Doletha M. E. Szebenyi

X-ray Laue Diffraction from Protein Crystals

In conventional x-ray diffraction experiments on single crystals, essentially monochromatic x-rays are used. If polychromatic x-rays derived from a synchrotron radiation spectrum are used, they generate a Laue diffraction pattern. Laue patterns from single crystals of macromolecules can be obtained in less-than 1 second, and significant radiation damage does not occur over the course of an exposure. Integrated intensities are obtained without rotation of the crystal, and individual structure factors may be extracted for most reflections. The Laue technique thus offers advantages for the recording of diffraction patterns from short-lived structural intermediates; that is, for time-resolved crystallography.

Evidence for Small Ubiquitin-like Modifier-dependent Nuclear Import of the Thymidylate Biosynthesis Pathway

Perturbations in folate-mediated one-carbon metabolism increase rates of uracil misincorporation into DNA during replication, impair cellular methylation reactions, and increase risk for neural tube defects and cancer. One-carbon metabolism is compromised by folate deficiency and common genetic polymorphisms. In this study, the mechanism for the preferential partitioning of cytoplasmic serine hydroxymethyltransferase (cSHMT)-derived methylenetetrahydrofolate to de novo thymidylate biosynthesis was investigated. The cSHMT enzyme was shown to interact with UBC9 and was a substrate for UBC9-catalyzed small ubiquitin-like modifier (SUMO) modification in vitro. SUMOylated cSHMT was detected in extracts from S phase MCF-7 cells, and cSHMT was shown to localize to the nucleus and nuclear periphery during the S and G2/M phases of the cell cycle. A common single nucleotide polymorphism (L474F-cSHMT) impaired the UBC9-cSHMT interaction and inhibited cSHMT SUMOylation in vitro. The three folate-dependent enzymes that constitute the de novo thymidylate biosynthesis pathway, cSHMT, thymidylate synthase, and dihydrofolate reductase, all contain SUMO modification consensus sequences. Compartmentation of the folate-dependent de novo thymidylate biosynthesis pathway in the nucleus accounts for the preferential partitioning of cSHMT-derived folate-activated one-carbon units into thymidylate biosynthesis; the efficiency of nuclear folate metabolism is likely to be modified by the cSHMT L474F polymorphism.

Insights into the Mode of Action of a Putative Zinc Transporter CzrB in Thermus thermophilus

The crystal structures of the cytoplasmic domain of the putative zinc transporter CzrB in the apo and zinc-bound forms reported herein are consistent with the protein functioning in vivo as a homodimer. NMR, X-ray scattering, and size-exclusion chromatography provide support for dimer formation. Full-length variants of CzrB in the apo and zinc-loaded states were generated by homology modeling with the Zn2+/H+ antiporter YiiP. The model suggests a way in which zinc binding to the cytoplasmic fragment creates a docking site to which a metallochaperone can bind for delivery and transport of its zinc cargo. Because the cytoplasmic domain may exist in the cell as an independent, soluble protein, a proposal is advanced that it functions as a metallochaperone and that it regulates the zinc-transporting activity of the full-length protein. The latter requires that zinc binding becomes uncoupled from the creation of a metallochaperone-docking site on CzrB.

Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

An emulsion-based serial crystallographic technology has been developed, in which single crystals are grown in nanolitre-sized droplets inside an X-ray semi-transparent microfluidic chip exploiting a negative feedback mechanism. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored in the chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals to solve the structure of glucose isomerase to 2.1 Å.

Regulation of de Novo Purine Biosynthesis by Methenyltetrahydrofolate Synthetase in Neuroblastoma

5-Formyltetrahydrofolate (5-formylTHF) is the only folate derivative that does not serve as a cofactor in folate-dependent one-carbon metabolism. Two metabolic roles have been ascribed to this folate derivative. It has been proposed to 1) serve as a storage form of folate because it is chemically stable and accumulates in seeds and spores and 2) regulate folate-dependent one-carbon metabolism by inhibiting folate-dependent enzymes, specifically targeting folate-dependent de novo purine biosynthesis. Methenyltetrahydrofolate synthetase (MTHFS) is the only enzyme that metabolizes 5-formylTHF and catalyzes its ATP-dependent conversion to 5,10-methenylTHF. This reaction determines intracellular 5-formylTHF concentrations and converts 5-formylTHF into an enzyme cofactor. The regulation and metabolic role of MTHFS in one-carbon metabolism was investigated in vitro and in human neuroblastoma cells. Steady-state kinetic studies revealed that 10-formylTHF, which exists in chemical equilibrium with 5,10-methenylTHF, acts as a tight binding inhibitor of mouse MTHFS. [6R]-10-formylTHF inhibited MTHFS with a Ki of 150 nm, and [6R,S]-10-formylTHF triglutamate inhibited MTHFS with a Ki of 30 nm. MTHFS is the first identified 10-formylTHF tight-binding protein. Isotope tracer studies in neuroblastoma demonstrate that MTHFS enhances de novo purine biosynthesis, indicating that MTHFS-bound 10-formylTHF facilitates de novo purine biosynthesis. Feedback metabolic regulation of MTHFS by 10-formylTHF indicates that 5-formylTHF can only accumulate in the presence of 10-formylTHF, providing the first evidence that 5-formylTHF is a storage form of excess formylated folates in mammalian cells. The sequestration of 10-formylTHF by MTHFS may explain why de novo purine biosynthesis is protected from common disruptions in the folate-dependent one-carbon network.

Quantitive analysis of Laue diffraction patterns recorded with a 120 ps exposure from an X-ray undulator

X-ray Laue diffraction patterns with an exposure time of 120 ps have been obtained from single crystals of an indole alkaloid and of the enzyme lysozyme using the X-rays emitted as a single bunch of electrons traverses a hard X-ray undulator inserted in CESR, the Cornell Electron–Positron Storage Ring. The patterns were recorded on a sensitive storage-phosphor detector. Despite complexities posed by the sharp variation of the incident X-ray spectrum with wavelength and the weakness of the diffraction patterns, accurate crystallographic structure amplitudes were extracted from the Laue intensities by the generalized scale-factor approach to the determination of the wavelength- and position-dependent correction factors. The results show that crystallography is feasible on the 100 ps time scale and open up the prospect of time-resolved measurements of ultra-rapid changes in molecular structure.

Structural Basis for the Interaction between the Growth Factor-binding Protein GRB10 and the E3 Ubiquitin Ligase NEDD4.

In addition to inhibiting insulin receptor and IGF1R kinase activity by directly binding to the receptors, GRB10 can also negatively regulate insulin and IGF1 signaling by mediating insulin receptor and IGF1R degradation through ubiquitination. It has been shown that GRB10 can interact with the C2 domain of the E3 ubiquitin ligase NEDD4 through its Src homology 2 (SH2) domain. Therefore, GRB10 might act as a connector, bringing NEDD4 close to IGF1R to facilitate the ubiquitination of IGF1R by NEDD4. This is the first case in which it has been found that an SH2 domain could colocalize a ubiquitin ligase and its substrate. Here we report the crystal structure of the NEDD4 C2-GRB10 SH2 complex at 2.0 Å. The structure shows that there are three interaction interfaces between NEDD4 C2 and GRB10 SH2. The main interface centers on an antiparallel β-sheet composed of the F β-strand of GRB10 SH2 and the C β-strand of NEDD4 C2. NEDD4 C2 binds at nonclassical sites on the SH2 domain surface, far from the classical phosphotyrosine-binding pocket. Hence, this interaction is phosphotyrosine-independent, and GRB10 SH2 can bind the C2 domain of NEDD4 and the kinase domain of IGF1R simultaneously. Based on these results, a model of how NEDD4 interacts with IGF1R through GRB10 has been proposed. This report provides further evidence that SH2 domains can participate in important signaling interactions beyond the classical recognition of phosphotyrosine.

Time-resolved laue diffraction from protein crystals: instrumental considerations

Abstract A serious limitation of macromolecular crystallography has been its inability to determine changes in structure on a biochemical time scale of milliseconds or less. Recently, we have shown that X-ray exposures on single crystals of macromolecules may be obtained in the millisecond time range through the use of intense, polychromatic radiation with Δλ/λ ∼ 0.2 derived from the Cornell High Energy Synchrotron Source, CHESS. Such radiation falling on a stationary crystal yields a Laue diffraction pattern, in which almost all Laue reflections arise from a unique set of Miller indices and where their intensities are automatically integrated over wavelength. This Laue technique requires wide band pass optics, which may be obtained by a combination of reflection and transmission mirrors, filters or layered synthetic microstructures. Time-resolved macromolecular crystallography may be achieved by several data collection schemes: “one-shot” recording coupled to a simple streak camera, repetitive sample perturbation coupled to a detector with temporal resolution and repetitive perturbation which uses the synchrotron pulses for stroboscopic triggering and detection. These schemes are appropriate for different time scales, roughly the milli-, micro- and nanosecond regimes. It appears that time-resolved crystallography is entirely feasible, with an ultimate time resolution limited only by the length of a synchrotron light pulse, some 150 ps at CHESS.

Protein crystallographic data acquisition and preliminary analysis using kodak storage phosphor plates

Abstract X-ray diffraction data from single crystals of typical proteins are very weak, numerous, and subject to systematic errors arising from radiation damage at long exposure times. Compared with films, the Kodak storage phosphor technology described in the accompanying paper [1] offers the prospect of greatly improved signal-to-noise, increased sensitivity particularly at shorter wavelengths, and wide dynamic range, though with more modest spatial resolution. To assess the suitability of this technology for protein crystallographic data collection, we have collected both monochromatic oscillation and wide bandpass Laue data at CHESS on crystals ranging in unit cell size from ∼ 50 A (lysozyme) to ∼ 300 A (viruses). A direct comparison of the Kodak storage phosphor with conventional Kodak Direct Exposure Film (DEF-5) was obtained by making immediately sequential exposures on the same crystal with the two detector systems. Even with an exposure time one order of magnitude less than with the corresponding film, the storage phosphor yielded data with improved signal-to-noise. Thus, storage phosphors enable more data to be acquired per crystal, with less radiation damage, and with better precision. Such detectors appear extremely well suited to protein crystallographic applications, both static and time-resolved, with both monochromatic and polychromatic X-ray sources.

Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS

Three research initiatives pursued by the Macromolecular Diffraction Facility at the Cornell High Energy Synchrotron Source (MacCHESS) are presented.