B6: Structural elucidation of the GPCR allosteric machine

We apply complementary in silico and in vitro structural biology methods to obtain insights into the dynamic modulation of G protein coupled receptors by ligands or signal transducers. To address the key question of G protein coupling specificity we investigate the role of the open cytoplasmic crevice of the human β2-adrenoceptor or bovine rhodopsin in selective binding of Gi, Gs or arrestins. We use native and mutant peptides derived from the key binding sites of the Gα subunit (GαCT) or arrestin (finger loop, ArrFL) to elucidate their role in the selective (on/off) switching of downstream signaling pathways. Our long term goal is to obtain high affinity variants of GαCT and ArrFL, enabling modelling, MD simulations and protein X-ray crystallography of complexes of R* with Gi or arrestin.

Selected Publications

Ismer J, Rose AS, Tiemann JK, Goede A, Preissner R, Hildebrand PW
SL2: an interactive webtool for modeling of missing segments in proteins.
Nucleic Acids Res 2016; :pii: gkw297. [Epub ahead of print].
Müller A, Berkmann JC, Scheerer P, Biebermann H, Kleinau G
Insights into Basal Signaling Regulation, Oligomerization, and Structural Organization of the Human G-Protein Coupled Receptor 83.
PLoS One 2016; 11(12):e0168260. doi: 10.1371/journal.pone.0168260. eCollection 2016.
Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P.
Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.
Angew Chem Int Ed Engl 2016; 55(18):5586-90. doi: 10.1002/anie.201508976. Epub 2016 Feb 23.
Sprink T, Ramrath DJ, Yamamoto H, Yamamoto K, Loerke J, Ismer J, Hildebrand PW, Scheerer P, Bürger J, Mielke T, Spahn CM
Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.
Sci Adv 2016; 2(3):e1501502. doi: 10.1126/sciadv.1501502. eCollection 2016.
Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Bürger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CM
Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA.
EMBO J 2015; 34(24):3042-58. doi: 10.15252/embj.201592469..
Behrmann E, Loerke J, Budkevich TV, Yamamoto K, Schmidt A, Penczek PA, Vos MR, Bürger J, Mielke T, Scheerer P, Spahn CM
Structural snapshots of actively translating human ribosomes.
Cell 2015; 161(4):845-57.
Barucker C, Bittner HJ, Chang PK, Cameron S, Hancock MA, Liebsch F, Hossain S, Harmeier A, Shaw H, Charron FM, Gensler M, Dembny P, Zhuang W, Schmitz D, Rabe JP, Rao Y, Lurz R, Hildebrand PW, McKinney RA, Multhaup G
Aβ42-oligomer Interacting Peptide (AIP) neutralizes toxic amyloid-β42 species and protects synaptic structure and function.
Sci Rep 2015; 5:15410. doi: 10.1038/srep15410.
Brehm A, Liu Y, Sheikh A, Marrero B, Omoyinmi E, Zhou Q, Montealegre G, Biancotto A, Reinhardt A, Almeida de Jesus A, Pelletier M, Tsai WL, Remmers EF, Kardava L, Hill S, Kim H, Lachmann HJ, Megarbane A, Chae JJ, Brady J, Castillo RD, Brown D, Casano AV, Gao L, Chapelle D, Huang Y, Stone D, Chen Y, Sotzny F, Lee CC, Kastner DL, Torrelo A, Zlotogorski A, Moir S, Gadina M, McCoy P, Wesley R, Rother K, Hildebrand PW, Brogan P, Krüger E, Aksentijevich I, Goldbach-Mansky R
Additive loss-of-function proteasome subunit mutations in CANDLE/PRAAS patients promote type I IFN production.
J Clin Invest 2015; 26(2):795. doi: 10.1172/JCI86020. Epub 2016 Feb 1.
Oestereich F, Bittner HJ, Weise C, Grohmann L, Janke LK, Hildebrand PW, Multhaup G, Munter LM
Impact of amyloid precursor protein hydrophilic transmembrane residues on amyloid-beta generation.
Biochemistry 2015; 54(17):2777-84.
Rose AS, and Hildebrand PW
NGL Viewer: a web application for molecular visualization.
Nucleic Acids Res 2015; 43(W1):W576-W579.
Prade E., Bittner H.J., Sarkar R., Amo J.M.L., Althoff-Ospelt G., Hildebrand P.W. and Reif B
Structural mechanism of the interaction of Alzheimer’s disease Aβ fibrils with the NSAID sulindac sulfide.
JBC 2015; 290(48):28737-45. doi: 10.1074/jbc.M115.675215.
Rose AS, and Hildebrand PW
NGL Viewer: a web application for molecular visualization.
Nucleic Acids Res 2015; 43(W1):W576-W579.
Sommer ME, Elgeti M, Hildebrand PW, Szczepek M, Hofmann KP, Scheerer P
Structure-based biophysical analysis of the interaction of rhodopsin with g protein and arrestin.
Methods Enzymol 2015; 556:563-608.
Alexander S. Rose, Ulrich Zachariae, Helmut Grubmüller, Klaus Peter Hofmann, Patrick Scheerer, Peter W. Hildebrand
Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction.
PLoS One 2015; 10(11):e0143399. doi: 10.1371/journal.pone.0143399. eCollection 2015.
Kazmin R, Rose A, Szczepek M, Elgeti M, Ritter E, Piechnick R, Hofmann KP, Scheerer P, Hildebrand PW, Bartl FJ
The Activation Pathway of Human Rhodopsin in Comparison to Bovine Rhodopsin.
J Biol Chem 2015; 290(33):):20117-27. doi: 10.1074/jbc.M115.652172.
Szczepek M, Beyrière F, Hofmann KP, Elgeti M, Kazmin R, Rose A, Bartl FJ, von Stetten D, Heck M, Sommer ME, Hildebrand PW, Scheerer P
Crystal structure of a common GPCR-binding interface for G protein and arrestin.
Nat Commun 2014; 5(4801):doi: 10.1038/ncomms5801.
Budkevich, T, Giesebrecht, J, Ramrath, D, Mielke, T, Ismer J, Hildebrand, P, Tung, C-S, Nierhaus, KH, Sanbonmatsu, KY and Spahn, CM
Regulation of the Mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.
Cell 2014; 158(1):121-131.
Rose AS, Elgeti M, Zachariae U, Grubmüller H, Hofmann KP, Scheerer P, Hildebrand PW
Position of Transmembrane Helix 6 Determines Receptor G Protein Coupling Specificity.
J Am Chem Soc 2014; 136(32):11244-11247.
Elgeti M, Rose AS, Bartl FJ, Hildebrand PW, Hofmann KP, Heck M
Precision vs Flexibility in GPCR signaling.
J Am Chem Soc 2013; 21(135):12305-12.
Yong Ju Kim, Klaus Peter Hofmann, Oliver P. Ernst, Patrick Scheerer, Hui-Woog Choe & Martha E. Sommer
Crystal structure of pre-activated arrestin p44.
Nature 2013; 497(7447):142-6.
Ismer, J., Rose, A., Goede, A., Johanna K. S. Tiemann, Rother, K. and Hildebrand, P.W.
Voronoia4RNA – A database of atomic packing densities of RNA structures and their complexes.
Nucleic Acids Res 2013; 41:D280-4. doi: 10.1093/nar/gks1061.
Ramrath D, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, Loerke J, Scheerer P, Ivanov P, Teraoka Y, Shpanchenko O, Nierhaus K, Spahn CM
The complex of tmRNA-SmpB and EF‐G on translocating ribosomes.
Nature 2012; 485(7399):526-9.
Kaden,D., Harmeier,A., Weise,C., Munter,L.M., Althoff,V., Rost,B.R., Hildebrand,P.W., Schmitz,D., Schaefer,M., Lurz,R., et al.
Novel APP/Aβ mutation K16N produces highly toxic heteromeric Aβ oligomers.
EMBO Mol Med 2012; 7:647-59.
Piechnick, R., Ritter, E., Hildebrand, P.W., Ernst, O.P., Scheerer, P., Hofmann, K. and Heck, M.
Effect of channel mutations on the uptake and release of the retinal ligand in opsin.
Proc Natl Acad Sci U S A 2012; 109(14):5247-52.
Botev A, Munter LM, Wenzel R, Richter L, Althoff V, Ismer J, Gerling U, Weise C, Koksch B, Hildebrand PW, Bittl R, Multhaup G
The Amyloid Precursor Protein C-Terminal Fragment C100 Occurs in Monomeric and Dimeric Stable Conformations and Binds gamma-Secretase Modulators.
Biochemistry 2011; 50:828-835.
Fritsch J, Scheerer P, Frielingsdorf S, Kroschinsky S, Friedrich B, Lenz O, Spahn CM
The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre.
Nature 2011; 479(7372):249-52.
Elgeti M, Kazmin R, Heck M, Morizumi T, Ritter E, Scheerer P, Ernst OP, Siebert F, Hofmann KP, Bartl FJ
Conserved Tyr223(5.58) plays different roles in the activation and G-protein interaction of rhodopsin.
J Am Chem Soc 2011; 133(18):7159-65.
Muhs M, Yamamoto H, Ismer J, Takaku H, Nashimoto M, Uchiumi T, Nakashima N, Mielke T, Hildebrand PW, Nierhaus KH, Spahn CM
Structural basis for the binding of IRES RNAs to the head of the ribosomal 40S subunit. Nucleic Acids Res..
Nucleid Acids Research 2011; 39(12):5264-75.
Hui-Woog Choe, Yong Ju Kim, Jung Hee Park, Takefumi Morizumi, Emil F. Pai, Norbert Krauß, Klaus Peter Hofmann, Patrick Scheerer & Oliver P. Ernst
Crystal structure of metarhodopsin II.
Nature 2011 Mar 9; 471(7340):651-5.