Publications


2022


104. Searching for Blockers of Dengue and West Nile Virus Viroporins. Lahiri, H., and Arkin, I.T. Viruses 14:1750.


103. Targeting Viral Ion Channels: A Promising Strategy to Curb SARS-CoV-2. Singh, A., and Arkin, I.T. Pharmaceuticals 15:396.


102. Zika M—A Potential Viroporin: Mutational Study and Drug Repurposing. Tomar, P.P.S., Krugliak, M., Singh, A., and Arkin, I.T. biomedicines 10:646. Supporting information.


2021


101. Isotope-Edited Amide II Mode: A New Label for Site-Specific Vibrational Spectroscopy. Brielle, E.S., and Arkin, I.T. J Phys Chem Lett 13:6634. Supporting information.


100. Identification of SARS-CoV-2 E Channel Blockers From a Repurposed Drug Library. Tomar, P.P.S., Krugliak, M., and Arkin, I.T. Pharmaceuticals 14:604. Supporting information.


99. Blockers of the SARS-CoV-2 3a Channel Identified by Targeted Drug Repurposing. Tomar, P.P.S., Krugliak, M., and Arkin, I.T. Viruses 13:532


98. MutagenPred‐GCNNs: A Graph Convolutional Neural Network‐Based Classification Model for Mutagenicity Prediction with Data‐Driven Molecular Fingerprints. Li, S., Zhang, L., Feng, H., Meng, J., Xie, D., Yi, L., Arkin, I.T., Liu, H. Int Sci Comp Lif Sci 13:25-33.


97. Predicting 2021 the reproductive toxicity of chemicals using ensemble learning methods and molecular fingerprints. Feng, H., Zhang, L., Li, S., Liu, L., Yang, T., Yang, P., Zhao, J., Arkin, I.T., Liu, H. Toxicol Lett 340:4-14.


2020


96. Quantitative Analysis of Multiplex H-bonds. Brielle, E.S., and Arkin, I.T. J Amer Chem Soc. 142:14150-14157. Supporting information.


95. A Balance Between Side-chain and Backbone Driven Association in Folding of the α-Helical Influenza A Transmembrane Peptide - Folding MD Simulations and DFT Calculations. Stylianakis, I., Scheiner, S., Faza, O.N., Sigalas, M.P., Shalev, A., Arkin, I.T., Glykos, N. and Kolocouris, A. J Comp Chem. ‭41:2177‭–‬2188‬.


94. SARS-CoV-2 E Protein is a Potential Ion Channel That Can Be Inhibited by Gliclazide and Memantine. Tomar, P.P.S., and Arkin, I.T. Biochem Biophys Res Comm. 530:10-14.


2019


93. Potential Viroporin Candidates From Pathogenic Viruses Using Bacteria-Based Bioassays. Tomar, P.P.S., Oren, R., Krugliak, M., and Arkin, I.T. Viruses 11:632.


2018


92. A robust proton flux (pHlux) assay for studying function and inhibition of the Influenza A M2 proton channel. Santner, P., Silva Martins, J.M., Laursen, J.S., Behrendt, L., Riber, L., Olsen, C.A., Arkin, I.T., Winther, J.R., Willemoës, M., and Lindorff-Larsen, K. Biochem 57(41):5949-5956.


91. Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants. Santner, P., Silva Martins, J.M., Kampmeyer, C., Hartmann-Petersen, R., Laursen, J.S., Stein, A., Olsen, C.A., Arkin, I.T., Winther, J.R., Willemoës, M., and Lindorff-Larsen. K. Biochem 7(41):5957-5968.


90. Site-Specific Hydrogen Exchange in a Membrane Environment Analyzed by Infrared Spectroscopy. Brielle, E.S., and Arkin, I.T. J Phys Chem Lett 9:4059–4065. Supporting information.


2016


89. Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker. Assa, D., Alhadeff, R., Krugliak, M., and Arkin, I.T. J Mol Biol. 428:4209-4217


2015


88. Enzyme mediated encapsulation of gold nanoparticles by polyaniline nanoshell. Sfez, R., Natan, E., Bardavid, Y., Ikbal, M., Arbeli, E., Arkin, I.T., Popov, I, and Yitzchaik, S. Journal of Self-Assembly and Molecular Electronics 3:1-16.


87. Mechanistic studies of the apical sodium-dependent bile acid transporter. Alhadeff, R., Ganoth, A., and Arkin, I.T. Proteins 83:1107-17.


2014


86. Bacteria-based analysis of HIV-1 Vpu channel activity. Taube, R., Alhadeff, R., Assa, D., Krugliak, M., and Arkin, I.T. PLoS ONE 10:e105387.


85. Use of isotope-edited FTIR to derive a backbone structure of a transmembrane protein. Manor, J., Arbely, E., Beerlink, A., Akkawi, M., and Arkin, I.T. J Phys Chem Lett 5:2573−2579. Supplementary data.


84. Strength of a bifurcated H bond. Feldblum, E.S., and Arkin, I.T. Proc Nat Acad Sci 111:4085-90.


83. Computational and experimental analysis of drug binding to the Influenza M2 channel. Alhadeff, R., Assa, D., Astrahan, P., Krugliak, M., and Arkin, I.T. Biochim Biophys Acta Biomemb 1838:1068-73.


2013


82. Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins. Kirrbach, J., Krugliak, M., Ried, C.L., Pagel, P., Arkin, I.T., and Langosch, D. Bioinformatics 29:1623-30. Supplementary data.


81. Editorial Preface: FTIR in membrane proteins and peptide studies. Arkin, I.T. Biochim Biophys Acta 1828:2255.


80. Gaining insight into membrane protein structure using isotope-edited FTIR. Manor, J., and Arkin, I.T. Biochim Biophys Acta 1828:2256-64.


2012


79. Environment polarity in proteins mapped noninvasively by FTIR spectroscopy. Manor, J., Feldblum, E.S., Zanni, M.T., and Arkin, I.T. J Phys Chem Lett 3:939-944.


2011


78. Characterization of the Na+/H+ antiporter from Yersinia pestis. Ganoth, A., Alhadeff, R., Kohen, D., and Arkin, I.T. PLoS ONE 6:e26115 Supplementary figure S1.


77. Promiscuous binding in a selective protein: the bacterial Na+/H+ antiporter. Alhadeff, R., Ganoth, A., Krugliak, M., and Arkin, I.T. PLoS ONE 6:e25182 Supplementary figure S1, Supplementary figure S2, Supplementary figure S3.


76. Computational study of the Na+/H+ antiporter from Vibrio parahaemolyticus. Ganoth, A., Alhadeff, R., and Arkin, I.T. J Mol Mod 17:1877-90.


75. How do aminoadamantanes block the influenza M2 channel and how does resistance develop? Leonov, H., Astrahan, P., Krugliak, M., and Arkin, I.T. J Amer Chem Soc 133:9903-11. Supplementary information.


74. Science, music, literature and the one-hit wonder connection. Arkin, I.T. Research Trends 22:9-10.


73. Quantitative analysis of Influenza M2 channel blockers. Astrahan, P., Flitman-Tene, R., Bennett, E.R., Krugliak, M., Gilon, C., and Arkin, I.T. Biochem Biophys Acta Biomem 1808:394-8.


72. Resistance characteristics of Influenza to amino-adamantyls. Astrahan, P., and Arkin, I.T. Biochem Biophys Acta Biomem 1808:547-53.


2010


71. pH Driven Helix Rotations in the Influenza M2 H+ Channel: A Potential Gating Mechanism. Leonov, H., and Arkin, I.T. Eur Biophys J 39:1043–49.


2009


70. Structure and Dynamics of the Influenza A M2 Channel: a Comparison of Three Structure. Leonov, H., and Arkin, I.T. J Mol Mod 15:1317-28.


69. A model for the interaction between NF-κB and ASPP2 suggests and I-κ like mechanism. Benyamini, H., Leonov, H., Rotem, S., Katz, C., Arkin, I.T., and Friedler, F. Proteins 77:602-11.


68. Interaction and Conformational Dynamics of Membrane-Spanning Protein Helices. Langosch, D., and Arkin, I.T. Prot Sci 18:1343-58.


67. Gating mechanism of the Influenza A M2 channel revealed by 1 and 2D-IR spectroscopies. Manor, J., Mukherjee, P., Lin, Y., Leonov, H., Skinner, J.L., Zanni, M.T., and Arkin, I.T. Structure 2009 17:247-254. Supporting online material. News and views.


2008


66. Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens. Jensen, M.Ø., Dror, R.O., Xu, H., Borhani, D.W., Arkin, I.T., Eastwood, M.P., and Shaw, D.E. 2008 Proc Nat Acad Sci 105(38):14430-35.


65. Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins. Maragakis, P., Lindorff-Larsen, K., Eastwood, M.P., Dror, R.O., Klepeis, J.L., Arkin, I.T., Jensen, M.Ø., Xu, H., Trbovic, N., Friesner, R.A., Iii, A.G., and Shaw, D.E. 2008 J Phys Chem B 112(19):6155-6158.


2007


64. Mechanism of Na+/H+ antiporting. Arkin, I.T., Xu, H., Jensen, M.Ø., Arbely, E., Bennett, E.R., Bowers, K.J., Chow, E., Dror, R.O., Eastwood, M.P., Flitman-Tene, R., Gregersen, B.A., Klepeis, J.L., Kolossváry, I., Shan, Y., and Shaw, D.E. 2007 Science 317(5839):799-803. Supporting online material. News and views 2007 Nature Chem Biol 3(10):609-610.


63. How important are transmembrane helices of bitopic membrane proteins? Zviling, M., Kochva, U., and Arkin, I.T. 2007 2007 Biochim Biophys Acta. 1768(3):387-92.


2006


62. Picoseconds dynamics of a membrane protein revealed by 2D IR. Mukherjee, P., Kass, I., Arkin, I.T., and Zanni, M.T. 2006 J Chem Phys B Co 103(10):3528-33.


61. Viral ion channel proteins in model membranes: a comparative study by X-ray reflectivit.y Khattari, Z., Arbely, E., Arkin, I.T., and Salditt, T. 2006 Eur Biophys J 2006 36(1):45-55.


60. A Trimerizing GxxxG Motif Is Uniquely Inserted in the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Protein Transmembrane Domain. Arbely, E., Granot, Z., Kass, I., Orly, J., and Arkin IT. 2006 Biochemistry 2006 45(38):11349-56.


59. Isotope-edited IR spectroscopy for the study of membrane proteins. Arkin, I.T. 2006 Biochemistry. 2006 Curr Opin Chem Biol 2006 10(5):394-401.


58. Picoseconds dynamics of a membrane protein revealed by 2D IR. Mukherjee, P., Kass, I., Arkin, I.T., and Zanni, M.T. 2006 Proc Nat Acad Sci 103(10):3528-33.


57. SARS coronavirus E Protein in Phospholipid Bilayers: An X-ray Study. Khattari, Z., Brotons, G., Arbely, E., Arkin, I.T., and Salditt, T. 2006 Biophys J 90(6):2038-50.


2005


56. How pH opens a H+ channel: the gating mechanism of Influenza A M2. Kass, I., and Arkin, I.T. 2005 Structure 13:1789-98.


55. Disorder Influence on Linear Dichroism Analyses of Smectic Phases. Manor, J., Khattari, Z., Salditt, T., and Arkin, I.T. 2005 Biophys J 89:563-571.


54. Genetic Algorithm-Based Optimization of Hydrophobicity Tables. Zviling, M., Leonov, H., and Arkin, I.T. 2005 Bioinfo 21:2651-2656


53. A Periodicity Analysis of Transmembrane α-Helices. Leonov, H., and Arkin, I.T. 2005 Bioinfo 21:2604-2610 (Supplementary material)


52. SARS E protein in phospholipid bilayers: an anomalous X-ray reflectivity study. Khattari, Z., Brotons, G., Arbely, E., Arkin, I.T., and Salditt, T. 2005 Physica B 357:34-38


2004


51. Distinct Protein Interfaces in Transmembrane Domains Suggest an in vivo Folding Model. Stevens, T.J, Mizuguchi, K., and Arkin, I.T. 2004 Prot Sci 13:3028-37


50. A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein. Arbely, E., Khattari, Z., Brotons, G., Akkawi, M., Salditt, T., and Arkin, I.T. 2004 J Mol Biol 341:769-779


49. Structural conservation in the Major Facilitator Superfamily as revealed by comparative modeling. Vardy, E., Arkin, I.T., Gottschalk, K.E., Kaback, H.R., and Schuldiner, S. 2004 Prot Sci 13:1832-1840


48. Site-specific vibrational dynamics of the CD3ζ membrane domain using heterodyned 2D IR photon echo spectroscopy. Mukherjee, P.ζ Krummel, A.T., Fulmer, E.C., Kass, I., Arkin, I.T., and and Zanni, M.T. 2004 J Chem Phys 120:10215-10224


47. Experimental Measurement of The Strength of a Cα-HO Bond in a Lipid Bilayer. Arbely, E., and Arkin, I.T 2004 J Amer Chem Soc 126:5362-3


46. A novel method of resistance for influenza against a channel-blocking anti-viral drug. Astrahan, P., Kass, I., Cooper, M.A., and Arkin, I.T.2004 Prot Struct Func Gen 55:251-57


45. Modeling sample disorder in site specific dichroism studies of uniaxial systems. Kass, I., Arbely, E., and Arkin, I.T 2004 Biophys J 86:2502-7


2003


44. Modeling membrane proteins utilizing information from silent amino acid subsitutions. Kochva, U., Leonov, H., Adams, P.D., and Arkin, I.T. 2003 Curr Protoc Bioinfo 5.3.


43. Modeling the structure of the respiratory syncytial virus small hydrophobic protein by silent-mutation analysis of global searching molecular dynamics. Kochva, U., Leonov, H., and Arkin, I.T. 2003 Prot Sci 12:2668-74


42. Site specific dichroism analysis utilizing transmission FTIR. Arbely, E., Kass, I., and Arkin, I.T 2003 Biophys J 85:2476-83


41. Syntaxin 1A Modulates the Voltage-gated L-type Calcium Channel (Ca1.2) in a Cooperative Manner. Arien, H., Wiser, O., Arkin, I.T., Leonov, H., and and Atlas, D. 2003 J Biol Chem 278:29231-9


40. Monte Carlo estimation of the number of possible proteins folds: effects of sampling bias and folds distributions. Leonov, H., Mitchell, J.S.B., and Arkin, I.T. 2003 Prot. Struct. Func. Gen. 51:353-359


2002


39. Hydrogen/ Deuterium exchange of hydrophobic peptides in model membranes by electrospray ionization mass spectrometry. Hansen, R.K., Broadhurst, W.R., Skelton, P.C., and Arkin, I.T. 2002 J. Amer. Soc. Mass Spectrom. 13:1376-1387


38. A structure for the trimeric MHC class II-associated invariant chain transmembrane domain. Kukol, A., Torres, J., and Arkin, I.T. 2002 J. Mol. Biol. 320:1109-1117.


37. Structural aspects of oligomerization taking place between the transmembrane -helices of bitopic membrane proteins. Arkin, I.T. 2002 Biochem. Biophys. Acta 1565:347-363


36. C-deuterated alanine, a new label to study membrane protein structure using site specific infrared dichroism. Torres, J., Kukol, A., and Arkin, I.T. 2002 Biophys J. 82 1068-1075


35. Multiple site-specific infrared dichroism of CD3-ζ, a transmembrane helix bundle. Torres, J., Brigss, J.A.G., and Arkin, I.T. 2002 J. Mol. Biol. 316:365-374


34. Convergence of experimental, computational and evolutionary approaches predicts the presence of a tetrameric form for CD3-ζ. Torres, J., Brigss, J.A.G., and Arkin, I.T. 2002 J. Mol. Biol. 316:375-384


33. The orientation of the antibiotic peptide maculatin 1.1 in DMPG and DMPC lipid bilayers. Support for a pore-forming mechanism. Chia, C.S.B., Torres, J., Cooper, M.A., Arkin, I.T., and Bowie J.H. 2002 FEBS Lett 512:47-51


32. Contribution of energy values to the analysis of global searching molecular dynamics simulations of transmembrane helical bundles. Torres, J., Brigss, J.A.G., and Arkin, I.T. 2002 Biophys. J. 82:3063-3071


31. Prediction of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A genomic analysis. Borner, G.H.H., Sherrier, D.J., Stevens, T.J., Arkin, I.T., and Dupree, P. 2002 Plant Physiol. 129:486-499.


2001


30. Mapping the energy surface of transmembrane helix-helix interactions. Torres, J., Kukol, A., and Arkin, I.T. 2001 Biophys. J. 81:2681-2692


29. A new method to model membrane protein structure based on silent amino-acid substitutions. Brigss, J.A.G., Torres, J., Kukol, A., and Arkin, I.T. 2001 Prot. Struct. Func. Gen. 44:370-375


28. The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. Cordes, F., Kukol, A., Forrest, L.R., Arkin, I.T., Sansom, M.S.P., and Fischer W.B. 2001 Biochem. Biophys. Acta 1512:291-298


27. Site specific examination of secondary structure and orientation determination in membrane proteins: The peptidic 13C=18O group as a novel infrared probeץ Torres, J., Kukol, A., and Arkin, I.T. 2001 Biopolyemrs 59:396-401


26. Substitution rates in α-helical transmembrane proteins. Stevens, T.J., and Arkin, I.T. 2001 Prot. Sci. 10:2507-2517


2000


25. Turning an opinion ``inside-out'': Rees and Eisenberg's commentary (Prot. Struct. Func. Gen. 2000,38:121-2) on ``Are membrane proteins ``inside-out'' proteins?'' (Prot. Struct. Func. Gen. 1999,36:135-43). Stevens, T.J., and Arkin, I.T. 2000 Prot. Struct. Func. Gen. 40:463-464


24. Use of a New Label, 13C=18O, in the Determination of a Structural Model of Phospholamban in a Lipid Bilayer. Spatial Restraints Resolve the Ambiguity Arising from Interpretations of Mutagenesis Data Torres, J., Adams, P.D., and Arkin, I.T. 2000 J. Mol. Biol. 300:677-685.


23. The use of a single glycine residue to determine the tilt and orientation of a transmembrane helix. A new structural label for infrared spectroscopy. Torres, J., Kukol, A., and Arkin, I.T. 2000 Biophys J. 79:3139-3143


22. Do more complex organisms have a greater proportion of membrane proteins? Stevens, T.J., and Arkin, I.T. 2000 Proteins Struct Func Gen. 39:417-420


21. The effect of nucleotide bias upon the composition and prediction of transmembrane helices. Stevens, T.J., and Arkin, I.T. 2000 Proteins Science. 9:505-511


20. Recursive use of evolutionary conservation data in molecular modelling of membrane proteins: A model of the multidrug H antiporter EmrE. Torres, J., and Arkin, I.T. 2000 Euro. J. Biochem. 267:3422-3431


19. Structure of the Influenza C CM2 protein transmembrane domain obtained by site-specific infrared dichroism and global molecular dynamics searching. Kukol, A., and Arkin, I.T. 2000 J Biol Chem. 275:4225-4229


18. Exploring models of the Influenza A M2 channel - MD simulation in a phospholipid bilayer. Forrest, L.R., Kukol, A., Arkin, I.T., Tieleman, D.P., and Sansom, M.S.P. 2000 Biophys J. 78:55-69.


1999


17. vpu Transmembrane Peptide Structure Obtained by Site-Specific Fourier Transform Infrared Dichroism and Global Molecular Dynamics Searching. Kukol, A., and Arkin, I.T. 1999 Biophys J. 77:1594-1601


16. Are membrane proteins ``inside-out'' proteins? Stevens, T.J., and Arkin, I.T. 1999 Prot. Struct. Func. Gen. 36:135-143


15. Experimentally based orientational refinement of membrane protein models: A structure for the Influenza A M2 H channel. Kukol, A., Adams, P.D., Rice, L.M., Brünger, A.T., and Arkin, I.T. 1999 J. Mol. Biol. 286:951-962.


1998


14. Statistical Analysis of Predicted Transmembrane α-Helices. Arkin, I.T., and Brünger, A.T. 1998 Biochem. Biophys. Acta 1429:113-128


13. Helicity, membrane incorporation, orientation and thermal stability of the large conductance mechanosensitive ion channel from E. coli. Arkin, I.T., Sukharev, S.I., Blount, P., Kung, C., and Brünger, A.T. 1998 Biochem. Biophys. Acta 1369:131-140


1997


12. Site directed dichroism as a method for obtaining rotational and orientational constraints for oriented polymers. Arkin, I.T., MacKenzie, K.R., and Brünger, A.T. 1997 J. Amer. Chem. Soc. 119:8973-8980


11. Are there dominant membrane protein families with a given number of helices? Arkin, I.T., Brünger, A.T., and Engelman, D.M. 1997 Prot. Struct. Func. Gen. 28:465-466


10. Transmembrane a-helix interactions in folding and oligomerization of integral membrane proteins. Lemmon, M.A., MacKenzie, K.R., Arkin, I.T., and Engelman, D.M. 1997 in ``Membrane protein assembly'' G. von Heijne (ed.) Springer New York.


9. Structural perspectives of phospholamban, a helical transmembrane pentamer. Arkin, I.T., Adams. P.D., Brünger, A.T, Smith, S.O., and Engelman, D.M. 1997 Annu. Rev. Biophys. Biomol. Struct. 26:157-179


8. Structure of the transmembrane cysteine residues in the phospholamban ion channel. Arkin, I.T., Adams. P.D., Aimoto, S., Brünger, A.T., Engelman, D.M., and Smith, S.O. 1997 J. Membr. Biol. 155:199-206


1996


7. Determining the secondary structure and orientation of EmrE, a multi-drug transporter, indicates a transmembrane four helix bundle. Arkin, I.T., Russ, W.P., Lebendiker, M., and Schuldiner, S. 1996 Biochem. 35:7233-7238.


6. Coassembly of synthetic segments of shaker channel within phospholipid membranes. Peled-Zehavi, H., Arkin, I.T., Engelman, D.M., and Shai, Y. 1996 Biochem. 35:6828-6838.


5. FTIR spectroscopy and site-directed isotope labelling as a probe of local secondary structure in the transmembrane domain of phospholamban. Ludlam, C.F.C., Arkin. I.T., Liu, X., Rothman, M.S., Rath, P., Aimoto, S., Smith, S.O., Engelman, D.M., and Rothschild K.J. 1996 Biophys. J. 70:1728-1736.


4. Mapping the lipid exposed surfaces of membrane proteins. Arkin, I.T., MacKenzie, K.R., Fisher, L., Aimoto, S., Engelman, D.M., and Smith, S.O. 1996 Nature Struct. Biol. 3:240-243.


1995


3. Structural model of the phospholamban ion channel complex in phospholipid membranes. Arkin, I.T., Rothman, M., Ludlam, C.F.C., Aimoto, S., Engelman, D.M., Rothschild, K.J., and Smith, S.O. 1995 J. Mol. Biol. 248:824-834.


2. Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Adams, P.D., Arkin, I.T., Engelman, D.M., and Brünger A.T. 1995 Nature Struct. Biol. 2:154-159.


1994


1. Structural organisation of the pentameric transmembrane ɑ-helices of phospholamban, a cardiac ion channel. Arkin, I.T., Adams, P.D., MacKenzie, K.R., Lemmon, M.A., Brünger A.T., and Engelman, D.M. 1994 EMBO J. 13:4757-4764.

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