University of Toronto
NMR Centre




Philipp Neudecker

Postdoctoral Fellow

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Contact:



Curriculum Vitae


Research Interests


Gallery of Structures

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Pru av 1 wild-type, 22 conformers (PDB 1E09)
Pru av 1 E45W, 24 conformers (PDB 1H2O)
Gly m 4, 20 conformers (PDB 2K7H)

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Holo Bet v 4, 25 conformers (PDB 1H4B)

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Human proguanylin, 30 conformers (PDB 1O8R)

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Folding/misfolding intermediate of the Fyn SH3 A39V/N53P/V55L, 10 conformers (PDB 2L2P)


Theses


Publications

Original articles in peer-reviewed journals

(selected publications highlighted by larger font size)

  1. P. Neudecker, K. Schweimer, J. Nerkamp, M. Boehm, S. Scheurer, S. Vieths, H. Sticht & P. Rösch:
    Sequence-specific 1H, 13C and 15N resonance assignments of the major cherry allergen Pru a 1
    J. Biomol. NMR 18, 71-72 (2000)

  2. P. Neudecker, K. Schweimer, J. Nerkamp, S. Scheurer, S. Vieths, H. Sticht & P. Rösch:
    Allergic Cross-reactivity Made Visible: Solution Structure of the Major Cherry Allergen Pru av 1
    J. Biol. Chem. 276, 22756-22763 (2001)

  3. P. Neudecker, H. Sticht & P. Rösch:
    Improving the efficiency of the Gaussian conformational database potential for the refinement of protein and nucleic acid structures
    J. Biomol. NMR 21, 373-375 (2001)

  4. P. Neudecker, K. Lehmann & P. Rösch:
    Sequence-specific 1H, 13C and 15N resonance assignments of SAM22, an allergenic stress-induced protein from soy bean
    J. Biomol. NMR 26, 191-192 (2003)

  5. T. Lauber, P. Neudecker, P. Rösch & U. C. Marx:
    Solution Structure of Human Proguanylin: The Role of a Hormone Prosequence
    J. Biol. Chem. 278, 24118-24124 (2003)

  6. K. Lehmann, S. Hoffmann, P. Neudecker, M. Suhr, W.-M. Becker & P. Rösch:
    High-yield expression in Escherichia coli, purification, and characterization of properly folded major peanut allergen Ara h 2
    Protein Expr. Purif. 31, 250-259 (2003)

  7. P. Neudecker, K. Lehmann, J. Nerkamp, T. Haase, A. Wangorsch, K. Fötisch, S. Hoffmann, P. Rösch, S. Vieths & S. Scheurer:
    Mutational epitope analysis of Pru av 1 and Api g 1, the major allergens of cherry (Prunus avium) and celery (Apium graveolens): correlating IgE reactivity with three-dimensional structure
    Biochem. J. 376, 97-107 (2003)

    Commentary article by R. Crameri
    Biochem. J. 376, e1-e2 (2003)

  8. K. Lehmann, K. Schweimer, P. Neudecker & P. Rösch:
    Sequence-specific 1H, 13C and 15N resonance assignments of Ara h 6, an allergenic 2S albumin from peanut
    J. Biomol. NMR 29, 93-94 (2004)

  9. P. Neudecker, J. Nerkamp, A. Eisenmann, A. Nourse, T. Lauber, K. Schweimer, K. Lehmann, S. Schwarzinger, F. Ferreira & P. Rösch:
    Solution Structure, Dynamics, and Hydrodynamics of the Calcium-bound Cross-reactive Birch Pollen Allergen Bet v 4 Reveal a Canonical Monomeric Two EF-Hand Assembly with a Regulatory Function
    J. Mol. Biol. 336, 1141-1157 (2004)

  10. A. Eisenmann, P. Neudecker, P. Rösch & S. Schwarzinger:
    Treatment of Peak Intensity Uncertainties in NMR Relaxation Data Analysis Can Lead to Severe Artifacts
    Monatsh. Chem. 135, 1089-1099 (2004)

  11. D. Mittag, V. Batori, P. Neudecker, R. Wiche, E. P. Friis, B. K. Ballmer-Weber, S. Vieths & E. L. Roggen:
    A novel approach for investigation of specific and cross-reactive IgE epitopes on Bet v 1 and homologous food allergens in individual patients
    Mol. Immunol. 43, 268-278 (2006)

  12. D. M. Korzhnev, P. Neudecker, A. Mittermaier, V. Y. Orekhov & L. E. Kay:
    Multiple-Site Exchange in Proteins Studied with a Suite of Six NMR Relaxation Dispersion Experiments: An Application to the Folding of a Fyn SH3 Domain Mutant
    J. Am. Chem. Soc. 127, 15602-15611 (2005)

  13. P. Neudecker, D. M. Korzhnev & L. E. Kay:
    Assessment of the effects of increased relaxation dispersion data on the extraction of 3-site exchange parameters characterizing the unfolding of an SH3 domain
    J. Biomol. NMR 34, 129-135 (2006)

  14. D. M. Korzhnev, P. Neudecker, A. Zarrine-Afsar, A. R. Davidson & L. E. Kay:
    Abp1p and Fyn SH3 Domains Fold through Similar Low-Populated Intermediate States
    Biochemistry 45, 10175-10183 (2006)

  15. JMB Cover Nov. 10, 2006 P. Neudecker, A. Zarrine-Afsar, W.-Y. Choy, D. R. Muhandiram, A. R. Davidson & L. E. Kay:
    Identification of a Collapsed Intermediate with Non-Native Long-Range Interactions on the Folding Pathway of a Pair of Fyn SH3 Domain Mutants by NMR Relaxation Dispersion Spectroscopy
    J. Mol. Biol. 363, 958-976 (2006)

    Cover Illustration: The kinetics and thermodynamics of the folding pathway of the Fyn SH3 domain can be studied in great detail by NMR relaxation dispersion spectroscopy, which allows detection and structural characterization of a previously undetected low-populated on-pathway intermediate. See article by Neudecker et al. in this issue, pp. 958-976.

  16. P. Neudecker, A. Zarrine-Afsar, A. R. Davidson & L. E. Kay:
    Φ-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy
    Proc. Natl. Acad. Sci. (USA) 104, 15717-15722 (2007)
    (track II - direct submission to the editorial office)

    Faculty of 1000 evaluation

  17. D. F. Hansen, P. Vallurupalli, P. Lundström, P. Neudecker & L. E. Kay:
    Probing Chemical Shifts of Invisible States of Proteins with Relaxation Dispersion NMR Spectroscopy: How Well Can We Do?
    J. Am. Chem. Soc. 130, 2667-2675 (2008)

  18. A. Zarrine-Afsar, S. Wallin, A. M. Neculai, P. Neudecker, P. L. Howell, A. R. Davidson & H. S. Chan:
    Theoretical and Experimental Demonstration of the Importance of Specific Nonnative Interactions in Protein Folding
    Proc. Natl. Acad. Sci. (USA) 105, 9999-10004 (2008)
    (track II - direct submission to the editorial office)

    Faculty of 1000 evaluation

  19. P. Filippakopoulos, M. Kofler, O. Hantschel, G. D. Gish, F. Grebien, E. Salah, P. Neudecker, L. E. Kay, B. E. Turk, G. Superti-Furga, T. Pawson & S. Knapp:
    Structural Coupling of SH2-Kinase Domains Links Fes and Abl Substrate Recognition and Kinase Activation
    Cell 134, 793-803 (2008)

  20. H. Berkner, P. Neudecker, D. Mittag, B. K. Ballmer-Weber, K. Schweimer, S. Vieths & P. Rösch:
    Cross-reactivity of pollen and food allergens: soybean Gly m 4 is a member of the Bet v 1 superfamily and closely resembles yellow lupine proteins
    Biosci. Rep. 29, 183-192 (2009)

  21. R. Auer, P. Neudecker, D. R. Muhandiram, P. Lundström, D. F. Hansen, R. Konrat & L. E. Kay:
    Measuring the Signs of 1Hα Chemical Shift Differences Between Ground and Excited Protein States by Off-Resonance Spin-Lock R NMR Spectroscopy
    J. Am. Chem. Soc. 131, 10832-10833 (2009)

  22. R. Auer, D. F. Hansen, P. Neudecker, D. M Korzhnev, D. R. Muhandiram, R. Konrat & L. E. Kay:
    Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R methods
    J. Biomol. NMR 46, 205-216 (2010)

  23. D. F. Hansen, P. Neudecker, P. Vallurupalli, F. A. A. Mulder & L. E. Kay:
    Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion
    J. Am. Chem. Soc. 132, 42-43 (2010)

  24. P. Walsh, P. Neudecker & S. Sharpe:
    Structural Properties and Dynamic Behaviour of Nonfibrillar Oligomers Formed by PrP(106-126)
    J. Am. Chem. Soc. 132, 7684-7695 (2010)

  25. D. F. Hansen, P. Neudecker & L. E. Kay:
    Determination of Isoleucine Side-Chain Conformations in Ground and Excited States of Proteins from Chemical Shifts
    J. Am. Chem. Soc. 132, 7589-7591 (2010)

  26. G. Bouvignies, D. M. Korzhnev, P. Neudecker, D. F. Hansen, M. H. J. Cordes & L. E. Kay:
    A simple method for measuring signs of 1HN chemical shift differences between ground and excited protein states
    J. Biomol. NMR 47, 135-141 (2010)

  27. L. Cardarelli, L. G. Pell, P. Neudecker, N. Pirani, A. Liu, L. A. Baker, J. L. Rubinstein, K. L. Maxwell & A. R. Davidson:
    Phage have adapted the same protein fold to fulfill multiple functions in virion assembly
    Proc. Natl. Acad. Sci. (USA) 107, 14384-14389 (2010)
    (track II - direct submission to the editorial office)

  28. L. G. Pell, G. M. C. Gasmi-Seabrook, M. Morais, P. Neudecker, V. Kanelis, D. Bona, L. W. Donaldson, A. M. Edwards, P. L. Howell, A. R. Davidson & K. L. Maxwell:
    The Solution Structure of the C-terminal Ig-like Domain of the Bacteriophage Lambda Tail Tube Protein
    J. Mol. Biol. 403, 468-479 (2010)

  29. This week in Science Apr. 20, 2012 P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundström, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo & L. E. Kay:
    Structure of an Intermediate State in Protein Folding and Aggregation
    Science 336, 362-366 (2012)

    Protein Tipping Point: Amyloid fibrils are insoluble protein aggregates that play a role in various degenerative diseases. Recent experiments have provided insight into fibrillar structures; however, the mechanisms of aggregation remain unclear. Neudecker et al. (p. 362; see the Perspective by Eliezer) report the structure of a transient folding intermediate in a protein SH3 domain known to undergo aggregation. The intermediate is stabilized by non-native interactions and exposes an aggregation-prone β strand. Thus, for this protein, folding from the intermediate state will compete with aggregation.

    Perspective: Visualizing Amyloid Assembly by D. Eliezer
    Science 336, 308-309 (2012)

    Faculty of 1000 evaluation

  30. R. Bobby, K. Medini, P. Neudecker, T. V. Lee, M. A. Brimble, F. J. McDonald, J. S. Lott & A. J. Dingley:
    Structure and dynamics of human Nedd4-1 WW3 in complex with the αENaC PY motif
    Biochim. Biophys. Acta 1834, 1632-1641 (2013)

Review articles in peer-reviewed journals

  1. P. Neudecker, P. Lundström & L. E. Kay:
    Relaxation Dispersion NMR Spectroscopy as a Tool for Detailed Studies of Protein Folding
    Biophys. J. 96, 2045-2054 (2009)

  2. A. Zarrine-Afsar, S. L. Lin & P. Neudecker:
    Mutational investigation of protein folding transition states by Φ-value analysis and beyond: Lessons from SH3 domain folding
    Biochem. Cell Biol. 88, 231-238 (2010)

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Conference Contributions and Seminar Presentations


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Last Update: October 14th, 2010
© 2003-2010 Philipp Neudecker
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