Edda Kloppmann

PostDoc at Rostlab at TUM Computer Science, until February 2017
Email: edda.kloppmann. ( at ) .mytum.de


Research Interests
  • Structure and function of (transmembrane) proteins
  • Target selection for structural genomics, in particular for the New York Consortium on Membrane Protein Structure (NYCOMPS)
  • Transembrane proteins, proton pumps, (archaeal) rhodopsins
  • Methods: various (machine-learning based) methods to predict aspects of protein structure and function usually from protein sequences, (Metropolis) Monte Carlo, dead-end elimination (DEE), X-DEE (extended DEE), molecular dynamics, Poisson-Boltzmann electrostatics, Normal Mode Analysis
  • Among the databases I use are: UniProt, RefSeq, PDB, OPM and PDBTM


Publications

[1] E Kloppmann, T Becker and G M Ullmann. Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra. Proteins 61:953-965 (2005). [pdf]
[2] E Kloppmann, G M Ullmann and T Becker. An extended dead-end elimination algorithm to determine gap-free lists of low energy states. J Comput Chem 28:2325-2335 (2007). [pdf]
[3] G M Ullmann, E Kloppmann, T Essigke, E-M Krammer, A R Klingen, T Becker and E Bombarda. Investigating the mechanisms of photosynthetic proteins using continuum electrostatics. Photosynth Res 97:33-53 (2008). [pdf]
[4] E Kloppmann. Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics. PhD Thesis, Faculty of Biology, Chemistry and Earth Science, University of Bayreuth (2010). [pdf]
[5] M Punta and E Kloppmann. Membrane Protein Structure. Gordon C. K. Roberts (ed.) Encyclopedia of Biophysics, Springer (2012). [weblink]
[6] E Kloppmann, P Hoenigschmid and Rost. Protein Secondary Structure Prediction in 2012. Gordon C. K. Roberts (ed.) Encyclopedia of Biophysics, Springer (2012). [weblink]
[7] E Kloppmann, M Punta and B Rost. Structural genomics plucks high-hanging membrane proteins. Curr Op Struct Biol 22:326-332 (2012). [pdf]
[8] U Pieper, A Schlessinger, E Kloppmann, G A Chang, J J Chou, M E Dumont, B G Fox, P Fromme, W A Hendrickson, M G Malkowski, D C Rees, D L Stokes, M H B Stowell, M C Wiener, B Rost, R M Stroud, R C Stevens and A Sali. Coordinating the impact of structural genomics on the human alpha-helical transmembrane proteome. Nat Struct Mol Biol 20:135-138 (2013). [pdf]
[9] J Mistry, E Kloppmann, B Rost and M Punta. An estimated 5% of new protein structures solved today represent a new Pfam family. Acta Crystallogr D Biol Crystallogr 69(Pt 11):2186-2193 (2013). [pdf]
[10] Yachdav G, Kloppmann E, Kajan L et al. PredictProtein - an open resource for online prediction of protein structural and functional features. Nucleic Acids Res 42(Web Server issue):W337-343 (2014). [pdf]
[11] Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, Liu Q. Structural basis for a pH-sensitive calcium leak across membranes. Science 344:1131-1135 (2014). [pdf]
[12] Yang T, Liu Q, Kloss B, Bruni R, Kalathur RC, Guo Y, Kloppmann E, Rost B, Colecraft HM, Hendrickson WA. Structure and selectivity in bestrophin ion channels. Science 346:355-359 (2014). [pdf]
[13] Reeb J, Kloppmann E, Bernhofer M, Rost B. Evaluation of transmembrane helix predictions in 2014. Proteins 83:473-484 (2015). [pdf]
[14] Guo Y, Kalathur RC, Liu Q, Kloss B, Bruni R, Ginter C, Kloppmann E, Rost B, Hendrickson WA. Structure and activity of tryptophan-rich TSPO proteins. Science 347:551-555 (2015). [pdf]
[15] Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest AR. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 6:7866 (2015). doi: 10.1038/ncomms8866 [pdf]
Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest AR. Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 7:10706 (2016). doi: 10.1038/ncomms10706. [pdf]
[16] Graessel A, Hauck SM, von Toerne C, Kloppmann E, Goldberg T, Koppensteiner H, Schindler M, Knapp B, Krause L, Dietz K, Schmidt-Weber CB, Suttner K. A combined omics approach to generate the surface atlas of human naive CD4+ T cells during early T-cell receptor activation. Mol Cell Proteomics. 14:2085-102 (2015). [pdf]
[17] Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun. 7:10175 (2016). [pdf]
[18] Petrou VI, Herrera CM, Schultz KM, Clarke OB, Vendome J, Tomasek D, Banerjee S, Rajashankar KR, Belcher Dufrisne M, Kloss B, Kloppmann E, Rost B, Klug CS, Trent MS, Shapiro L, Mancia F. Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Science 351:608-612 (2016). [pdf]
[19] Bernhofer M, Kloppmann E, Reeb J, Rost B. TMSEG: Novel prediction of transmembrane helices. Proteins 84:1706-1716 (2016). [pdf]


nycomps98_fasta
nycomps98_all-DNAs
nycomps98_FILT-NEW-all-DNAs
nycomps98_list
nycomps98_genomes
nycomps98_genomes_old


Curriculum Vitae

since 03/2017 Data Scientist at the Arvato Health Analytics GmbH, Munich, Germany
01/2011 - 02/2017 Postdoc in the Bioinformatics and Computational Biology group of Prof. Dr. Burkhard Rost, TU Munich, Germany
01/2011 - 06/2015 Target selection for New York Consortium on Membrane Protein Structure (NYCOMPS) as part of the Protein Structure Initiative (PSI)
05/2010 Dr. rer. nat. (PhD), University of Bayreuth, Germany, 1. Referee: Prof. Dr. G. Matthias Ullmann, 2. Referee: Prof. Dr. Franz X. Schmid
12/2003 - 04/2007 PhD student in the Computational Biochemistry/Bioinformatics group of Prof. Dr. G. Matthias Ullmann, University of Bayreuth, Germany
11/2002 - 11/2003 PhD student in the Computational Molecular Biophysics group of Prof. Dr. Jeremy C. Smith, IWR Heidelberg, Germany, Supervisor: Dr. G. Matthias Ullmann
02/2002 - 08/2002 Master thesis in the Computational Molecular Biophysics group of Prof. Dr. Jeremy C. Smith, IWR, Heidelberg, Germany
10/2000 - 09/2002 MSc in Molecular and Cellular Biology, University of Heidelberg, Germany
10/1997 - 09/2000 Studies in biology, chemistry and physics, University of Rostock, Germany