Publications

2016


89. Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker. Assa D, Alhadeff R, Krugliak M, Arkin IT. 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 & 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. & 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. & 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. & Arkin, I.T. J Phys Chem Lett 5:2573−2579. Supplementary data.


84. Strength of a bifurcated H bond. Feldblum, E.S. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & Arkin, I.T. Biochem Biophys Acta Biomem 1808:394-8.


72. Resistance characteristics of Influenza to amino-adamantyls. Astrahan, P. & 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. & 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. & 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. & Friedler, F. Proteins 77:602-11.


68. Interaction and Conformational Dynamics of Membrane-Spanning Protein Helices. Langosch, D. & 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. & 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. & 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. & 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. & 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. & 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. & 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 reflectivity Khattari, Z., Arbely, E., Arkin, I.T. & 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. & 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. & 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. & 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. & Arkin, I.T. 2005 Structure 13:1789-98.


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


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


53. A Periodicity Analysis of Transmembrane α-Helices. Leonov, H. & 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. & 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. & 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. & 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. & 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 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. & 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. & 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. & 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. & 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. & Arkin, I.T. 2003 Prot Sci 12:2668-74


42. Site specific dichroism analysis utilizing transmission FTIR. Arbely, E., Kass, I. & 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 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. & 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. & 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. & 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. & 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. & 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. & 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., & 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. & 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. & Dupree, P. 2002 Plant Physiol. 129:486-499.


2001


30. Mapping the energy surface of transmembrane helix-helix interactions. Torres, J., Kukol, A. & 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. & 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. & 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 probe Torres, J., Kukol, A. & Arkin, I.T. 2001 Biopolyemrs 59:396-401


26. Substitution rates in α-helical transmembrane proteins. Stevens, T.J. & 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. & 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. & 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. & Arkin, I.T. 2000 Biophys J. 79:3139-3143


22. Do more complex organisms have a greater proportion of membrane proteins? Stevens, T.J. & 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. & 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. & 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. & 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. & Sansom, M.S.P. 2000 Biophys J. 78:55-69.


1999


17. Structure of the HIV-1 Vpu transmembrane complex determined by site-specific FTIR dichroism and global molecular dynamics searching. Kukol, A. & Arkin, I.T. 1999 Biophys J. 77:1594-1601


16. Are membrane proteins ``inside-out'' proteins? Stevens, T.J. & 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. & Arkin, I.T. 1999 J. Mol. Biol. 286:951-962.


1998


14. Statistical Analysis of Predicted Transmembrane α-Helices. Arkin, I.T. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & Brünger A.T. 1995 Nature Struct. Biol. 2:154-159.


1994


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