University of Toronto NMR Centre

University of Toronto
NMR Centre

Philipp Neudecker

Postdoctoral Fellow

Contact:

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Phone:              +1 416 978 0642
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Fax:                +1 416 978 6885
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E-Mail:             philipp@pound.med.utoronto.ca

Office and          University of Toronto
Mailing Address:    Department of Medical Genetics and Microbiology
		    NMR Centre, Medical Sciences Building, Room 1233
                    1 King's College Circle
                    Toronto, ON, M5S 1A8
                    Canada

Research Interests

NMR Relaxation Dispersion Experiments for the Study of Protein Dynamics for Folding and Function
NMR Structural Biology of Allergens

Gallery of Structures

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

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

Human proguanylin, 30 conformers (PDB 1O8R)

Theses

P. Neudecker:
Strukturbestimmung von Pru a 1
Diploma Thesis, Universität Bayreuth, Bayreuth (2000)
P. Neudecker:
Strukturbestimmung von Birkenpollenallergenen und birkenpollenassoziierten Nahrungsmittelallergenen mit NMR-Spektroskopie
Doctoral Thesis, Universität Bayreuth, Bayreuth (2003)

Publications

Original articles in peer-reviewed journals

(selected publications highlighted by larger font size)

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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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.
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
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)
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
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)
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)
R. Auer, P. Neudecker, D. R. Muhandiram, P. Lundström, D. F. Hansen, R. Konrat & L. E. Kay:
Measuring the Signs of ¹H^α Chemical Shift Differences Between Ground and Excited Protein States by Off-Resonance Spin-Lock R_1ρ NMR Spectroscopy
J. Am. Chem. Soc. 131, 10832-10833 (2009)
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_1ρ methods
J. Biomol. NMR, in press (2009)
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)

Review articles in peer-reviewed journals

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)
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., in press (2009)

Search PubMed for publications and abstracts

Conference Contributions and Scientific Talks

Last Update: December 14th, 2008
© 2003-2008 Philipp Neudecker
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