Lecture Series:

�Electron microscopy of amyloid fibrils and spontaneous generation of anchorless prions�

Summary:
To investigate the role of the glycosylphosphatidyl inositol (GPI) anchor on the folding landscape of the cellular prion protein (PrP^C) in vivo, we established transgenic mice expressing PrP lacking the GPI signal sequence (PrP-ΔGPI).Mice expressing PrP-ΔGPI at ~2✕ the level of PrPC in wild-type (wt) mice developed late-onset, spontaneous neurological illness accompanied by the deposition of large amounts of amyloids throughout the brain. Proteinase K treatment of brain tissue revealed the presence of an unusual, 10 kDa proteinase K-resistant PrP fragment. This 10 kDa PK resistant fragment is an N- and C-terminal truncated product of the full length PrP as shown by western blotting using antibodies directed against different PrP epitopes. Purification using a combination of Phosphotungsten acid (PTA) and Proteinase K showed clearly the presence of amyloid fibrils in electron microscopy studies. Serial passage in mice expressing anchorless PrP of these amyloids led to the discovery that this spontaneously formed amyloid can transmit to mice expressing anchorless PrP accelerating the course of the amyloidosis from ~600 d to ~250 days. In 70% of our transmission attempts we were able to induce a prion disease in mice expressing anchored full length PrP with the appearance of PK resistant fragments of prototypical prion strains in addition to a novel amyloidogenic strain. Both strains have a significant different molecular structure which correlates with a novel disease phenotype. Therefore we conclude that at least two different propagating prion structures can be found in animals with this spontaneous disease. Our findings shows for the first time that PrP detached from the cell membrane spontaneously forms a variety of β-sheet rich infectious prions and that correct GPI anchoring stabilizes the α-helix dominated structure of PrP^C.

Speaker:
Dr. Jan Stöhr, University of California, San Francisco, USA

Time and Location:
Monday, July 4^th, 5p.m., s.t.
Location: Lecture hall 6D

Inviting BioStruct Group:
Birkmann Group

Lecture Series:

�Structure and ligand recognition of riboswitches and ribosome assembly factors�

Summary:
to be announced

Speaker:
Prof. Dr. Jens Wöhnert, Goethe University Frankfurt

Time and Location:
Tuesday, January 11^th, 5p.m., s.t.
Location: HS 6A

Inviting BioStruct Group:
Willbold Group

Lecture Series:

�Insights into the activation pathway of the adenovirus protease enzyme: Large scale nudged elastic band simulations using AMBER�

Summary:
The adenovirus proteinase (AVP) is essential for adenovirus replication and hence is a target for antiviral drugs aimed at treating infections such as bird-flu and SARS. The enzyme is activated upon the binding of a small peptide via a 53 amino acid signal transduction pathway. Recently obtained crystal structures of both the inactive and active forms of AVP provide the two end points of this pathway. This talk will highlight attempts, in combination with experimentalists at Brookhaven National Laboratory, to characterize this pathway. This includes a combination of standard molecular dynamics simulations, replica exchange simulations and a complete characterization of the structural motions involved in the activation pathway using a simulating annealing based Nudged Elastic Band (NEB) algorithm that is implemented within the AMBER software. Simulations to date, carried out on NSF supercomputers, have revealed some interesting features of this pathway and it is hoped that this insight, coupled with experimental feedback, will provide valuable data that can aid in identifying novel drug targets other than the active site and in finding drugs that prevent the utilization of the pathway.

Speaker:
Prof. Ross Walker, PhD, San Diego Supercomputer Center, University of California, San Diego

Time and Location:
Monday, April 26^th, 5p.m., s.t.
Location: HS 6B

Inviting BioStruct Group:
Gohlke Group

Lecture Series:

Electron microscopy applied to membrane protein complexes

Summary:
Transmission electron microscopy (EM) can be used in various ways to study protein structures. One way is single particles averaging. Projections arising from randomly oriented single molecules can be aligned, sorted and subsequently averaged. With semi-automated data collection it is now possible to analyze sets of about half a million particles. We have applied this method to study supercomplexes from plant photosynthetic membranes and mitochondria. Another application is electron tomography (ET). Cryo-ET is an emerging EM technique for reconstructing 3D volumes by incremental tilting and imaging a specimen in discrete steps over a relatively large range of angles around a tilt axis under cryogenic conditions. In a reconstruction of an organelle like the mitochondrion the larger protein complexes are detectable and sub-volumes can be selected and averaged. The fine structure of intact, close-to spherical mitochondria from the alga Polytomella was visualized by dual-axis cryo-ET. The supramolecular organization of dimeric ATP synthase in the cristae membranes was investigated by averaging sub-volumes of tomograms and 3D details at ~ 6 nm resolution were revealed.

Speaker:
Prof. Egbert J. Boekema, University of Groningen

Time and Location:
Tuesday, January 19^th, 5p.m., c.t.
Location: HS 6A

Inviting BioStruct Group:
Groth Group

Symposium:

Structural biology of amyloidogenic proteins

Program and Speakers::
01:15 p.m.:     �Structure-activity relationship of amyloids�
                         Prof. Dr. Roland Riek, Biological Nuclear Magnetic Resonance Group,                          Laboratory of Physical Chemistry, ETH Zürich, Switzerland

02:00 p.m.:     �Full-length alpha synuclein and its mutants �a solid-state NMR view�
                         Prof. Dr. Henrike Heise, Institut for Physical Biology, Heinrich-Heine-University                          Düsseldorf, Germany

02:45 p.m.:     Coffee break

03:15 p.m.:    �Prions: What do we know about the structure of the infectious prion                           protein?�
                          Prof. Dr. Holger Wille, Institute for Neurodegenerative Diseases, University of                           California, San Francisco, USA

04:00 p.m.:      �Studies on the structure of the mammalian prion, PrP^Sc�
                          Prof. Dr. Jesus Requena, Prion Research Unit, Department of Microbiology,                           School of Medicine, Universidade de Santiago de Compostela, Santiago,                           Spain

05:00 p.m.:      End of the BioStruct mini symposium

Time and Location:
Monday, November 30^th, 1p.m. - 5p.m
Location: Building 26.11, level O0, Lecture hall 6A,

Inviting BioStruct Group:
AG Dr. Eva Birkmann
AG Prof. Dr. Carsten Korth

For further information please contact:
Dr. Eva Birkmann:
Prof. Dr. Carsten Korth:
BioStruct:

Lecture Series:

Activation in 3D: the Domain Architecture of a Glutamate Receptor

Summary:
Crystallographic studies of glutamate receptor ligand-binding domains have focused attention on the functional importance of an agonist-associated cleft closure in triggering channel activation and in regulating relative agonist efficacy. However, recent studies suggest that additional factors are important as well, including the stability of the closed-cleft state and the precise orientation of the axis of rotation. In all cases, it has appeared that the mechanism of channel activation involves the extent, direction, and stability of separation between transmembrane attachment points within subunit dimer pairs. However, the domain architecture of AMPA receptors has not been clearly defined, preventing analysis of interactions between dimer pairs and with the transmembrane domains. Here, we present the single-particle electron microscopic analysis of recombinant AMPA-Rs, alone and with domain-specific fusion tags, permitting a first look at the domain architecture and subunit packing interactions in this ligand-gated ion channel. Our model suggests the importance of rotation as well as separation in channel activation and has implications for the mechanism of subunit assembly.

Speaker:
Prof. Dean Madden, Dartmouth College, Hanover, USA

Time and Location:
Monday, November 16^nd, 6 p.m., c.t.
Location: HS 6A

Inviting BioStruct Group:
Schmitt Group

Lecture Series:

Protein Flexibility, Pathways and Folding

Summary:
Many interesting phenomena occur in material structures that are poised between rigid and flexible. In this talk, we describe the modern theory of rigidity and show how it can be used to analyze networks of constraints. These results can be used as input to geometrical simulation, where the various rigid parts of a system are moved, while maintaining the local stereochemistry. These approaches have been tuned to proteins to determine pathways and to fold proteins de novo. Results are compared with experiments and with molecular dynamics simulations.

Speaker:
Prof. Mike Thorpe, Imperial College, London and Arizona State University, Tempe

Time and Location:
Monday, November 2^nd, 5p.m., c.t.
Location: to be announced

Inviting BioStruct Group:
Gohlke Group

Lecture Series:

Transport and regulation in the trimeric Na⁺-coupled betaine symporter BetP

Summary:
The Na⁺-coupled symporter BetP, a member of the Betaine-Choline-Carnitine-Transporter (BCCT) family catalyzes uptake of the osmolyte betaine in Corynebacterium glutamicum. BetP also senses hyperosmotic stress and regulates its own activity according to the stress level. The X-ray structure to 3.35Å reveals a trimeric architecture of BetP and a break in three-fold non crystallographic symmetry by the osmosensing C-terminal helices. BetP has the same overall fold as four other unrelated Na⁺-coupled symporters, but the BetP structure shows a unique intermediate conformation in the Na⁺-coupled transport cycle. Betaine is bound in a tryptophan box occluded from both sides of the membrane with aromatic side chains lining the transport pathway. A three-dimensional map at 8Å resolution of BetP in a membrane environment was determined by electron cryo-microscopy of 2D crystals. BetP is an asymmetric homotrimer in the membrane in which each monomer adopts a distinct conformation. Fitting of the X-ray structure of BetP to the map allowed assignment of transmembrane helices and reveal differences in monomer-monomer interaction. Flexible fitting of helices lining the substrate pathway gave different conformations of BetP for each monomer map, which we assign to distinct states in an alternating-access cycle of transport. The presence of asymmetry in the trimer suggests a mechanism of conformational coupling between monomers during transport.

Speaker:
Dr. Christine Ziegler, Max Planck Institute for Biophysics, Frankfurt am Main, Germany

Time and Location:
Monday, October 19^th, 5p.m.
Location: Building 26.32.03

Inviting BioStruct Group:
Schmitt Group

Lecture Series:

Protein regulation at a distance: allostery, phosphorylation, and pH

Summary:
Protein activity can be regulated by several different mechanisms including posttranslational modification and ligand binding. In many cases, the regulation can be described as allosteric in that the regulatory site is distant from the functional site being regulated. I will describe my group's efforts to understand mechanisms of such "regulation at a distance" using atomistic computational models. Examples will include: myosin regulation by post-translational phosphorylation; the regulation of talin-actin interactions by changes in cytoplasmic pH; and interactions between small-molecule binding sites in interleukin-2.

Speaker:
Matthew P. Jacobson, PhD, Associate Professor and Vice Chair, Department of Pharmaceutical Chemistry, University of California, San Francisco

Time and Location:
Thursday, June 25^th, 5p.m., c.t.
Lecture room: 6A

Inviting BioStruct Group:
Gohlke Group

Lecture Series:

Markov models for understanding folding, binding and conformational changes from MD and single molecule experiments:

Summary:
Markov models capturing the metastable dynamics of macromolecules can be built from both MD simulations and single molecule experiments. Here we present methods for the construction and validation of such Markov models and for the computation of observables of interest from them. In particular, we will focus on the ensemble of transition pathways for folding.

Speaker:
Dr. Frank Noe, Computational Molecular Biology, DFG Research Center Matheon, Freie Universität Berlin, Germany

Time and Location:
Friday, June 19^th, 2p.m.
Building 26.32, level O3, room 11

Inviting BioStruct Group:
AG Seidel