Publications
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, in press.
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 -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.
