UNIO Publications Read more about published UNIO results

Publications from 1998 - 2019

1. Herrmann, T., Rosenfelder, R. "A consistent calculation of dispersion corrections in elastic electron-deuteron scattering." Eur. Phys. J. A 1998 May, 2(1): 29–40.

2. Wimmer, R., Herrmann, T., Solioz M., Wüthrich K. "NMR structure and metal interactions of the CopZ copper chaperone." J. Biol. Chem. 1999 Aug, 274(32): 22597–22603.

3. Ellgaard, L., Riek, R., Braun, D., Herrmann, T., Helenius, A., Wüthrich, K. "Three-dimensional structure topology of the Calreticulin P-domain based on NMR assignment." FEBS Lett. 2001 Jan, 488(1-2): 69–73.

4. Ellgaard, L., Riek, R., Herrmann, T., Güntert, P., Braun, D., Helenius, A., Wüthrich, K. "NMR structure of the calreticulin P-domain." Proc. Natl. Acad. Sci. USA 2001 Mar, 98(6): 3133–3138.

5. Ellgaard, L., Riek, R. Frickel, E., Herrmann, T., Braun, D. Güntert P., Wüthrich, K. “NMR structure of the calreticulin P-domain: Implications for chaperone function“. Mol. Biol. Cell 2001 Nov: 12, 132-132.

6. Herrmann, T. “New approaches for automated protein NMR structure determination based on experimental NOESY data.” 2002, Mar, published by ETH Zurich, Switzerland. Doctoral and Habilitation thesis, doi:10.3929/ethz-a-004370762.

7. Herrmann, T., Güntert, P., Wüthrich, K. "Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA." J. Mol. Biol. 2002 May, 319(1): 209–227.

8. Ellgaard, L., Bettendorff, P., Braun, D., Herrmann, T., Fiorito, F., Güntert, P., Helenius, A., Wüthrich, K. "NMR structures of 36- and 73-residue fragments of the calreticulin P-domain." J. Mol. Biol. 2002 Sept, 322(4): 773–784.

9. Herrmann, T., Güntert, P., Wüthrich, K. "Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS." J. Biomol. NMR 2002 Nov, 24(3): 171–189.

10. Hiller, S., Kohl, A., Fiorito, F., Herrmann, T., Wider, G., Tschopp, J., Grütter, M. G., Wüthrich, K. "NMR structure of the apoptosis- and inflammation-related NALP1 pyrin domain." Structure 2003 Oct, 11(4): 1199–1205.

11. Peti, W., Etezady-Esfarjani, T., Herrmann, T., Klock, H. E., Lesley, S. A., Wüthrich, K. "NMR for structural proteomics of Thermotoga maritima: Screening and structure determination." J. Struct. Funct. Genom. 2004 July, 5(3): 205–215.

12. Etezady-Esfarjani, T., Herrmann, T., Peti, W., Klock, H. E., Lesley, S. A., Wüthrich, K. "NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis." J. Biomol. NMR 2004 July, 29(3): 403–406.

13. Lysek, D. A., Schorn, C., Nivon, L. G., Esteve-Moya, V., Christen, B., Calzolai, L., von Schroetter, C., Fiorito, F., Herrmann, T., Güntert, P., Wüthrich, K. "Prion protein NMR structures of cats, dogs, pigs and sheep." Proc. Natl. Acad. Sci. USA 2005 Jan, 102(3): 640–645.

14. Peti, W., Herrmann, T., Zagnitko, O., Grzechnik, S. K., Wüthrich, K. "NMR structure of the conserved hypothetical protein TM0979 from Thermotoga maritima." Proteins: Structure, Function and Bioinformatics 2005 May, 59(2): 387–390.

15. Columbus, L., Peti, W., Etezady-Esfarjani, T., Herrmann, T., Wüthrich K. "NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima." Proteins: Structure, Function and Bioinformatics 2005 Aug, 60(3): 552–557.

16. Nishiyama, M., Horst, R., Eidam, O., Herrmann, T., Ignatov, O., Vetsch, M., Bettendorff, P., Jelesarov, I., Grütter, G. M., Wüthrich, K., Glockshuber, R., Capitani G. "Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD." EMBO J. 2005 Jun, 24(12): 2075–2086.

17. Peti, W., Johnson, M. A., Herrmann, T., Neumann, B. W., Buchmeier, M. J., Nelson, M., Joseph, J., Page, R., Stevens, R. C., Kuhn, P., Wüthrich, K. "Structural genomics of SARS Coronavirus: NMR structure of the protein nsP7." J. Virol. 2005 Oct, 79(20): 12905–12913.

18. Fadel, V., Bettendorff, P., Herrmann, T., de Azevedo Jr, W. F., Oliveira, E. B., Yamane, T., Wüthrich, K. "Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus." Toxicon 2005 Dec, 46(7): 759–767.

19. Almeida, A. S., Herrmann, T., Peti, W., Wilson, I. A., Wüthrich, K. "NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins." Protein Sci. 2005 Nov, 14(11): 2880–2886.

20. Etezady-Esfarjani, T., Herrmann, T., Horst, R., Wüthrich, K. "Automated protein NMR structure determination in crude cell extract." J. Biomol. NMR 2006 Jan, 34(1): 3–11.

21. Johnson, M. A., Peti, W., Herrmann, T., Wilson, I. A., Wüthrich, K. "Solution structure of Asl1650, an Acyl carrier protein from Anabaena sp. PCC7120 with a variant phosphopantetheinylation-site sequence." Protein Sci. 2006 May, 15(5): 1030–1041.

22. Etezady-Esfarjani, T., Placzek, W. J., Herrmann, T., Wüthrich, K. "Solution structures of the putative anti-sigma-factor antagonist TM1442 from Thermotoga maritima in the free and phosphorylated states." Magn. Reson. Chem. 2006 July, 44(S1): 61–70.

23. Banci, L., Bertini, I., Cantini, C., DellaMalva, N., Rosato, A., Herrmann, T., Wüthrich, K. "Solution structure and intermolecular interactions of the third metal-binding domain of ATP7A, the Menkes disease protein." J. Biol. Chem. 2006 Sept, 281(39): 7220–7227.

24. Almeida, M. S., Johnson, M. A., Herrmann, T., Geralt, M., Saikatendu, K., Joseph, J. Subramanian, V., Neuman, B. W., Buchmaeier, M. J.,Stevens, R. C., Kuhn, P., Wüthrich, K. "Novel b–barrel fold in the NMR structure of the replicase nonstructural protein 1 from the SARS Coronavirus." J. Virol. 2007 April, 81(7): 3151–3161.

25. Johnson, M. A., Southworth, M. W., Herrmann, T.,
Brace, L., Perler, F. B., Wüthrich, K. "NMR structure of a KlbA intein precursor from Methanococcus jannaschii." Protein Sci. 2007 July, 16: 1316–1328.

26. Placzek, W.J., Etezady-Esfarjani, T., Herrmann, T., Pedrini, B., Peti, W., Alimenti, C., Luporini, P., Wüthrich, K. "Cold-adapted signal proteins: NMR structures of pheromones from the Antarctic Ciliate Euplotes nobilii." IUBMB Life 2007 Aug&Sept, 59(8&9): 578–585.

27. Serrano, P., Johnson, M. A., Almeida, M. S., Horst, R. Herrmann, T., Joseph, J. S., Neumann, B. W., Subramamaian, V., Saikatendu, K. S., Buchmeier, M. J., Stevens, R. C., Kuhn, P., Wüthrich, K. "NMR structure of the N-terminal domain of the nonstructural protein 3 from the SARS Coronavirus.” J. Virol. 2007 Nov, 81(21): 12049–12060

28. Gossart, A., Bettendorff, P., Puorger, C., Vetsch, M., Herrmann, T., Glockshuber, R., Wüthrich, K. "NMR solution structure and interaction studies of the protein FimF from type I pili of E. coli." J. Mol. Biol. 2008 Jan, 375(3): 752–763.

29. Manolikas, T., Herrmann, T., Meier, B. H. "Protein structure determination from solid state NMR using only proton-driven
13C spin-diffusion experiments." J. Am. Chem. Soc. 2008 Mar, 130(12): 3959–3966.

30. Volk, J., Herrmann, T., Wüthrich, K. "Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH." J. Biomol. NMR 2008 Jul, 41 (3): 127–138.

31. Manolikas, T., Herrmann, T., Meier, B. H. “Protein structure determination from solid state NMR using only proton-driven 13C spin-diffusion experiments“. Chimia 2008 Mar, 62(5): 439–439.

32. Fiorito, F., Damberger, F. F., Herrmann, T., Wüthrich, K. "Automated side-chain NMR assignment directly from [
1H, 1H]-NOESY spectra." J. Biomol. NMR 2008 Sep, 42(1): 23–33.

33. Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Güntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A, Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., van der Schot, G., Vranken, W.F., Vuister, G.W., Bonvin, A.M.J.J. “CASD-NMR: critical assessment of automated structure determination by NMR.” Nature Methods 2009 Sep, 6, 625-626.

34. Herrmann, T. “Protein structure calculation and automated NOE restraints.” Encycl. Magn. Res. 2010, DOI: 10.1002/9780470034590.emrstm1151.

35. Loureiro-Ferreira, N., Wassenaar, T.A., de Vries, S.J., van Dijk, M., van der Schot, G., van der Zwan, J., Boelens, R., Giachetti, A., Carotenuto, D., Rosato, A., Bertini, I., Herrmann, T., Bagaria, A., Jaravine, V., Jonker, H.R.A, Güntert, P., Schwalbe, H., Vranken, W.F., Dal Pra, S., Mazzucato, M., Frizziero, E., Traldi, S., Verlato, M., Bonvin, A.M.J.J. “e-NMR gLite grid enabled infrastructure“. Proceedings of Ibergrid 2010 May, 360-382.

36. Pontoizeau, C., Herrmann, T., Toulhoat, P., Elena, B., Emsley, L. “Projection NMR spectroscopy for unambiguous metabolic profiling of complex mixtures.”
Magn; Reson. Chem. 2010 July, 48(9): 727-733.

37. Herrmann, T. “Protein structure calculation and automated NOE restraints“. Solid State NMR Studies of Biopolymers. McDermott, A.E., Polenova, T. (eds) John Wiley & Sons Ltd., Chichester, UK, 2010 Aug.: 405-414.

38. Mohanty, B., Serrano, P., Pedrini, P., Jaudzems, K., Geralt, M., Horst, R., Herrmann, T., Elsliger M.-A., Wilson, I.A., Wüthrich, K. “Comparison of NMR structure and crystal structures for the proteins TM1112 and TM1367“. Acta Cryst. F 2010 Oct., 66(10): 1381-1391.

39. Serrano, P., Pedrini, P., Geralt, M., Jaudzems, K., Mohanty, B., Horst, R., Herrmann, T., Elsliger M.-A., Wilson, I.A., Wüthrich, K. “Comparison of NMR structure and crystal structures highlights conformational isomerism in protein active sites“. Acta Cryst. F 2010 Oct., 66(10): 1393-1405.

40. Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., Wider, G. “Structural analysis of the conserved UBM domains of the translesion polymerase iota in complex with ubiquitin“. J. Biol. Chem. 2011 Jan., 285: 1364-1373.

41. Wassenaar, T.A., van Dijk, M., Loureiro-Ferreira, N.,, van Der Schot, G., de Vries, S., Schmitz, C., van Der Zwan, J., Boelens, R., Giachetti, A., Ferella, L., Rosato, A., Bertini, I., Herrmann, T., Jonker, H., Bagaria, A., Jaravine, V., Güntert, P., Schwalbe, H., Vranken, W., Verlato, M., Badoer, S., Mazzucato, M., Bonvin, A., Frizziero, E. “WeNMR: Structural Biology on the Grid“. CEUR-WS, Vol. 819, Proceedings of IWSG-Life  2011 June, London, UK.

42. Guerry, P., Herrmann, T. “Advances in automated NMR protein structure determination“. Quart. Rev. Biophys. 2011 Aug., 44(3): 257-309.

43. Knight, M.J., Webber, A.L., Pell, A.J., Guerry, P., Barbet-Massin, E., Bertini, I., Felli, I.C., Gonnelli, L., Pierattelli, R., Emsley, L., Lesage, A., Herrmann, T., Pintacuda, G. “Fast resonance assignment and fold determination of the 153-residue protein superoxide dismutase by high-resolution proton-detected solid-state MAS NMR spectroscopy“. Angew. Chem. - Int. Edit. 2011 Oct., 50(49): 11697-11701.

44. Guerry, P., Herrmann, T. “Comprehensive automation for NMR structure determination of proteins“. Methods Mol. Biol. 2012 April, 831: 429-451.

45. Rosato. A., Aramini, J., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J.F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Güntert, P., He, Y., Herrmann, T., Huang, Y.J., Jaravine, V., Jonker, H.R.A., Kennedy, M.A., Lange, O.F., Liu, L., Malliavin, T.E., Mani, R., Mao, B., Montelione, G.T., Nilges, M., Rossi, P., van der Schot, G., Schwalbe, H., Szyperski, T., Vendruscolo, M., Vernon, R., Vranken; W.F., de Vries, S., Vuister, G.W., Wu, B.,Yang, Y., Bonvin, A.M.J.J.
“Blind testing of routine, fully automated determination of protein structures from NMR data“. Structure 2012 Feb., 20(2): 227-236.

46. Guerry, P., Herrmann, T. “Automated protein structure determination methods“. NMR of biomolecules: Towards mechanistic systems biology. Bertini, I., McGreevy, K. (eds.) John Wiley & Sons Ltd., 2012 March: 537-548.

47. Knight, M, Pell, A.J., Bertini, I., Felli, I.C., Gonnelli, L., Pierattelli, R., Herrmann, T., Emsley, L., Pintacuda, G. “Structure and site-specific backbone dynamics of a microcrystalline metalloprotein by solid-state NMR“. Proc. Natl. Acad. Sci. USA 2012 July, 109(28): 111095-11100.

48. Serrano, P., Pedrini, B., Mohanty, B., Geralt, M., Herrmann, T., Wüthrich, K. “The J-UNIO protocol for automated protein structure determination by NMR in solution“. J. Biomol. NMR 2012 Aug. 53(4): 341-354.

49. Knight, M, Felli, I.C., Pierattelli, R., Bertini, I., Emsley, L., Herrmann, T., Pintacuda, G. “Rapid measurement of pseudocontact shifts in metalloproteins by proton-detected solid-state NMR“. J. Am. Chem. Soc. 2012 Aug., 136(36): 14730-14733.

50. Wang, X., Lord, D.M., Cheng, H.-Y., Osbourne, D.O., Hong, S.H., Sanchez-Torres, V., Quiroga, C., Zheng, K., Herrmann, T., Peti, W., Denedik, M.J., Page, R., Wood, T.K. “A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS“. Nature Chem. Biol. 2012 Sept., 8(10): 855-861.

51. Wassenaar, T.A., van Dijk, M., Loureiro-Ferreira, N., van Der Schot, G., de Vries, S., Schmitz, C., van Der Zwan, J., Boelens, R., Giachetti, A., Ferella, L., Rosato, A., Bertini, I., Herrmann, T., Jonker, H., Bagaria, A., Jaravine, V., Güntert, P., Schwalbe, H., Vranken, W., Doreleijers, J.F., Vriend, G., Vuisters, G., Franke, D., Kikhney, A., Svergun, D.I., Fogh, R., Ionides, J., Laue, E.D., Spronk, C., Jurksa, S., Verlato, M., Badoer, S., Dal Pra, S., Mazzucato, M., Frizziero, E., Bonvin, A.M.J.J. WeNMR: “Structural biology on the grid”. J. Grid Comp. 2012 Dec., 10: 743-767.

52. Montelione, G. T., Nilges, M., Bax, A., Guntert, G., Herrmann, T., Richardson, J.S., Schwieters, C.D., Vranken, W.F., Vuister, G.W., Wishart, D.S., Berman, H.M., Kleywegt, G., Markley, J.L. Recommendations of the wwPDB NMR validation task force. Structure 2013 Sept., 21(9): 1563-1570.

53. Herrmann, T., Elena-Herrmann, B. Applications of projection NMR techniques. Annu. Rep. NMR Spectrosc. 2013 Jan., 78:55-102.

54. Barbet-Massin, E., Pell, A.J., Retel, J.S., Andreas, L.B., Jaudzems, K., Franks, W.T., Nieuwkoop, A.J., Hiller, M., Higman, V., Guerry, P., Bertarello, A., Knight, M.J., Felletti, M., Le Marchand, T., Kotelovica, S., Akopjana, I., Tars, K., Stoppini, M., Bellotti, V., Bolognesi, M., Ricagno, S., Chou, J.J., Griffin, R.G., Oschkinat, H., Lesage, A., Emsley, L., Herrmann, T, Pintacuda, G. “Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning”. J. Am. Chem. Soc. 2014 Sept., 136(35): 12489-12497.

55. Dutta, S.K., Serrano, P., Proudfoot, A., Geralt, M., Pedrini, B., Herrmann, T., Wuthrich, K. “APSY-NMR for protein backbone assignment in high-throughput structural biology”. J. Biomol. NMR 2015 Jan, 61(1): 47-53.

56. Guerry, P., Duong, V.D., Herrmann, T. “CASD-NMR 2: Robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO”. J. Biomol. NMR 2015 April, 62(4): 473-480.

57. Gutmanas, A., Adams, P.D., Bardiaux, B., Berman, H.M., Case, D.A., Fogh, R.H., Güntert, P., Hendrickx, P.M.S., Herrmann, T., Kleywegt, G.J., Kobayashi, N., Lange, O.F., Markley, J.L., Montelione, G.T., Nilges, M., Ragan, T.J., Schwieters, C.D., Tejero, R., Ulrich, E., Velankar, S., Vranken, W.F., Wedell, J., Westbrook, J., Wishart, D.S., Vuister, G.W. “NMR exchange format: a community-driven unified representation of NMR restraints data”. Nature Struct. Mol. Biol. 2015 June, 22: 433-434.

58. Andreas, L.B., Stanek, J., Le Marchand, T., Bertarello, A., Cala-De Paepe, D., Lalli, D., Krejčíková, M., Doyen, C., Öster, C., Knott, B., Wegner, S., Engelke, F., Felli, I.C., Pierattelli, R., Dixon, N.E., Emsley, L., Herrmann, T.,
Pintacuda, G. “Protein residue linking in a single spectrum for magic-angle spinning NMR assignment”. J. Biomol. NMR 2015 July, 62(3): 253-261.

59. Latgé
C., Cabral, K.M.S., Oliveira, G.A.P., Raymundo, D.P., Freitas, J.A., Palhano, F.L., Herrmann, T., Almeida, M.S., Foguel, D. “The solution structure and dynamics of full-length human cerebral dopamine neurotrophic factor and its neuroprotective role against alpha-synuclein oligomers”. J. Biol. Chem. 2015 Aug., 290(33): 20527-20540

60. Augustyniak, R., Stanek, J.,
Colaux, H., Bodenhausen, G., Koźmiński, W., Herrmann, T., Ferrage, F. “Nuclear Overhauser spectroscopy of chiral methylene groups”. Chem. Bio. Chem. 2016 Jan., 64(1): 27-37.

61. Andreas L.B., Jaudzems, K., Stanek, J., Lalli, D., Bertarello, A.,
Le Marchand, T., Cala-De Paepe, D., Kotelovica, S., Akopjana, S., Knott, B., Wegner, S., Engelke, F., Lesage, A., Emsley, L., Tars, K., Herrmann, T., Pintacuda, G. “Structure of fully protonated proteins by proton-detected magic-angle spinning NMR”. Proc. Natl. Acad. Sci. USA 2016 Aug., 113(33): 9187-9192.

62. Birkou
M., Chasapis C.T., Marousis K.D., Loutsidou A.K., Bentrop D., Lelli M., Herrmann T., Carthy J.M., Episkopou V., Spyroulias G.A. “A residue-specific insight on the Arkadia E3 ubiquitin ligase activity and conformational plasticity upon replacement of the conserved RING domain Tryptophan residue”., J. Mol. Biol. 2017 July, 429(15): 2373-2386.

63. Oster, C., Walkowiak, G.P., Hughes, D.E., Spoering, A.L., Peoples, A.J., Catherwood, A.C., Tod, J.A., Lloyd, A.J., Herrmann, T., Lewis, K., Dowson, C.G., Lewandowski, J.R.  “Structural studies suggest aggregation as one of the modes of action for teixobactin”. Chem. Sci. 2018 Sept. 9(47): 8850-8859.




UNIO References

Stacks Image 124
UNIO - Key References