On this page, you will find a list of the structural biology services available through Instruct-ERIC and associated providers in the ISIDORe project.
To start your application, select the service you would like to access in our catalogue of services and click on the red button “Apply for access” located at the bottom right of your service drop-down.
Find additional information about the ISIDORe transnational call on our ISIDORe help page.
Please contact us if you have any question regarding ISIDORe call and the application process at isidore@instruct-eric.org
Access to software for data analysis, organisation and interpretation.
Studying biological structures and their function using complementary visual techniques
The Imaging Centre at EMBL Heidelberg gives access to state-of-the-art cryo-EM equipment for structure determination projects using the latest technology and methods in single-particle analysis, cryo-electron tomography (cryo-ET) and Cryo-correlative light and electron microscopy (Cryo-CLEM).
Crystallisation allows the 3D structure of macromolecules to be revealed through X-ray diffraction. Instruct offer a fully automated crystallisation pipeline to achieve high-throughput with short crystallisation plate processing times, high reproducibility, and increased efficiency of the screening process.
The 'From Sample to X-ray Diffraction' platform at EMBL Hamburg offers services for obtaining crystal structures from molecules of interest. Services include: sample characterization by various biophyscial methods, sample optimization, high-throughput crystallization, robotic crystal harvesting, diffraction data collection on synchrotron beamlines, data processing, and support in structure solution and refinement.
EMBL Hamburg operates three beamlines at the PETRA III synchrotron ring, two for macromolecular X-ray crystallography and one for small angle X-ray scattering on biological macromolecules. Academic access to the beamlines is available to all research groups, and is prioritised on scientific grounds only. All proposals for beamline access are evaluated by the Project Evaluation Committee.
EMBL beamlines also offer possibilities for mail-in and remote access. Users are encouraged to contact the beamline responsibles for further details.
The Sample Preparation and Characterisation (SPC) facility supports users on the beamline and in addition offers expertise to check and improve the samples that are submitted to the crystallisation facility and the SAXS beamline.
The Protein Facility of the Netherlands Cancer Institute (NKI) in Amsterdam has a strong record in structural biology using macromolecular X-ray crystallography, Electron Microscopy and sample preparation, and is also extremely well-equipped for studying molecular biophysics.
We are very experienced in macromolecular crystallization and offer to our users:
- Robotics for preparation of nanoliter crystallization drops in 96-well format.
- Storage of crystallization plates at 4°C or 20°C.
- Screening and ranking of crystallization conditions in 96-well format (TOPAZ, AutoInspex station).
Solving crystal structures is beyond the scope of the facility!
The platform at the Biomolecular Interactions and Crystallography core facility (BIC) at CEITEC Instruct centre provides services for biophysical and structural characterisation of biomolecules, and studying (bio)molecular interactions. It is equipped with the instrumentation to set up crystallisation conditions of biomolecules and their complexes, basic characterisation of physical properties of the molecules (analytical ultracentrifugation, dynamic light scattering, CD spectroscopy, differential scanning calorimetry, differential scanning fluorimetry, size-exclusion chromatography), and to study thermodynamics and/or kinetics of interactions (isothermal titration calorimetry, surface plasmon resonance, bio-layer interferometry, microscale thermophoresis, CD spectroscopy, analytical ultracentrifugation). The facility is accessible each working day upon previous agreement.
More information can be found on the Biomolecular Interactions and Crystallography core facility webpage.
EMBL Grenoble offers access to automated nano-volume crystallization screening and optimization services. Additional services include sample quality assessment and buffer optimization through TSA and estimation of crystallization likelihood. This platform is remotely operated through the web via the Crystallographic Information Management System (CRIMS) providing real-time access to results and experimental parameters.
Biocenter Oulu Protein Crystallography core facility offers crystallization using nanoliter dispensers and a collection of commercial and self maintained crystallization screens. Crystallization is followed using the IceBear software and remote access to monitor the experiments can be provided following the visit.
The high throughput crystallisation platform offers vapour diffusion as well as crystallisation under oil screening and optimisation in sitting drops. Flexible methods have been developed to adapt each step to individual project requirements. At the crystallisation level, we have especially focused on developing techniques to optimise crystal growth.
Crystallization of Proteins and Nucleic Acids core facility provides services focused on obtaining crystals of biomacromolecules and their complexes. We support both manual and robotic crystallization drops setting under various conditions. Remote control of crystal growth in the crystallization hotel is provided using the web interface over Internet.
Expertise
The macromolecular crystallisation platform enables in-drop dynamic light scattering measurement to check the quality of the protein sample, robotic setup of 96-well crystallisation plates, incubation at selected temperature from a wide range, and automated monitoring of the crystallisation experiments. Experiments can be stored at 4-30°C (or higher). Dedicated rooms with stereomicroscopes for crystal manipulation are available at 20°C, 10°C and 25°C (or higher).
Crystallisation screening: Utilizing the sitting and hanging drop by vapor diffusion methods for crystallising soluble proteins, using the Mosquito, and LCP Mosquito crystallisation robots.
Lipidic cubic phase (LCP) crystallisation is an alternative to standard crystallisation for membrane proteins. It allows membrane proteins to crystallise in a close to native and stable environment, in a lipidic bilayer. G-protein-coupled receptors (GCPR) protein crystallisation demonstrated the power of this approach; Cherezov V et al. High Resolution Crystal Structure of an Engineered Human β2-Adrenergic G protein-Coupled Receptor. As LCP is described as infinite 3D periodic structure, membrane proteins (MP) can freely diffuse laterally along the membrane. Diffusion is one of the important pre-crystallisation characteristic of the MP embedded into lipidic bilayer, which could be checked by Fluorescence recovery After Photobleaching (FRAP) technique available at HTMPC platform.
The high-resolution electron microscope has evolved into a sophisticated instrument that is capable of routinely providing quantitative structural information on the atomic scale.
The Imaging Centre at EMBL Heidelberg gives access to state-of-the-art cryo-EM equipment for structure determination projects using the latest technology and methods in single-particle analysis, cryo-electron tomography (cryo-ET) and Cryo-correlative light and electron microscopy (Cryo-CLEM).
The Instruct Image Processing Center (I2PC), part of Instruct-ES, offers an extended duration service "FlexibilityHub” targeted to the exploration of the conformational landscape of flexible macromolecules from sets of cryo Electron Microscopy images of purified samples. A continuous flexibility analysis will be performed using recently developed tools (including Zernike3D, developed at I2PC, among several other methods). This service is especially suited for samples presenting large structural flexibility.
This platform will provide personalised support to Instruct projects requiring specialised processing of either electron or X-ray microscopy images. It will also help developers in integrating their methods into generally accessible analysis workflows. The Instruct Image Processing Centre (I2PC) in Madrid will assign personnel to this analysis, as well as the required computational resources.
The Cryo-electron microscopy and tomography core facility (CEMCOF) at CEITEC Instruct centre is an open access facility providing access to state-of-the-art instrumentation for cryo-electron microscopy, support with cryo-EM sample preparation, and data analysis. The facility handles BSL1 and BSL2 samples, respectively, and is available to its users for both service and collaborative projects.
More information can be found on the Cryo-electron microscopy and tomography core facility (CEMCOF) webpage
The Electron Bio-Imaging Centre (eBIC) provides scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for both single particle analysis and cryo-tomography. Currently eBIC houses five Titan Krios microscopes, a Talos Arctica, Glacios, and a Scios and Aquilos cryo-FIB/SEM.
The EM platform at IBS provides access to a full range of instruments (three in total) for national and European users via FRISBI and Instruct respectively. This includes classical quality control negative staining experiment (Tecnai 12 EM) prior to setting up cryo conditions (F20 EM equipped for cryo and tomography). Data acquisition can also be carried out on the F20 EM. Our third EM: the Glacios is equipped with a direct electron detector ((Falcon II). The Glacios is able to do single particle imaging and single axis tomo.
The PF is also offering cellular EM service
CryoEM unit provides high-resolution imaging of nanoparticles, such as virus and protein complexes in the order of 100 kDa upwards (~5 to 300 nm in diameter). CryoEM is particularly useful for objects that are too large, unstable or variable to be studied by X-ray crystallography or NMR. It can be used to understand the structure, assembly and function of various biological macromolecule complexes. The site has over 20 years experience in the preparation and optimisation of samples for cryoEM. Access is especially suitable for those wanting to screen samples and get small prelimianary datasets that can be used as proof of principle for access to 300 kV machines or for longer data collection. Both genetically modified organisms and biosafety level 2 samples (Finnish criteria) can be handled but may require acquisition of permits per sample upto 40 days prior to handling. Correlative light microscopy and cryoEM is possible. We accept both visits and shipped samples. Biomolecular complexes studied by cryoEM can be purified in the Biocomplex purification facility located in the same building (see Biomolecular Complex Purification, Helsinki). Please contact grp-cryoemservice@helsinki.fi for enquiries.
NeCEN is an open access facility for high resolution cryo-electron microscopy of biological samples. A state-of-the-art Titan Krios transmission electron microscope allows efficient and automated high resolution data collection in its two most broadly used forms, single particle analysis (SPA) and cryo-electron tomography (cryo-ET). These imaging techniques allow visualisation of biomolecular structures, such as proteins, macromolecular complexes, bacteria, and cell organelles at subnanometer resolution in close-to-native conditions. The facility is equipped with a BSL2 lab and microscope rooms.
OPIC houses state-of-the-art equipment for cryo-EM single particles analysis, in-situ FIB-SEM and cryo-ET of biological specimens, from small macromolecular complexes to cells. Our facilities are available to all researchers from across the University of Oxford as well as external users from both academia and industry.
Our facility includes a series of plunging devices (Vitrobots, GP2 Leica plunger), grids micro-patterning (Primo, Alveole) for preparing and optimizing grids to image both purified macromolecular complexes or cells. A 200-kV Glacios (Thermo Fisher Scientific) cryo-TEM equipped with a Falcon III direct electron detector for sample screening, grid optimizations and initial data collection. A 300-kV Titan Krios G3i (Thermo Fisher Scientific) cryo-TEM equipped with Falcon 4 direct electron detector and a Selectris-X imaging filter for high resolution single particles and tomography data collection. A Thermo Fisher Scientific Aquilos 2, which is a dual beam system dedicated to the preparation of thin, electron-transparent cellular lamellas for high-resolution cryo-electron tomography or MicroED of micro-crystals.
Equipment provided in OPIC are located within biosafety containment laboratories at ACDP category 3 and DEFRA 4 levels of containment which facilitates the study of live pathogenic viruses that are important to human and animal health.
The center offers access for three-dimensional structure determination using cryo-electron microscopy (cryo-EM). The centre has expertise in all aspects of single particle analysis from the automated acquisition of large data sets to image analysis.
The Astbury Biostructure Laboratory includes the electron microscopy facility within the Faculty of Biological Sciences. We have a range of state-of-the-art equipment for transmission electron microscopy of biological specimens, from small macromolecular complexes to cells, tissues and organisms.
Our facilities are available to researchers from across the University of Leeds, and external users form academia and industry.
Our facility can operate at Biosafety Level II.
Imaging techniques including fluorescence microscopy provide an efficient and unique approach to study fixed and living cells because of their versatility, specificity, and high sensitivity.
The Leica SR GSD microscope allows to perform single-molecule localization microscopy (SMLM) experiments, such as dSTORM, STORM, PALM, or SPT, in standard epifluorescence or TIRF mode. A dichroic image splitter is used for spectral demixing of fluorophore emission in multi-color SMLM. The optional mounting of cylindrical lenses allows for 3D-imaging based on astigmatism, or alternatively, astigmatism can be induced with a MicAO 3DSR adaptive optics system.
NMR allows three-dimensional structural and dynamic information to be obtained in conditions as close as possible to physiological ones. Functional processes can be followed in living cells, and transient protein-protein interactions can be investigated.
Electron Paramagnetic Resonance (EPR)-based methods have been used to map local dynamic and structural features of biomolecules, to explore different modes of biomolecule-ligand interaction, to obtain long-range structural restraints and to probe metal-ion-binding sites.
The Center of Magnetic Resonance (CERM) facility includes two EPR instruments (Continuous-wave X-Band and Continuous-wave/Pulse Q-Band), the necessary sample preparation wet lab (including glove-box) and the necessary processing computer. EPR measurements can be performed on biological samples containing paramagnetic metal ions (i.e. Fe, Cu, Mn etc.) or on samples opportunely labelled with paramagnetic tags (i.e. spin labels). The pulse Q-band EPR instrumentation present at CERM permit to measure DEER, HYSCORE and ESEEM experiments.
The NMR facility provides services on the field of liquid NMR. The main focus area includes studies of structure and dynamics of biomacromolecules, but also other types of analyses are very well possible e.g. with broadband probe on 600 MHz.
Relaxometry is a technique that has been developed to obtain structural and dynamical information on nuclear spin systems. In the presence of a paramagnetic metal ion in the compound under investigation, relaxometry may provide information on the coordination of the nuclear spin with respect to the paramagnetic metal and, indirectly, information on the electron spin system. In fact, if the water proton exchange rate is fast or of the same order as the NMR timescale, the magnetic properties of the paramagnetic center are carried over from the water in bound position to the bulk.
CERM/CIRMMP (Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine) offers unique research capabilities in the field of solid-state NMR of biomolecules by providing state of the art instrumentation and expertise to perform, at the highest level, the most comprehensive array of experiments needed for the structure and dynamic characterisation of biological macromolecules and their complexes.
Solid-state NMR available at CERM/CIRMMP is typically applied for the determination of fibril structures and to obtain atomic-level structural information of biomolecules when they are bound to or trapped in solid matrices that lack long-range three-dimensional order. Detailed structural studies can be accomplished by exploiting the effects induced by the presence of paramagnetic metal ions. CERM/CIRMMP has a long tradition in the determination of paramagnetic effects in the solid state to access structural information.
Solid state nuclear magnetic resonance equipment available through Instruct at Grenoble include a 950 MHz and several 600 MHz instruments, equipped with state-of-the-art magic-angle spinning (MAS) capabilities, and triple-resonance probes for different rotor sizes and spinning speeds.
The Bijvoet Centre houses solid state 1200, 800, 700, 500 and 400 MHz NMR equipment for the characterisation of biomolecules, their structure determination and dynamical and functional studies. All of the NMR instruments are state-of-the-art digital Bruker NMR spectrometers.
Not only are the standard pulse sequences for spectroscopic, structural, dynamical, and functional characterisation available, the Bijvoet Centre also offers tailored pulse sequences for structural determination of high molecular weight proteins and other special applications such as in-cell NMR experiments. Dynamic Nuclear Polarization (DNP) capabilities on the 800 and 400 MHz instruments provide a significant boost in sensitivity.
The Core Facility of High Field NMR Spectroscopy at CEITEC Instruct centre provides access to NMR spectrometers in the range of proton frequencies from 500 MHz to 950 MHz. The equipment is suited mainly to the studies of structure, dynamics and interactions of biomolecules, i.e. proteins, nucleic acids and carbohydrates. However, the instrumentation is flexible enough to cover various research needs in material science, organic and inorganic chemistry, biochemistry, biology and biophysics.
More information can be found on the Core Facility of High Field NMR Spectroscopy webpage
CERM/CIRMMP provides state of the art instrumentation and expertise to perform the most comprehensive array of experiments needed for the structure and dynamic characterisation of biological macromolecules and their complexes. All the standard pulse sequences for spectroscopic, structural and dynamical characterisation are available for attaining fundamental atomic level information. CERM/CIRMMP have developed 13C direct detection protocols for “protonless” NMR experiments and for in-cell NMR spectroscopy, and tailored pulse sequences for structural determination of paramagnetic systems.
NMR of proteins, RNA, ligand-protein and ligand-RNA complexes using these NMR Spectrometers:
600 MHz NMR Spectrometer I / NMR-Screening
600 MHz NMR Spectrometer II/ NMR-Screening
600 MHz NMR Spectrometer III / Liquid State NMR
600 MHz NMR Spectrometer IV/ Liquid State NMR
700 MHz NMR Spectrometer / Liquid State NMR
800 MHz NMR Spectrometer I / Liquid State NMR
800 MHz NMR Spectrometer II/ Liquid State NMR
900 MHz NMR Spectrometer / Liquid State NMR
950 MHz NMR Spectrometer / Liquid State NMR
Researchers can gain access to 950, 850, 700, and several 600 MHz instruments, equipped with most recent Bruker electronics (Avance III HD) and cryogenically cooled probes for high-sensitivity solution-state NMR applications. Standard Bruker experiment libraries, as well as additional in-house libraries for optimised fast NMR data acquisition (e.g. SOFAST, BEST, and HADAMAC-type experiments) are available. Fast-mixing equipments required for real-time studies of kinetic processes such as protein folding are also available.
The NMR facility of the Astbury BioStructure Laboratory in Leeds has several unique capabilities available at 950 MHz. The first is based on direct heteronuclear detection (15N and 13C, 5mm TXO Cryoprobe). The combination of high field and Carbon detection has advantages for complex or large intrinsically disordered proteins. There are also new developments in characterising protein sidechains utilising Carbon detection. Techniques using 15N detection are under development and are of interest in chemically exchanging systems, as an alternative to Ca detection and when deuteration is not feasible. The second is based on using a smaller diameter probe (3mm TCI Cryoprobe) for mass limited samples and high ionic strength samples for optimised sensitivity.
The Bijvoet Center at UU offers access and support for solution NMR studies of biomolecules at field strengths ranging from 500 MHz up to 1.2 GHz. The instruments are well-equipped for all standard structural and dynamical characterization of proteins or other biomolecules, with cryoprobes for enhanced sensitivity on three machines.
The Facility has extensive expertise in the study of protein structure, dynamics and interactions. Applications involving high molecular weight proteins or protein complexes, such as nucleosome-protein complexes (200-250 kDa) for instance, benefit from the available tailored pulse sequences, provided these samples are appropiately isotope-labelled. We can now also offer dedicated support for applications involving interactions of intrinsically disordered proteins. Finally, support for medium to high-througput screening will be offered mid 2022.
Mass spectrometry is the dominant technology in the field of proteomics, enabling the identification and quantification of cellular proteins and their modified forms.
Glycan analysis with:
Protein Mass spectrometry using an Orbitrap Elite mass spectrometer, coupled with HPLC/nanoLC or
Native Mass Spectrometry using an UltrafleXtreme II MALDI mass spectrometer, coupled with nanoLC
The mass spectrometry facility runs routine HDX analyses to determine protein folding states, effects of ligand binding and protein interactions (e.g. epitope mapping). Further advanced instrumentation offers bespoke high-resolution native MS and ion mobility capabilities: Ultra-high mass range Q-Exactive Plus Orbitrap enabling native analysis of heterogeneous systems at high mass-to-charge ratios, e.g. membrane protein lipid complexes, and Tofwerk high-resolution ion mobility TOF (in late 2018) as well as several Waters Synapt HDMS systems.
UEF core facility offers two state-of-the-art mass spectrometers for versatile utilization of native mass spectrometry for studies of protein folding and assembly of biological macromolecules as well as for quantitative biological interaction studies with large dynamic range.
Structural mass spectrometry (MS3D) offers various methodologies for characterisation of protein structure. The Institute of Biotechnology/Centre of Molecular Structure (IBT/CMS) at BIOCEV offers different labelling approaches including hydrogen/deuterium exchange, covalent labelling, chemical cross-linking and limited proteolysis. The facility is equipped with cutting-edge technologies including high-resolution mass spectrometer, HPLC system, H/D system and in-house software for data processing.
The service provided includes data processing and reporting ready for publication. The platform also offers: identification and quantification of proteins, precise determination of protein molecular mass, and characterisation of various post translational modifications.
The Proteomics core facility at CEITEC Instruct centre provides the academic and other entities with access to advanced proteomic technologies based on shared resources and the know-how of highly trained staff. Effective utilization of the state-of-the-art mass spectrometric instrumentation promotes understanding proteome complexity according to the demands of research community. Thus, the facility is involved in broad range of projects requiring protein characterisation covering fields of biochemistry, molecular and structural biology, human and veterinary medicine, microbiology, plant, agriculture and food sciences. The facility staff can offer a complete mass spectrometry-assisted proteomics services including sample preparation, separation of protein/peptide mixtures, qualitative and quantitative characterisation of proteins and their modifications by mass spectrometry and data processing.
More information can be found on the Proteomics core facility webpage.
SCoPE-MS offers a revolutionary technique enabling global level identification and quantification of single cell proteome (>1000 proteins) using mass spectrometry, exceeding the by >ten-fold the identification capability of fluorescence or mass cytometry. Single cell technologies on DNA and RNA level have recently become extremely popular, the SCoPE-MS will extend this to protein/proteome level.
Instruct offer a wide range of techniques to study macromolecular interactions, including circular dichroism, surface plasmon resonance (SPR), thermal shift assay and calorimetry.
The Protein Facility of the Netherlands Cancer Institute (NKI) in Amsterdam has a strong record in structural biology using macromolecular X-ray crystallography, Electron Microscopy and sample preparation, and is also extremely well-equipped for studying molecular biophysics.
With respect to Molecular Biophysics we offer to our users fluorescence-based fast kinetics and high-throughput experiments, ITC, MST, MALS, SPR and Thermal Shift Assays.
The platform at the Biomolecular Interactions and Crystallography core facility (BIC) at CEITEC Instruct centre provides instruments and services leading to the biophysical characterization of (bio)molecules, the study of biomolecular interactions (determination of affinity, kinetic and thermodynamic parameters) and the sample quality control using analytical ultracentrifugation (AUC), isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), bio-layer interferometry (BLI), microscale thermophoresis (MST), dynamic light scattering (DLS), differential scanning calorimetry (DSC), differential scanning fluorimetry (DSF), and analytical size-exclusion chromatography (SEC-MALS). The platform is available to the entire INSTRUCT-ERIC community every working day upon previous agreement.
More information can be found on the Biomolecular Interactions and Crystallography core facility webpage
The Molecular Biophysics platform at EMBL Hamburg offers one of the most-well equipped biophysical laboratories in Europe. We support users with the design, execution and data analysis of biophysical experiments aimed at the characterization of proteins, protein complexes and interactions between proteins and other types of molecules.
Biocenter Oulu Molecular Biophysics core facility offers multiple technologies for analysing secondary structure and stability of biological macromolecules, biomolecular interactions and enzyme kinetics.
Techniques are available for the analysis of kinetic and thermodynamic parameters of biomolecular interactions and for the biophysical characterisation of the structure, function and stability of biological biological macromolecules like proteins, nucleic acids, lipids and their complexes.
The HT Robotein® facility at CIP and SBBC has the particularity to combine high technology laboratory instrumentation: a central liquid handling workstation, a colony picking instrument, various microplate spectrophotometers, an Octet HTX, a LabChip GXII, a protein spotter and an Infrared Imager. This specific combination of equipment offers versatile tools for the development of numerous HT applications. Here is a list of the main services that Robotein® can provide. Nonetheless, we are always open to develop new and innovative assays.
The combination of the central liquid handling platform with the microplate spectrophotometers offers the possibility to analyse in an automated and HT manner the conformational stability (△G0) of proteins in the presence of chaotropic agents (e.g. urea, guanidinium chloride).
Furthermore, a direct link can be created to build a protein array from hundreds of different proteins or proteins that have been submitted to different conditions. A unique combination of a HT protein arrayer (using 96 or 384 –well plates) and a state-of-the-art infrared imager allows hundreds of proteins to be quantitatively analysed in a few minutes for secondary structure, phosphorylation, glycosylation or any contaminant of known infrared spectrum.
The central robotic workstation linked to the Octet HTX instrument (fortéBio), enables real-time and label-free determination of binding affinity (Equilibrium dissociation constant: Kd) by measuring kinetics of association and dissociation of the complex (kon, koff). Using microtiter plates as liquid sample holders, the system can measure up to 96 samples in parallel. The Octet HTX is highly modular and can be easily adapted to measure interactions for a large range of antibodies, proteins, peptides or small molecules.
The combination of the central robotic workstation with the Octet HTX instrument (fortéBio) can also be used to perform fast and accurate protein quantitation from crude extracts (cell extracts, culture media, etc.), with no required purification steps. This method is particularly suitable to measure the concentration of full-length antibodies or various antibody fragments (although the modularity of the Octet system makes it compatible for the quantitation of many other proteins or peptides).
The combination of the central robotic workstation with a microplate spectrophotometer allows for the development of fully automated, easy, fast and robust enzymatic assays. For instance, we have performed automated quantification (i.e. determination of the relevant kinetic parameters: kcat, Km, and kcat/Km) of carbohydrate-isomerases, several dehydrogenases and various β-lactamases.
Using the central robotic workstation together with the microplate spectrophotometer and a quantitative PCR block, we developed protocols for automated screening of 164 buffers/pH conditions to improve protein stability and activity. This screen covers a pH range from 2 to 10, in 19 different buffers that are the most commonly used by pharmaceutical companies. This screen is coupled to HT and automated Differential Scanning Fluorimetry (DSF) thermal shift assays and enzymatic/binding affinity measurements in order to determine the best buffer/pH conditions that are compatible with the protein optimum stability and activity. We have validated this screen with several hydrogenases, oxygenases, ß-lactamases and antibody fragments.
We developed an automated screen of 96 refolding conditions for protein expressed as inclusion bodies. This screen, coupled to HT enzymatic/binding activity measurements, offers the possibility to significantly improve the refolding yield of active protein from inclusion bodies in a fast and reproducible manner.
Nanobodies are single chain antibodies which have revolutionary applications in structural biology. Our Nanobody Discovery service is accessible to all Instruct researchers.
Rapid selection of nanobodies by in vitro screening/affinity maturation complementary to VIB nanobodies by immunisation
The Nanobodies4Instruct center produces and characterises Nanobodies to be used as auxiliary tools in structural and cellular biology.
By learning more about the nature of each project, the team can advise in designing antigens and work out optimal immunisation schemes, panning strategies and screening methods.
The Nanobodies4Instruct center produces and characterises Nanobodies to be used as auxiliary tools in structural and cellular biology.
By learning more about the nature of each project, the team can advise in designing antigens and work out optimal immunisation schemes, panning strategies and screening methods.
Nanobodies can then be reformatted into Megabodies. Nanobodies are rigidly grafted into selected scaffold proteins to increase their molecular weight while retaining the full antigen binding specificity.
Instruct's services include protein expression, cloning and high throughput expression, and protein purification. Our techniques allow for expression of challenging proteins along with expert protein purification systems.
Biocomplex is specialized in macromolecular sample preparation and purification for functional and structural studies using preparative ultracentrifugation, monolithic chromatography and asymmetrical flow field-flow fractionation technologies. Biocomplex also actively develops new purification methods for large biopolymers, often in co-operation with manufacturers. Our technologies can be used in different combinations to purify large macromolecular complexes such as viruses, virus-like particles, viral subassemblies, exosomes, membrane vesicles, large protein complexes, and ribonucleoprotein complexes as an important first step in the structure analysis pipeline. Samples produced at Biocomplex can be further studied at the CryoEM facility located in the same building (see Electron Microscopy, Helsinki). We accept both visits and shipped samples. Please contact grp-biocomplexservice@helsinki.fi for enquiries.
The platform also provide access to gene tagging with the CRISPR-Cas9 system for introduction of affinity tags to facilitate the purification of endogenous complexes or for tagging proteins with fluorescent reporters in view of imaging and functional proteomics applications, in the frame of a partnership with the TacGene platform from the Museum d’Histoire Naturelle (Paris, France),
The Protein Facility of the Netherlands Cancer Institute (NKI) in Amsterdam has a strong record in structural biology using macromolecular X-ray crystallography, Electron Microscopy and sample preparation, and is also extremely well-equipped for studying molecular biophysics.
We are very experienced in protein production using insect and mammalian cells, and assist users with the design of their expression construct in terms of solubility, domain boundaries, etc. We offer a variety of expression vectors, including a set of LIC vectors (Ligand Independent Cloning) for protein expression in insect cells and mammalian cells. For expression in insect cells we have SF9 and SF21 systems for expression of intracellular and extracellular proteins. Our mammalian expression system has been optimized for HEK-293T cells, and we also have the glycosylation free, gnT1-deficient HEK293S variety.
Protein expression in bacteria (E. coli) is beyond the scope of the facility!
Sample preparation is not only a key issue for structural and molecular biology studies, but concerns life sciences development as a whole. Instruct centre France 1 offers state-of-the-art infrastructures for the expression and production of biomolecules and their complexes. The center proposes recombinant expression of protein and multi-protein complexes in prokaryotic and eukaryotic hosts as well as biomass production for isolation of poorly abundant proteins and endogenous complexes.
Protein production in bacteria, baculovirus, and mammalian cells. Proteins are typically purified following a standard 3 step protocol which includes: affinity capture, ion exchange and size exclusion. Specific techniques can be employed depending on the protein, the experimental requirements, tags and yields. Removal of tags with TEV protease can be employed.
Reference material RNA dn Protein preparation
Instruct-ERIC offer a wide range of X ray approaches to determine the three dimensional shape of proteins at the atomic level.
Biological Small-Angle X-Ray Scattering (Bio-SAXS) can be used to collect low resolution structural data, or for understanding the subunit arrangement of multi-subunit macromolecules including in the presence of a ligand. A Rigaku BioSAXS-1000 is attached to the right port of a Rigaku MicroMaxTM-007HF generator. The BioSAXS-1000 is fitted with Osmic optics and a 2D Kratky block for collimation. Data is collected on a Pilatus 100K photon counting detector (Dectris).
The 'From Sample to Bio-SAXS' platform at EMBL Hamburg offers services for sample preparation for SEC-SAXS and/or automated SAXS data collection, real-time determination of physical parameter of molecules in solution and automated pipelines for building low resolution models against SAXS data.
The 'From Sample to X-ray Diffraction' platform at EMBL Hamburg offers services for obtaining crystal structures from molecules of interest. Services include: sample characterization by various biophyscial methods, sample optimization, high-throughput crystallization, robotic crystal harvesting, diffraction data collection on synchrotron beamlines, data processing, and support in structure solution and refinement.
EMBL Hamburg operates three beamlines at the PETRA III synchrotron ring, two for macromolecular X-ray crystallography and one for small angle X-ray scattering on biological macromolecules. Academic access to the beamlines is available to all research groups, and is prioritised on scientific grounds only. All proposals for beamline access are evaluated by the Project Evaluation Committee.
EMBL beamlines also offer possibilities for mail-in and remote access. Users are encouraged to contact the beamline responsibles for further details.
The Sample Preparation and Characterisation (SPC) facility supports users on the beamline and in addition offers expertise to check and improve the samples that are submitted to the crystallisation facility and the SAXS beamline.
EMBL Grenoble offers access to a fully automated protein to structure pipeline based on the CrystalDirect technology an the CRIMS software. Starting from purified samples, this pipeline integrates automated crystallization screening, crystal growth optimisation, automated crystal harvesting and cryocooling and X-ray diffraction data collection in a continuous and fully automated workflow operated over the Internet.
Diamond provides a range of techniques for academic and industrial researchers studying the machines of life. As one of those techniques, Macromolecular Crystallography (MX) reveals the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function. This can be combined with complementary information from many other techniques available at Diamond alongside lab based investigations to reveal the broader picture of molecular interactions and their effects.
Small Angle X-ray Scattering (SAXS) covers the major disciplines of Biology, Chemistry and Physics delivering structural and dynamic information in nanoscience, mesoscopic architectures, supramolecular structures and nucleation/growth of crystals. SAXS is also proving important in archaeological, environmental and conservation sciences, indicating an ability to span a wide range of scientific disciplines.
The 'X-ray Diffraction and Bio-SAXS ' platform at EMBL Hamburg offers beamtime on one beamline for small-angle X-ray scattering (P12) and two beamlines for macromolecular crystallography (P13, P14). With both methods, static and time-resolved pump-probe experiments can be performed.
Diffraction techniques core facility provides services for characterization of protein structure using single crystal X-ray diffraction and small-angle X ray scattering for analysis of liquid samples. Both methodes are backer by advanced approaches available in laboratory. The quality of high-intense X-ray beams is ensured by using of MetalJet sources (Excillum). The provided services include assistance with data processing and reporting ready for publication.
Biocenter Oulu Protein Crystallography core facility offers home-source X-ray generator for macromolecular crystal diffraction experiments.
Fragment screening through Macromolecular Crystallography at Diamond’s XChem facility at beamline I04-1, supporting 1000+ compound screens
