R, Brady N, Atashova S, Rodionova M, Gabrielyan D, Kreslavski V, Zharmukhamedov S, Huseynova I, Shen JR, Bruce BD, Allakhverdiev S. (2019) Enhanced activity and stability of osmotically-stabilized thylakoids in a biohybrid solar cell. International Journal of Energy Research, 43(14): 8878-8889. doi: 10.1002/er.4866.
  70. Vural D, Smith JC, Petridis L. (2020) Polymer Principles Behind Solubilizing Lignin With Organic Cosolvents for Bioenergy. Green Chemistry 22: 4331-4340.
  71. Wang A, Burch-Smith TM, Li Y. (2020) Focus on Cell Biology of Virus-Plant and Virus-Vector Interactions. Mol Plant Microbe Interact. 33(1):5. doi: 10.1094/MPMI-11-19-0318-FI.
  72. Wang G, Lee G, Vuong R, Park JH. (2019) Two-factor specification of apoptosis: TGF-b signaling acts cooperatively with ecdysone signaling to induce cell- and stage-specific apoptosis of larval neurons during metamorphosis in Drosophila melanogaster. Apoptosis 24: 972-989. doi: 0.1007/s10495-019-01574-4.
  73. Wang J, Davis RE. (2020) Ascaris. Current Biology 30 R423-R425. doi: 10.1016/j.cub.2020.02.064.
  74. Wang J, Veronezi GMB, Kang Y, Zagoskin M, O’Toole ET, Davis RE. (2020) Comprehensive Chromosome End Remodeling During Programmed DNA Elimination. Current Biology 30: 1-17. doi: 10.1016/j.cub.2020.06.058.
  75. Westerfield JM, Barrera FN. (2019) Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem. 295(7):1792-1814. doi: 10.1074/jbc.REV119.009457.
  76. Yoo S, Nair S, Kim H-J, Kim Y, Lee C, Lee G, Park JH. (2020) Knock-in mutations of scarecrow, a Drosophila homolog of mammalian Nkx2.1 reveal a novel function required for development of the optic lone in Drosophila melanogaster. Dev. Biol. 461:145-159. doi: 10.1016/j.ydbio.2020.02.008.

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