Martin Warmer

A Flow Cytometry-Based FRET Assay to Identify and Analyse Protein-Protein Interactions in Living Cells

Background Försters resonance energy transfer (FRET) microscopy is widely used for the analysis of protein interactions in intact cells. However, FRET microscopy is technically challenging and does not allow assessing interactions in large cell numbers. To overcome these limitations we developed a flow cytometry-based FRET assay and analysed interactions of human and simian immunodeficiency virus (HIV and SIV) Nef and Vpu proteins with cellular factors, as well as HIV Rev multimer-formation. Results Amongst others, we characterize the interaction of Vpu with CD317 (also termed Bst-2 or tetherin), a host restriction factor that inhibits HIV release from infected cells and demonstrate that the direct binding of both is mediated by the Vpu membrane-spanning region. Furthermore, we adapted our assay to allow the identification of novel protein interaction partners in a high-throughput format. Conclusion The presented combination of FRET and FACS offers the precious possibility to discover and define protein interactions in living cells and is expected to contribute to the identification of novel therapeutic targets for treatment of human diseases.

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering

At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.

Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering.

A micro-patterned sample holder of single-crystalline silicon, loaded with multiple protein crystals which are exposed to a humidified gas stream, allows high-quality room-temperature data collection.

High-speed fixed-target serial virus crystallography

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.

Human cytomegaloviruses expressing yellow fluorescent fusion proteins--characterization and use in antiviral screening.

Recombinant viruses labelled with fluorescent proteins are useful tools in molecular virology with multiple applications (e.g., studies on intracellular trafficking, protein localization, or gene activity). We generated by homologous recombination three recombinant cytomegaloviruses carrying the enhanced yellow fluorescent protein (EYFP) fused with the viral proteins IE-2, ppUL32 (pp150), and ppUL83 (pp65). In growth kinetics, the three viruses behaved all like wild type, even at low multiplicity of infection (MOI). The expression of all three fusion proteins was detected, and their respective localizations were the same as for the unmodified proteins in wild-type virus–infected cells. We established the in vivo measurement of fluorescence intensity and used the recombinant viruses to measure inhibition of viral replication by neutralizing antibodies or antiviral substances. The use of these viruses in a pilot screen based on fluorescence intensity and high-content analysis identified cellular kinase inhibitors that block viral replication. In summary, these viruses with individually EYFP-tagged proteins will be useful to study antiviral substances and the dynamics of viral infection in cell culture.

Fast high-pressure freezing of protein crystals in their mother liquor.

High-pressure freezing (HPF) is a method which allows sample vitrification without cryoprotectants. In the present work, protein crystals were cooled to cryogenic temperatures at a pressure of 210 MPa. In contrast to other HPF methods published to date in the field of cryocrystallography, this protocol involves rapid sample cooling using a standard HPF device. The fast cooling rates allow HPF of protein crystals directly in their mother liquor without the need for cryoprotectants or external reagents. HPF was first attempted with hen egg-white lysozyme and cubic insulin crystals, yielding good to excellent diffraction quality. Non-cryoprotected crystals of the membrane protein photosystem II have been successfully cryocooled for the first time. This indicates that the presented HPF method is well suited to the vitrification of challenging systems with large unit cells and weak crystal contacts.

Development of an in-vacuum x-ray microscope with cryogenic sample cooling for beamline P11 at PETRA III

Beamline P11 at PETRA III is dedicated to structural investigations of biological samples. It provides two experimental stations, one for macromolecular crystallography and one for X-ray microscopy. The microscope will provide full field Zernike phase contrast and scanning microscopy both in 2D and in tomographic mode. Full field microscopy with a field of view of 50 x 50 μm2 will allow to generate an overview of the sample and to select regions of interest for later inspection of the element distribution by X-ray fluorescence and diffraction in scanning mode. Central part of the microscope is an inhouse developed flexure based x,y,z scanner on top of a rotation stage. The scanner is operated in closed loop with piezo motors, has a travel range of 4 mm in horizontal and of 3 mm in vertical direction. With laser interferometers for closed loop operation a positioning accuracy of better than 5 nm is achieved in all directions. For precise sample rotation an in-vacuum air-bearing has been developed. An open bore in the center of the air-bearing allows cryogenic sample cooling by a cold He or N2 gas stream. Different optical elements such as beam defining pinholes, a condensor, zone plates, OSA, phase rings, etc. can be centered in the beam path by piezomotor driven x,y flexure elements mounted on a rail system which allows further positioning along the beam path. Different 2D detectors and two fluoresence detectors can be attached to the microscope.

Towards tender X‐rays with Zernike phase‐contrast imaging of biological samples at 50 nm resolution

X-ray microscopy is a commonly used method especially in material science application, where the large penetration depth of X-rays is necessary for three-dimensional structural studies of thick specimens with high-Z elements. In this paper it is shown that full-field X-ray microscopy at 6.2 keV can be utilized for imaging of biological specimens with high resolution. A full-field Zernike phase-contrast microscope based on diffractive optics is used to study lipid droplet formation in hepatoma cells. It is shown that the contrast of the images is comparable with that of electron microscopy, and even better contrast at tender X-ray energies between 2.5 keV and 4 keV is expected.

Structure determination from a single high-pressure-frozen virus crystal

Successful cryogenic X-ray structure determination from a single high-pressure-frozen bovine enterovirus 2 crystal is reported. The presented high-pressure-freezing procedure is based on a commercially available device and allows the cryocooling of macromolecular crystals directly in their mother liquor without the time- and crystal-consuming search for optimal cryoconditions. The method is generally applicable and will allow cryogenic data collection from all types of macromolecular crystals.

X-ray Crystallography at Beamline P11 at PETRA III

The bio-imaging and diffraction beamline P11 at PETRA III is dedicated to structure determination of periodic (crystalline) and aperiodic biological samples. The beamline features two experimental endstations: an X-ray microscope and a crystallography experiment. Basis of design was to provide an extremely stable and flexible setup ideally suited for micro and nano beam applications. The X-ray optics consist of a HHL double crystal monochromator, followed by two horizontal deflecting and one vertical deflecting X-ray mirrors. All mirrors are dynamically bendable and used to generate an intermediate focus at 65.5 m from the source with a size of 37 × 221 μm2 FWHM (v × h). All experiments are installed on an 8 m long granite support which provides a very stable setup for micro beam experiments. The crystallography endstation is located at the end of the granite at 72.9 m from the source. The experiment is equipped with a high precision single axis goniostat with a combined sphere of confusion of less than 100 nm. X-ray energies are tunable between 5.5 and 30 keV. A second focusing bendable KB mirror system can be used for further demagnification of the secondary source. In this way the beam size can be freely adjusted between 4 × 9 μm2 and 300 × 300 μm2 FWHM (v × h) with 1013 ph/s at 12 keV. Smaller beam sizes down to 1 × 1 μm2 with more than 2 × 1011 ph/s in the focus can be realized by slitting down the secondary source at the cost of flux. The crystallography endstation is equipped with a Pilatus 6M-F detector which allows fast data collection with up to 25 Hz. Due to the very small beam divergence of the X-ray beam P11 is ideally suited to measure large unit cell systems, such as viruses or large molecular complexes. In addition, the beamline is capable of high-throughput crystallography and fast crystal screening. Crystals can be mounted in less than 10 s using an automatic sample changer. The large sample dewar provides space for 368 crystals.