Structural
Biology /
Bioinformatics Journal Club
of the
Görlach,
Sühnel
and Than
Labs
at the Leibniz
Institute for Age
Research - Fritz Lipmann Institute
Guests are welcome
Thursday, April 17, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Christoph Wiedemann (FLI; Görlach Lab)
Bellucci JJ, Amiram M, Bhattacharyya J, McCafferty D, Chilkoti A.
Three-in-One
Chromatography-Free Purification, Tag Removal, and Site-Specific
Modification of Recombinant Fusion Proteins Using Sortase A and
Elastin-like Polypeptides.
Angew Chem Int Ed Engl. 2013;52(13):3703-8. [PDF]
Sorting it out: Applied in tandem, elastin-like polypeptides (ELPs, see scheme) and the Sortase A (SrtA) transpeptidase provide a method for chromatography-free purification of recombinant proteins and optional, site-specific conjugation of the protein to a small molecule (yellow). This system provides an efficient mechanism for generating bioactive proteins at high yields and purities.
Thursday, March 28, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Torsten Thalheim (FLI; Sühnel Lab)
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Nature. 2013;494(7435):77-80. [PDF]
Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.
Thursday, March 14, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
NMR Coffee Room
Presenter: Sven Dahms (FLI; Than Lab)
Redecke L et al.,
Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.
Science. 201311;339(6116):227-30. [Paper | Supplementary Materials]
The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
Thursday, February 28, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Ramadurai Ramachandran (FLI; Görlach Lab)
Marchetti A, Jehle S, Felletti M, Knight MJ, Wang Y, Xu ZQ, Park AY, Otting G, Lesage A, Emsley L, Dixon NE, Pintacuda G.
Backbone assignment of fully protonated solid proteins by 1H detection and ultrafast magic-angle-spinning NMR spectroscopy.
Angew Chem Int Ed Engl. 2012;51(43):10756-9.[PDF]
No abstract available.
Thursday, February 14, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Oliver Ohlenschläger (FLI; Görlach Lab)
Woo JS, Zeltina A, Goetz BA, Locher KP.
X-ray structure of the Yersinia pestis heme transporter HmuUV.
Nat Struct Mol Biol. 2012;19(12):1310-5. [PDF]
HmuUV is a
bacterial ATP-binding cassette (ABC) transporter that catalyzes heme
uptake into the cytoplasm of the gram-negative pathogen Yersinia
pestis. We report the crystal structure of HmuUV at 3.0 Ċ resolution in a nucleotide-free state, which features a heme translocation pathway in an outward-facing conformation, poised to accept a heme from the cognate periplasmic binding protein HmuT. A new assay allowed us to determine in vitro rates of HmuUV-catalyzed heme transport into proteoliposomes and to establish the role of conserved residues in the translocation pathway of HmuUV and at the interface with HmuT. Differences in architecture relative to the related vitamin B(12) transporter BtuCD suggest an adaptation of HmuUV for its smaller substrate. Our study also suggests that type II ABC importers, which include bacterial iron-siderophore, heme and cobalamin transporters, have a coupling mechanism distinct from that of other ABC transporters.
Thursday, January 31, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Ina Coburger (FLI; Than Lab)
Kurouski D, Deckert-Gaudig T, Deckert V, Lednev IK.
Structure and composition of insulin fibril surfaces probed by TERS.
J Am Chem Soc. 2012;134(32):13323-9. [PDF]
Amyloid fibrils
associated with many neurodegenerative diseases are the most intriguing
targets of modern structural biology. Significant knowledge has been
accumulated about the morphology and fibril-core structure recently.
However, no conventional methods could probe the fibril surface despite
its significant role in the biological activity. Tip-enhanced Raman
spectroscopy (TERS) offers a unique opportunity to characterize the
surface structure of an individual fibril due to a high depth and
lateral spatial resolution of the method in the nanometer range.
Herein, TERS is utilized for characterizing the secondary structure and
amino acid residue composition of the surface of insulin fibrils. It
was found that the surface is strongly heterogeneous and consists of
clusters with various protein conformations. More than 30% of the
fibril surface is dominated by β-sheet secondary structure, further
developing Dobson's model of amyloid fibrils (Jimenez et al. Proc.
Natl. Acad. Sci. U.S.A. 2002, 99, 9196-9201). The propensity of various
amino acids to be on the fibril surface and specific surface secondary
structure elements were evaluated. β-sheet areas are rich in cysteine
and aromatic amino acids, such as phenylalanine and tyrosine, whereas
proline was found only in α-helical and unordered protein clusters. In
addition, we showed that carboxyl, amino, and imino groups are nearly
equally distributed over β-sheet and α-helix/unordered regions.
Overall, this study provides valuable new information about the
structure and composition of the insulin fibril surface and
demonstrates the power of TERS for fibril characterization.
Thursday, January 17, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Rolf Huehne (FLI; Suehnel Lab)
Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE.
The RCSB Protein Data Bank: new resources for research and education.
Nucleic Acids Res. 2013 Jan 1;41(D1):D475-D482. [PDF]
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
Thursday, January 10, 2013, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Sandra Hoefgen (FLI; Than Lab)
Vallée-Bélisle A, Michnick SW.
Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis.
Nat Struct Mol Biol. 2012;19(7):731-6. [PDF]
To understand how proteins fold, assemble and function, it is necessary to characterize the structure and dynamics of each state they adopt during their lifetime. Experimental characterization of the transient states of proteins remains a major challenge because high-resolution structural techniques,including NMR and X-ray crystallography, cannot be directly applied to study short-lived protein states. To circumvent this limitation, we show that transient states during protein folding can be characterized by measuring the fluorescence of tryptophan residues, introduced at many solvent-exposed positions to determine whether each position is native-like, denatured-like or non-native-like in the intermediate state. We use this approach to characterize a late-folding-intermediate state of the small globular mammalian protein ubiquitin, and we show the presence of productive non-native interactions that suggest a 'flycatcher' mechanism of concerted binding and folding.
Thursday, December 13, 2012, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Steffen Kemmerzehl (FLI; Görlach Lab)
Yang ZY, Moure VR, Dean DR, Seefeldt LC.
Carbon dioxide reduction to methane and coupling with acetylene to form propylene catalyzed by remodeled nitrogenase.
Proc Natl Acad Sci U S A. 2012;109(48):19644-8. [PDF]
A doubly substituted form of the nitrogenase MoFe protein (α-70(Val)(→Ala),α-195(His→Gln)) has the capacity to catalyze the reduction of carbon dioxide (CO(2)) to yield methane (CH(4)). Under optimized conditions, 1 nmol of the substituted MoFe protein catalyzes the formation of 21 nmol of CH(4) within 20
min. The catalytic rate depends on the partial pressure of CO(2) (or concentration of HCO(3)(-)) and the electron flux through nitrogenase. The doubly substituted MoFe protein also has the capacity to catalyze the unprecedented formation of propylene (H(2)C = CH-CH(3)) through the reductive coupling of CO(2)
and acetylene (HC≡CH). In light of these observations, we suggest that an emerging understanding of the mechanistic features of nitrogenase could be relevant to the design of synthetic catalysts for CO(2) sequestration and formation of olefins.
Thursday, December 6, 2012, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Peter Bellstedt (FLI; Görlach Lab)
Bonnet J, Subsoontorn P, Endy D.
Rewritable digital data storage in live cells via engineered control of recombination directionality.
Proc Natl Acad Sci U S A. 2012;109(23):8884-9.[PDF]
The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems.
Thursday, November 15, 2012, 11:00
Leibniz Institute for Age Research - Fritz Lipmann Institute
Beutenbergstr. 11, D-07745 Jena
Villa
Presenter: Nishit Bharat Goradia (FLI; Görlach Lab)
Itkin A, Dupres V, Dufrêne YF, Bechinger B, Ruysschaert JM, Raussens V.
Calcium ions promote formation of amyloid β-peptide (1-40) oligomers causally implicated in neuronal toxicity of Alzheimer's disease.
PLoS One. 2011;6(3):e18250. [PDF]
Amyloid
β-peptide (A