Protein Technologies

The NanoTemper Prometheus is a multi-purpose, label-free instrument measuring both intrinsic protein fluorescence and scattering while applying a defined temperature profile. Structural changes (folding/unfolding) as well as aggregation can be monitored over time, as a function of temperature, or under different chemical conditions. Since a sensitive fluorescence detection setup is used, only a minute protein sample is needed (>5µg/ml, 10µl). The Prometheus serves not only as a quality control instrument but also as a tool to find optimum conditions by using buffer screens to optimize stability. Using the Prometheus as a tool for day-to-day protein quality checks will improve the reproducibility of subsequent experiments that use purified proteins for structural and interaction studies while screening for potential binders can open up subsequent avenues of investigation.

The Creoptix^TM WAVE is a novel, highly sensitive label-free biosensor used to analyze the affinity and kinetics of molecular interactions. The Creoptix^TM WAVE provides similar information to the well-known Surface Plasmon Resonance biosensors but with increased sensitivity and lower noise, a superior “no-clog” microfluidics system allowing the detection and characterization of interactions in crude samples, and the ability to measure a very broad kinetic range (k_a=10³ – 3x10⁹ M^-1 sec^-1; k_d = 10^-5 – 5 sec^-1).  Additionally, sample consumption, although dependent on the system studied, is very low. Combined with user friendly and robust analysis software, the Creoptix^TM WAVE is ideal to study many different sample types and systems including those previously inaccessible using conventional biosensors.

The OmniSEC system combines analytical size exclusion chromatography with right angle light scattering and measurement of refractive index, to accurately determine protein molecular weights and concentrations. It can be used to analyze the oligomeric state of proteins and protein complexes and to quantify the different species present in a sample. A full UV-vis spectrum and intrinsic viscosity measurements enable the accurate determination of extinction coefficients and shape/size of protein samples.

The PEAQ-ITC instrument can be used to perform isothermal titration calorimetry experiments to measure biomolecular interaction parameters. The change in enthalpy upon ligand binding is directly measured by the instrument and can then be used to determine the dissociation constant, stoichiometry, and other thermodynamic parameters of the binding interaction. Interactions in the high nanomolar to high micromolar range can be determined using the PEAQ-ITC.

ProTech has three Aekta Purifier/Aekta PURE systems that can be booked by users after appropriate training, so that purifications can be performed by users in our lab. Additional purification equipment, such as a sonicator and centrifuges, can also be booked after training.

DLS is a label free technique that analyzes particle size distribution in a bulk sample. It is mainly used for protein quality control, as you can detect size distributions of molecules and therefore aggregation and oligomerization of your protein of interest. The Dynapro II plate reader can also be used for screening or long-term stability measurements. Experiments can be carried out for you; alternatively, you may receive training and can then book the instrument yourself.

Circular Dichroism is a spectroscopic technique that uses circularly polarized light to study the structure of chiral molecules, such as proteins. The CD spectrum of a protein can be used to determine protein secondary structure or some aspects of tertiary structure. CD can also be used to study protein stability using thermal melt analysis to determine protein melting temperatures (T_m). We perform CD on a Chirascan Plus CD spectrometer from Applied Photophysics.  Experiments can be carried out for you; alternatively, you may receive training and can then book the instrument yourself.

MST is a novel technique used to determine molecular affinities. Thermophoretic changes upon molecular interaction can be monitored by fluorescent labeling or via tryptophan fluorescence, revealing binding constants in the range of nM to mM.  Unlike many other methods, MST experiments can be performed rapidly and with small amounts of sample. We have two instruments for performing MST experiments, the NT.115 and the NT.LabelFree. MST experiments can be performed as a service, or you can receive training and then book the instruments yourself.

In general, we offer four types of access to our shared research infrastructure:

1. Research projects
2. Full research services
3. Trained user access | user labs
4. Shared technology platform

Typically, these are set but not limited by the offered technology or instrument, and differ in the required user expertise, the usability of a technology, the user’s pre- and postprocessing input, and the underlying operational models.

Research project

Research projects are the equivalent of contract research organizations (CRO). The customer submits the starting material/sample and receives the ready-to-use data for publication. Hence, core facility members are often co-authoring and involved in the entire publication process.

Full research service

The user submits the sample, we perform a pre-defined workflow (incl. QC) and process the raw data. Data interpretation or contributions to publications cannot be offered in this service mode.

Trained user access | User labs

VBCF experts maintain an instrument park and train users to operate it. This requires a certain level of expertise, maturity of the offered technology, a hands-on attitude and reliability from the user.

Shared technology platform | Instrument park

These technologies require expert knowledge to run the offered instruments. Experts are hired by one of the research institutes on the Vienna BioCenter Campus. The experts maintain an instrument park, run the experiments and train other trainers. Machines can only be operated by experts.

The ProTech Facility provides full research service and trained user access. The ProTech Facility Usage Policy can be downloaded HERE. It is assumed that users who order services have read and understood this policy as well as the VBCF General Cooperation Conditions.

If you are a new user, please contact David Drechsel (for ProTech core services) or Arthur Sedivy (for biophysical characterization services) to discuss your project requirements. To order services and book instruments, please use our web-based booking and request system. IMP, IMBA, GMI, and MPL users can log in with their usual institute network accounts. External users must register. For questions, please contact protech(at)vbcf.ac.at.

Pricing information, additional links, information on techniques, and other documents can be found on the ProTech MyVBCF Wiki site.

We require acknowledgement of facility use in publications. 
A simple statement is sufficient and can be placed in the Materials and Methods section or in the Acknowledgments section, depending on the journal format.

Suggested format:

The XXXXXX was performed by the Protein Technologies Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

In case of (co-)authorship:

The Vienna BioCenter Core Facilities (VBCF) Protein Technologies Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna.

Brillouin light scattering anisotropy microscopy for imaging the viscoelastic anisotropy in living cells. Keshmiri H, Cikes D, Samalova M, Schindler L, Appel LM, Urbanek M, Yudushkin I, Slade D, Weninger WJ, Peaucelle A, Penninger J, Elsayad K. Nat Photonics. 2024;18:276–285.

Two ARGONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis. Bradamante G, Nguyen VH, Incarbone M, Meir Z, Bente H, Donà M, Lettner N, Mittelsten Scheid O, Gutzat R. Plant Cell. 2024;36(4):863–880.

Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum. Mérai Z, Graeber K, Xu F, Donà M, Lalatović K, Wilhelmsson PKI, Fernandez-Pozo N, Rensing SA, Leubner-Metzger G, Mittelsten Scheid O, Dolan L. Curr Biol. 2024;34(13):2893–2906.e3.

A molecular network of conserved factors keeps ribosomes dormant in the egg. Leesch F, Lorenzo-Orts L, Pribitzer C, Grishkovskaya I, Roehsner J, Chugunova A, Matzinger M, Roitinger E, Belačić K, Kandolf S, Lin T, Mechtler K, Meinhart A, Haselbach D & Pauli A. Nature. 2023;613:712–720.

Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Ehrmann JF, Grabarczyk DB, Heinke M, Deszcz L, Kurzbauer R, Hudecz O, Shulkina A, Gogova R, Meinhart A, Versteeg GA, Clausen T. Science. 2023;379(6637):1117-1123.

Trapped Pore Waters in the Open Proton Channel H(V) 1. Boytsov D, Brescia S, Chaves G, Koefler S,Hanneschlaeger C, Siligan C, Goessweiner-Mohr, N, Musset B, Pohl P. Small. 2023;19:2205968.

Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of Na(+) and K(). Real-Hohn A, Groznica M, Kontaxis G, Zhu R, Chaves OA, Vazquez L, Hinterdorfer P, Kowalski H, Blaas D. Viruses. 2023; 15(4):1003.

The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate. Lackner A, Müller M, Gamperl M, Stoeva D, Langmann O, Papuchova H, Roitinger E, Dürnberger G, Imre R, Mechtler K, Latos Pa. Nat Commun. 2023;14:2559. 

RAF1 contributes to cell proliferation and STAT3 activation in colorectal cancer independently of microsatellite and KRAS status. Dorard C, Madry C, Buhard O, Toifl S, Didusch S, Ratovomanana T, Letourneur Q, Dolznig H, Garnett MJ, Duval A, Baccarini M. Oncogene. 2023;42:1649–1660.

Amplification of human interneuron progenitors promotes brain tumors and neurological defects. Eichmüller OL, Corsini NS, Vértesy Á, Morassut I, Scholl T, Gruber VE, Peer AM, Chu J, Novatchkova M, Hainfellner JA, Paredes MF, Feucht M, Knoblich JA. Science. 2022 375(6579):eabf5546.

Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. Andreev VI, Yu C, Wang J, Schnabl J, Tirian L, Gehre M, Handler D, Duchek P, Novatchkova M, Baumgartner L, Meixner K, Sienski G, Patel DJ, Brennecke J. Nat Struct Mol Biol. 2022 29(2):130-142.

Sperm membrane proteins DCST1 and DCST2 are required for sperm-egg interaction in mice and fish. Noda T, Blaha A, Fujihara Y, Gert KR, Emori C, Deneke VE, Oura S, Panser K, Lu Y, Berent S, Kodani M, Cabrera-Quio LE, Pauli A, Ikawa M. Commun Biol. 2022 5(1):332.

A mitotic chromatin phase transition prevents perforation by microtubules. Schneider MWG, Gibson BA, Otsuka S, Spicer MFD, Petrovic M, Blaukopf C, Langer CCH, Batty P, Nagaraju T, Doolittle LK, Rosen MK, Gerlich DW. Nature. 2022 609(7925):183-190.

Transient upregulation of IRF1 during exit from naive pluripotency confers viral protection. Romeike M, Spach S, Huber M, Feng S, Vainorius G, Elling U, Versteeg GA, Buecker C. EMBO Rep. 2022 23(9):e55375.

A Ca2+-Mediated Switch of Epiplakin from a Diffuse to Keratin-Bound State Affects Keratin Dynamics. Ratajczyk S, Drexler C, Windoffer R, Leube RE, Fuchs P. Cells. 2022 11(19):3077.

TMBIM5 is the Ca2+ /H+ antiporter of mammalian mitochondria. Austin S, Mekis R, Mohammed SEM, Scalise M, Wang WA, Galluccio M, Pfeiffer C, Borovec T, Parapatics K, Vitko D, Dinhopl N, Demaurex N, Bennett KL, Indiveri C, Nowikovsky K. EMBO Rep. 2022 23(12):e54978

Characterization of ATG8-Family Interactors by Isothermal Titration Calorimetry. Picchianti L, Sedivy A, Dagdas Y. Methods Mol Biol. 2023;2581:149-176.