Structural Biology / Bioinformatics Journal Club

Görlach, Sühnel and Than Labs

Leibniz Institute for Age Research - Fritz Lipmann Institute


Guests are welcome


Thursday, April 4, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Christoph Wiedemann (FLI, Goerlach Lab)

Xu G, Ye Y, Liu X, Cao S, Wu Q, Cheng K, Liu M, Pielak GJ, Li C.
Strategies for Protein NMR in Escherichia coli.
Biochemistry 2014;53(12):1971-81. [PubMed] [PDF]

Abstract: In-cell NMR spectroscopy provides insight into protein conformation, dynamics, and function at atomic resolution in living cells. Systematic evaluation of isotopic-labeling strategies is necessary to observe the target protein in the sea of other molecules in the cell. Here, we investigate the detectability, sensitivity, and resolution of in-cell NMR spectra of the globular proteins GB1, ubiquitin, calmodulin, and bcl-xl-cutloop, resulting from uniform (15)N enrichment (with and without deuteration), selective (15)N-Leu enrichment, (13)C-methyl enrichment of isoleucine, leucine, valine, and alanine, fractional (13)C enrichment, and (19)F labeling. Most of the target proteins can be observed by (19)F labeling and (13)C enrichment with direct detection because selectively labeling suppresses background signals and because deuteration improves in-cell spectra. Our results demonstrate that the detectability of proteins is determined by weak interactions with intercellular components and that choosing appropriate labeling strategies is critical for the success of in-cell protein NMR studies..



Thursday, March 27, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Bharat Goradia (FLI, Goerlach Lab)

Lin MH, Chang YC, Hsiao CD, Huang SH, Wang MS, Ko YC, Yang CW, Sun YJ.
LipL41, a hemin binding protein from Leptospira santarosai serovar Shermani.
PLoS One. 2013 ;8(12): e83246 [PubMed] [PDF]

Abstract: Leptospirosis is one of the most widespread zoonotic diseases in the world. It is caused by the pathogen Leptospira that results in multiple-organ failure, in particular of the kidney. Outer membrane lipoprotein is the suspected virulence factor of Leptospira. In Leptospira spp LipL41 is one major lipoprotein and is highly conserved. Previous study suggests that LipL41 bears hemin-binding ability and might play a possible role in iron regulation and storage. However, the characterization of hemin-binding ability of LipL41 is still unclear. Here the hemin-binding ability of LipL41 was examined, yielding a K d = 0.59 ± 0.14 ~M. Two possible heme regulatory motifs (HRMs), C[P/S], were found in LipL41 at (140)Cys-Ser and (220)Cys-Pro. The mutation study indicates that Cys140 and Cys220 might be cooperatively involved in hemin binding. A supramolecular assembly of LipL41 was determined by transmission electron microscopy. The LipL41 oligomer consists of 36 molecules and folds as a double-layered particle. At the C-terminus of LipL41, there are two tetratricopeptide repeats (TPRs), which might be involved in the protein-protein interaction of the supramolecular assembly.



Thursday, March 20, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Juergen Suehnel (FLI, Suehnel Lab)

Kosciolek T, Jones DT.
De novo structure prediction of globular proteins aided by sequence variation-derived contacts.
PLoS One. 2014 9(3): e92197 [PubMed] [PDF]

Abstract: The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm - FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical potentials or contacts alone. Results show up to nearly 80% of correct predictions (TM-score ~0.5) within analysed dataset and a mean TM-score of 0.54. Unsuccessful modelling cases emerged either from conformational sampling problems, or insufficient contact prediction accuracy. Nevertheless, a strong dependency of the quality of final models on the fraction of satisfied predicted long-range contacts was observed. This not only highlights the importance of these contacts on determining the protein fold, but also (combined with other ensemble-derived qualities) provides a powerful guide as to the choice of correct models and the global quality of the selected model. A proposed quality assessment scoring function achieves 0.93 precision and 0.77 recall for the discrimination of correct folds on our dataset of decoys. These findings suggest the approach is well-suited for blind predictions on a variety of globular proteins of unknown 3D structure, provided that enough homologous sequences are available to construct a large and accurate multiple sequence alignment for the initial contact prediction step.



Thursday, March 13, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Manual Than (FLI, Than Lab)

Song Y, Mittendorf KF, Lu Z, Sanders CR.
Impact of Bilayer Lipid Composition on the Structure and Topology of the Transmembrane Amyloid Precursor C99 Protein.
J Am Chem Soc. 2014 Mar 11. [Epub ahead of print]
[PubMed] [PDF]

Abstract: C99 (also known as beta-CTF) is the 99 residue transmembrane C-terminal domain (residues 672-770) of the amyloid precursor protein and is the immediate precursor of the amyloid-beta (Abeta) polypeptides. To test the dependence of the C99 structure on the composition of the host model membranes, NMR studies of C99 were conducted both in anionic lyso-myristoylphosphatidylglycerol (LMPG) micelles and in a series of five zwitterionic bicelle compositions involving phosphatidylcholine and sphingomyelin in which the acyl chain lengths of these lipid components varied from 14 to 24 carbons. Some of these mixtures are reported for the first time in this work and should be of broad utility in membrane protein research. The site-specific backbone (15)N and (1)H chemical shifts for C99 in LMPG and in all five bicelle mixtures were seen to be remarkably similar, indicating little dependence of the backbone structure of C99 on the composition of the host model membrane. However, the length of the transmembrane span was seen to vary in a manner that alters the positioning of the ~-secretase cleavage sites with respect to the center of the bilayer. This observation may contribute to the known dependency of the Abeta42-to-Abeta40 production ratio on both membrane thickness and the length of the C99 transmembrane domain.

Barrett PJ, Song Y, Van Horn WD, Hustedt EJ, Schafer JM, Hadziselimovic A, Beel AJ, Sanders CR.
The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol.
Science. 2012; 336(6805:1168-71.
[PubMed] [PDF]



Kosciolek T, Jones DT.
Impact of Bilayer Lipid Composition on the Structure and Topology of the Transmembrane Amyloid Precursor C99 Protein.
J Am Chem Soc. 2014 Mar 11. [Epub ahead of print]
[PubMed] [PDF]

Abstract: C99 (also known as beta-CTF) is the 99 residue transmembrane C-terminal domain (residues 672-770) of the amyloid precursor protein and is the immediate precursor of the amyloid-beta (Abeta) polypeptides. To test the dependence of the C99 structure on the composition of the host model membranes, NMR studies of C99 were conducted both in anionic lyso-myristoylphosphatidylglycerol (LMPG) micelles and in a series of five zwitterionic bicelle compositions involving phosphatidylcholine and sphingomyelin in which the acyl chain lengths of these lipid components varied from 14 to 24 carbons. Some of these mixtures are reported for the first time in this work and should be of broad utility in membrane protein research. The site-specific backbone (15)N and (1)H chemical shifts for C99 in LMPG and in all five bicelle mixtures were seen to be remarkably similar, indicating little dependence of the backbone structure of C99 on the composition of the host model membrane. However, the length of the transmembrane span was seen to vary in a manner that alters the positioning of the ~-secretase cleavage sites with respect to the center of the bilayer. This observation may contribute to the known dependency of the Abeta42-to-Abeta40 production ratio on both membrane thickness and the length of the C99 transmembrane domain.

Barrett PJ, Song Y, Van Horn WD, Hustedt EJ, Schafer JM, Hadziselimovic A, Beel AJ, Sanders CR.
The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol.
Science. 2012; 336(6805:1168-71.
[PubMed] [PDF]



Thursday, March 6, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Torsten Thalheim (FLI, Suehnel Lab)

Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D.
A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
Drug Discov Today. 2013;S1359-6446(13)00391-7
[PubMed] [PDF]

Abstract: In the Semantic Enrichment of the Scientific Literature (SESL) project, researchers from academia and from life science and publishing companies collaborated in a pre-competitive way to integrate and share information for type 2 diabetes mellitus (T2DM) in adults. This case study exposes benefits from semantic interoperability after integrating the scientific literature with biomedical data resources, such as UniProt Knowledgebase (UniProtKB) and the Gene Expression Atlas (GXA). We annotated scientific documents in a standardized way, by applying public terminological resources for diseases and proteins, and other text-mining approaches. Eventually, we compared the genetic causes of T2DM across the data resources to demonstrate the benefits from the SESL triple store. Our solution enables publishers to distribute their content with little overhead into remote data infrastructures, such as into any Virtual Knowledge Broker.



Thursday, February 27, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Ramadurai Ramachandran (FLI, Goerlach Lab)

Vajpai N, Nisius L, Wiktor M, Grzesiek S.
High-pressure NMR reveals close similarity between cold and alcohol protein denaturation in ubiquitin.
Proc Natl Acad Sci U S A. 2013;110(5):E368-76.
[PubMed] [PDF]

Abstract: Proteins denature not only at high, but also at low temperature as well as high pressure. These denatured states are not easily accessible for experiment, because usually heat denaturation causes aggregation, whereas cold or pressure denaturation occurs at temperatures well below the freezing point of water or pressures above 5 kbar, respectively. Here we have obtained atomic details of the pressure-assisted, cold-denatured state of ubiquitin at 2,500 bar and 258 K by high-resolution NMR techniques. Under these conditions, a folded, native-like and a disordered state exist in slow exchange. Secondary chemical shifts show that the disordered state has structural propensities for a native-like N-terminal ~-hairpin and ~-helix and a nonnative C-terminal ~-helix. These propensities are very similar to the previously described alcohol-denatured (A-)state. Similar to the A-state, (15)N relaxation data indicate that the secondary structure elements move as independent segments. The close similarity of pressure-assisted, cold-denatured, and alcohol-denatured states with native and nonnative secondary elements supports a hierarchical mechanism of folding and supports the notion that similar to alcohol, pressure and cold reduce the hydrophobic effect. Indeed, at nondenaturing concentrations of methanol, a complete transition from the native to the A-state can be achieved at ambient temperature by varying the pressure from 1 to 2,500 bar. The methanol-assisted pressure transition is completely reversible and can also be induced in protein G. This method should allow highly detailed studies of protein-folding transitions in a continuous and reversible manner.



Thursday, January 30, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Rolf Huehne (FLI, Suehnel Lab)

Fernández-Suárez XM, Rigden DJ, Galperin MY.
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.
Nucleic Acids Res. 2014; 42(1):D1-6.
[PubMed] [PDF]

Abstract: The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).



Thursday, January 16, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Sven Dahms (FLI, Than Lab)

Redecke et al.
Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.
Science 2013; 339(6116):146-7.
[PubMed] [PDF] [Supplementary Materials, PDF]

Abstract: 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, January 09, 2014, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Peter Bellstedt (FLI, Görlach Lab)

Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS.
Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.
Nature 2013; Ahead of print.
[PubMed] [PDF]

Abstract: Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions. Aprataxin (APTX) reverses DNA adenylation but the context for deadenylation repair is unclear. Here we examine the importance of APTX to RNase-H2-dependent excision repair (RER) of a lesion that is very frequently introduced into DNA, a ribonucleotide. We show that ligases generate adenylated 5' ends containing a ribose characteristic of RNase H2 incision. APTX efficiently repairs adenylated RNA-DNA, and acting in an RNA-DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint activation in budding yeast undergoing RER. Structure-function studies of human APTX-RNA-DNA-AMP-Zn complexes define a mechanism for detecting and reversing adenylation at RNA-DNA junctions. This involves A-form RNA binding, proper protein folding and conformational changes, all of which are affected by heritable APTX mutations in ataxia with oculomotor apraxia 1. Together, these results indicate that accumulation of adenylated RNA-DNA may contribute to neurological disease.



Thursday, November 28, 2013, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Nishit Bharat Goradia (FLI, Görlach Lab)

Mukherjee S, Dey SG.
Heme bound amylin: spectroscopic characterization, reactivity, and relevance to type 2 diabetes.
Inorg Chem. 2013;52(9):5226-35.
[PubMed] [PDF]

Abstract: Deposition of human amylin or islet amyloid polypeptide (hIAPP) within the beta-cells of the pancreatic islet of Langerhans is implicated in the etiology of type 2 diabetes mellitus (T2Dm). Accumulating evidences suggest that increased body iron stores, iron overload, and, in particular, higher heme-iron intake is significantly associated with higher risk of Type 2 diabetes mellitus (T2Dm)(PloS One2012, 7, e41641). Some key pathological features of T2Dm, like iron dyshomeostasis, iron accumulation, mitochondrial dysfunction, and oxidative stress are very similar to the cytopathologies of Alzheimer's disease, which have been invoked to be due to heme complexation with amyloid beta-peptides. The similar etiology and pathogenic features in both Alzheimer's disease(AD) and T2Dm indicate a common underlying mechanism, with heme playing an important role. In this study we show that hIAPP can bind heme. His18 residue of hIAPP binds heme under physiological conditions and results in an axial high-spin active site with a trans-axial water derived ligand. Arg11 is a key residue that is also essential for heme binding. Heme(Fe(2+))-hIAPP complexes are prone to produce partially reduced oxygen species (PROS). The His18 residue identified in this study is absent in rats which do not show T2Dm, implicating the significance of thiresidue as well as heme in the pathology of T2Dm.



Thursday, December 5, 2013, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Ina Coburger (FLI, Than Lab)

Li X, Dang S, Yan C, Gong X, Wang J, Shi Y.
Structure of a presenilin family intramembrane aspartate protease.
Nature 2013;493(7430):56-61.
[PubMed] [PDF]

Abstract: Presenilin and signal peptide peptidase (SPP) are intramembrane aspartyl proteases that regulate important biological functions in eukaryotes. Mechanistic understanding of presenilin and SPP has been hampered by lack of relevant structural information. Here we report the crystal structure of a presenilin/SPP homologue (PSH) from the archaeon Methanoculleus marisnigri JR1. The protease, comprising nine transmembrane segments (TMs), adopts a previously unreported protein fold. The amino-terminal domain, consisting of TM1-6, forms a horseshoe-shaped structure, surrounding TM7-9 of the carboxy-terminal domain. The two catalytic aspartate residues are located on the cytoplasmic side of TM6 and TM7, spatially close to each other and approximately 8?Å into the lipid membrane surface. Water molecules gain constant access to the catalytic aspartates through a large cavity between the amino- and carboxy-terminal domains. Structural analysis reveals insights into the presenilin/SPP family of intramembraproteases.



Thursday, December 12, 2013, 11:00

Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena
Villa

Presenter: Christoph Wiedemann (FLI, Than Lab)

Lu JX, Qiang W, Yau WM, Schwieters CD, Meredith SC, Tycko R
Molecular structure of beta-amyloid fibrils in Alzheimer's disease brain tissue.
Cell 2013;493(7430): 154(6):1257-68.
[PubMed] [PDF]

Abstract: In vitro, beta-amyloid (Abeta) peptides form polymorphic fibrils, with molecular structures that depend on growth conditions, plus various oligomeric and protofibrillar aggregates. Here, we investigate structures of human brain-derived Abeta fibrils, using seeded fibril growth from brain extract and data from solid-state nuclear magnetic resonance and electron microscopy. Experiments on tissue from two Alzheimer's disease (AD) patients with distinct clinical histories showed a single predominant 40 residue A? (Abeta40) fibril structure in each patient; however, the structures were different from one another. A molecular structural model developed for Abeta40 fibrils from one patient reveals features that distinguish in-vivo- from in-vitro-produced fibrils. The data suggest that fibrils in the brain may spread from a single nucleation site, that structural variations may correlate with variations in AD, and that structure-specific amyloid imaging agents may be an important future goal.