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CV and Publications

 

Short CV Alexander Schug

04/2011+

Helmholtz Young Investigator Group Leader, Steinbuch Centre for Computing & Department of Physics, Karlsruhe Institute of Technology (KIT), Germany

09/2010-03/2011

Assistant Professor (“Forskarassistent”), Department of Chemistry, Umeå University, Sweden

01/2006-08/2010

Postdoctoral Scholar, University of California, San Diego, USA

05/2005-11/2005

Postdoctoral Scholar, Kobe University, Japan

02/2002-04/2005

Graduate Researcher, Research Center Karlsruhe, Germany

 

Selected Research Articles

G. Uguzzoni*, S. John Lovis*, F. Oteri, A. Schug+, H. Szurmant+, M. Weigt+, Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis Proc. Natl. Acad. Sci. U.S.A.  (accepted) *Contributed equally; + joint corresponding authors 

M. Figliuzzi, H. Jacquier, A.  Schug, O. Tenaillon, M. Weigt. Coevolutionary inference of mutational landscapes: Capturing the context-dependence of mutations in the beta-lactamase TEM-1, Mol. Bio. Evol., msv211, 2016.

E. De Leonardis*, B. Lutz*, S. Cocco, R. Monasson, A. Schug+, M. Weigt+. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA tertiary structure prediction, Nucl. Ac. Res., gkv932, 2015. *Contributed equally; + joint corresponding authors.

E. Stanganello, A.I.H. Hagemann, B. Mattes, C. Sinner, D. Meyen, S. Weber, A. Schug, E. Raz and S. Scholpp. Filopodia based Wnt transport during vertebrate tissue patterning, Nature Communication 6, doi:10.1038/ncomms6846, 2015.

A. E. Dago*, A. Schug*, A. Procaccini, J. A. Hoch, M. Weigt, and H. Szurmant. The Structural Basis of Histidine Kinase Autophosphorylation deduced by Integrating Genomics, Molecular Dynamics and Mutagenesis. Proc. Natl. Acad. Sci. U.S.A., 109:1733-1742, 2012 *contributed equally

A. Schug, M. Weigt, J.N. Onuchic, T. Hwa, and H. Szurmant. High resolution protein complexes from integrating genomic information with molecular simulation. Proc. Nat. Acad. Sci. U.S.A., 106:22124– 22129, 2009.

A. Schug, P.C. Whitford, Y. Levy, and J.N. Onuchic. Mutations as trapdoors to two competing native conformations of the rop-dimer. Proc. Nat. Acad. Sci. U.S.A., 104:17674–17679, 2007.

A. Schug, T. Herges, and W. Wenzel. Predictive in silico all-atom folding of a four-helix protein with a free-energy model. Phys. Rev. Letters, 91(15):158102, 2003.

Publication List

  1. G. Uguzzoni*, S. John Lovis*, F. Oteri, A. Schug+, H. Szurmant+, M. Weigt+, Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis Proc. Natl. Acad. Sci. U.S.A.  (accepted) *Contributed equally; + joint corresponding authors 
  2. A.L. Winkler, J. von Wulffen, L. Rödling, A. Raic, I. Reinartz, A. Schug, R. Gralle-Koser, U. Geckle, A. Welle, C. Lee-Thedieck. Bi-functional nanopatterned hydrogels control hematopoietic stem cell maintenance and proliferation, Advanced Functional Materials (accepted).
  3. M. Figliuzzi, H. Jacquier, A.  Schug, O. Tenaillon, M. Weigt. Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1, Mol. Bio. Evol. 33:268-280, msv211, 2016.
  4. C. Sinner, B. Lutz, A. Verma, A. Schug. Revealing the Global Map of Protein Folding Space by Large-Scale Simulations, J. Chem. Phys. 143, 243154, 2015.
  5. H. Lammert, J.K. Noel, E. Haglund, A. Schug, J.N. Onuchic. Constructing a folding model for protein S6 guided by dynamics deduced from NMR structures, J. Chem. Phys. 143, 243141, 2015.
  6. E. De Leonardis*, B. Lutz*, S. Cocco, R. Monasson, A. Schug+, M. Weigt+. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA tertiary structure prediction, Nucl. Ac. Res., gkv932, 2015. *Contributed equally; + joint corresponding authors.
  7. M. Figliuzzi, H. Jacquier, A.  Schug, O. Tenaillon, M. Weigt. Coevolutionary inference of mutational landscapes: Capturing the context-dependence of mutations in the beta-lactamase TEM-1, Mol. Bio. Evol., msv211, 2015.
  8. E. De Leonardis*, B. Lutz*, S. Cocco, R. Monasson, A. Schug+, M. Weigt+. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA tertiary structure prediction, Nucl. Ac. Res., gkv932, 2015. *Contributed equally; + joint corresponding authors.
  9. S. Kirmizialtin, S. Hennelly, A. Schug, J. Onuchic and K. Sanbonmatsu. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT, Methods Enzym 553, 215-234, 2015.
  10. E. Stanganello, A.I.H. Hagemann, B. Mattes, C. Sinner, D. Meyen, S. Weber, A. Schug, E. Raz and S. Scholpp. Filopodia based Wnt transport during vertebrate tissue patterning, Nature Communication 6, doi:10.1038/ncomms6846, 2015.
  11. B. Lutz, C. Sinner, S. Bozic, I. Kondov, A. Schug. Native structure-based modeling and simulation of biomolecular systems per mouse click, BMC Bioinformatics 2014, 15:292.
  12. C. Sinner, B. Lutz, S. John, I. Reinartz, A. Verma, A. Schug. Simulating Biomolecular Folding and Function by Native Structure Based/ Go-type Models, Isr. J. Chem. 54 (8-9), 165–1175.
  13. B. Lutz, M. Faber, A. Verma, S. Klumpp, A. Schug. Differences between co-transcriptional and free riboswitch folding, Nucl. Ac. Res., 42 (4), 2687–2696, 2014, doi: 10.1093/nar/gkt1213.
  14. P. Anand, A. Schug, W. Wenzel. Structure-Based Design of Protein Linkers for Zinc Finger Nuclease Based Gene Manipulation, FEBS Letters, 587 (19), 3231–3235, 2013.
  15. B. Lutz, C. Sinner, G. Heuermann, A. Verma, A. Schug. ESBMTools 1.0: enhanced native structure-based modeling tools, Bioinf., 29 (21): 2795-2796, 2013.
  16. J. Ådén, A. Verma, A. Schug, M. Wolf-Watz. Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity . J. Am. Chem. Soc., 134: 16562–16570, 2012.
  17. A. E. Dago*, A. Schug*, A. Procaccini, J. A. Hoch, M. Weigt, and H. Szurmant. The Structural Basis of Histidine Kinase Autophosphorylation deduced by Integrating Genomics, Molecular Dynamics and Mutagenesis. Proc. Natl. Acad. Sci. U.S.A., 109:1733-1742, 2012 *contributed equally
  18. J. K. Noel, A. Schug, A. Verma, W. Wenzel, A. E. Garcia, J. N. Onuchic. Mirror images as naturally competing conformations in protein folding. J. Phys. Chem. B, 116(23): 6880-6888, 2012.
  19. R. Nechushtaia, H. Lammert, D. Michaeli, Y. Eisenberg-Domovich, J. Zuris, M. A. Luca, D. T. Capraro, A. Fisha, O. Shimshon, M. Roy, A. Schug, P. C. Whitford, O. Livnah, J. N. Onuchic, and P. A. Jenning. Allostery in the ferredoxin protein motif does not involve a conformational switch. Proc. Natl. Acad. Sci. U.S.A., 108:2240-2245, 2011.
  20. A. Schug and J.N. Onuchic. From protein folding to protein function and biomolecular binding by energy landscape theory. Curr. Opin. Pharm. 10:709-714,2010.
  21. A. Schug, M. Weigt, J.A. Hoch, J.N. Onuchic, T. Hwa, and H. Szurmant. Computational modeling of phosphotransfer complexes in two-component signaling. Meth. Enzymol., 471:43-58, 2010.
  22. A. Schug, M. Weigt, J.N. Onuchic, T. Hwa, and H. Szurmant. High resolution protein complexes from integrating genomic information with molecular simulation. Proc. Nat. Acad. Sci. U.S.A., 106:22124– 22129, 2009.
  23.  H. Lammert, A. Schug, and J.N. Onuchic. Robustness and Generalization of Structure-Based Models for Protein Folding. Prot.: Struct., Funct., and Bioinf., 77:881–891, 2009.
  24.  Y. Gambin*, A. Schug*, E.A. Lemke, J.J. Lavinder, A.C.M. Ferreon, T.J. Magliery, J.N. Onuchic, and A.A. Deniz. Direct single-molecule observation of a protein living in two opposed native structures. Proc. Nat. Acad. Sci. U.S.A., 106:10153–10158, 2009. *contributed equally, selected as “must read” by Faculty of 1000 Biology
  25. P.C. Whitford, A. Schug, J. Saunders, S.P. Hennelly, K. Sanbonmatsu, and J.N. Onuchic. Non-local helix formation is key to understanding SAM-1 riboswitch function. Biophys. J. Letters, 96:7–9, 2009. Cover Picture
  26.  P.C. Whitford, J.K. Noel, S. Gosavi, A. Schug, K. Sanbonmatsu, and J.N. Onuchic. An all-atom structure- based potential for proteins: Bridging minimal models with empirical forcefields. Prot.: Struct., Funct., and Bioinf., 75:430–441. 2009.
  27. L. Oliveira, A. Schug, and J.N. Onuchic. Geometrical features of the protein folding mechanism are a robust property of the energy-landscape- a detailed investigation for several reduced models. J. Phys. Chem. B, 112:6131–6136, 2008.
  28. A. Schug, P.C. Whitford, Y. Levy, and J.N. Onuchic. Mutations as trapdoors to two competing native conformations of the rop-dimer. Proc. Nat. Acad. Sci. U.S.A., 104:17674–17679, 2007.
  29. K. Maeda, A. Schug, H. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka. Effects of point mutations on the binding energies of estrogen receptor with estradiol. J. Comp. Chem. Jpn., 6:33–46, 2007.
  30. A. Schug and W. Wenzel. An evolutionary strategy for all-atom protein folding of the sixty-amino acid bacterial ribosomal protein l20. Biophys. J., 90:4273–4280, 2006.
  31. A. Verma, A. Schug, K. H. Lee, and W. Wenzel. Basin hopping simulations for all-atom protein folding. J. Chem. Phys., 124:044515, 2006.
  32. A. Schug, W. Wenzel, and U.H.E. Hansmann. Energy landscape paving simulations of the trp-cage protein. J. Chem. Phys., 122:194711, 2005.
  33. A. Schug, T. Herges, A. Verma, and W. Wenzel. Investigation of the parallel tempering method for protein folding. J. Phys. Cond. Matter, special issue: Structure and Function of Biomolecules, 17:1641–1650, 2005.
  34. A. Schug, B. Fischer, A. Verma, H. Merlitz, W. Wenzel, and G. Schoen. Biomolecular structure prediction with stochastic optimization methods. Adv. Eng. Materials, 11:1005–1009, 2005.
  35. A. Schug, A. Verma, T. Herges, K.H. Lee, and W. Wenzel. Comparison of stochastic optimization methods for all-atom folding of the trp-cage protein. ChemPhysChem, 6(12): 2640–2646, 2005.
  36. T. Herges, A. Schug, and W. Wenzel. Exploration of the free energy surface of a three helix peptide with stochastic optimization methods. Int. J. Quant. Chem., 99:854–863, 2004.
  37. A. Schug and W. Wenzel. All-atom folding of the trp-cage protein with an adaptive parallel tempering method. Europ. Phys. Lett., 67:307–313, 2004.
  38. A. Schug, T. Herges, and W. Wenzel. All atom folding of the three helix hiv accessory protein with an adaptive parallel tempering method. Prot.: Struct., Funct., and Bioinf., 57(4):792–798, 2004.
  39. A. Schug, T. Herges, and W. Wenzel. Predictive in silico all-atom folding of a four-helix protein with a free-energy model. J. Am. Chem. Soc., 126(51):16736–16737, 2004.
  40. T. Herges, A. Schug, H. Merlitz, and W. Wenzel. Stochastic optimization methods for structure prediction of biomolecular nanoscale systems. Nanotechnology, 14:1161–1167, 2003.
  41. A. Schug, T. Herges, and W. Wenzel. Predictive in silico all-atom folding of a four-helix protein with a free-energy model. Phys. Rev. Letters, 91(15):158102, 2003. Cover Picture, selected as “recommended” by Faculty of 1000 Biology