Gergely Katona

University of Gothenburg | GU · Department of Chemistry & Molecular Biology

Whether long-range quantum coherent states could exist in biological systems, and beyond low-temperature regimes where quantum physics is known to be applicable, has been the subject to debate for decades. It was proposed by Fröhlich that vibrational modes within protein molecules can order and condense into a lowest-frequency vibrational mode in a...

Although virtual and augmented reality (VR and AR) techniques have been used extensively in specialized laboratories, only recently did they become affordable, reaching wider consumer markets. With increased availability, it is timely to examine the roles that VR and AR may play in teaching structural biology and in experiencing complex data sets s...

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography¹ using an X-ray free-electron laser² to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridi...

This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We observed differential expression of PRC2 subunits in CD4+ T cells with varying levels of survivin e...

In the realm of atomic physics and chemistry, composition emerges as the most powerful means of describing matter. Mendeleev’s periodic table and chemical formulas, while not entirely free from ambiguities, provide robust approximations for comprehending the properties of atoms, chemicals, and their collective behaviours, which stem from the dynami...

Electrodynamic interactions between biomolecules are of potential biological interest for signaling warranting investigation of their activation through various mechanisms in living systems. Here, using as model system a light harvesting protein within the phycobilisome antenna system of red algae, we proved that not only light exposure but also th...

Background Bivalent regions of chromatin (BvCR) are characterized by trimethylated lysine 4 (H3K4me3) and lysine 27 on histone H3 (H3K27me3) deposition which aid gene expression control during cell differentiation. The role of BvCR in post-transcriptional DNA damage response remains unidentified. Oncoprotein survivin binds chromatin and mediates IF...

With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchro...

Protein dynamics is shaped by interactions between thermal fluctuations, external forces, and molecular structures. Thermal fluctuations have high frequencies and are hence very challenging to quantify. We were able to record femtosecond X-ray diffraction snapshots and determine atomic displacements of crystalline bovine trypsin atoms either in the...

Background Immunomodulating treatment in rheumatoid arthritis (RA) prevent aberrant proliferation and activation of CD4+T cells by various mechanisms. Yet, drug choice remains empirical. In RA, unrepaired DNA damage promote the arthritogenic potential of effector T cells [1]. DNA damage response (DDR) combines cell cycle check points, DNA repair an...

This study explores a regulatory role of oncoprotein survivin on the bivalent regions of chromatin (BvCR) characterized by concomitant deposition of trimethylated lysine of histone H3 at position 4 (H3K4me3) and 27 (H3K27me3). Intersect between BvCR and chromatin sequences bound to survivin demonstrated their co-localization on cis-regulatory eleme...

In the realm of atomic physics and chemistry, composition emerges as the most powerful means of describing matter. Mendeleev’s periodic table and chemical formulas, while not entirely free from ambiguities, provide robust approximations for comprehending the properties of atoms, chemicals, and their collective behaviours, which stem from the dynami...

Background Rheumatoid arthritis (RA) is associated with aberrant epigenomic control which obstructs the proper function of CD4 T cells. Bivalent chromatin regions (BvCR), containing histone H3 tail trimethylation at lysine 4 (H3K4me3) and lysine 27 (H3K27me3), act as a major organizer of the 3D nuclear environment required for efficient T cell deve...

In this study, we explore the role of nuclear survivin in maintaining the effector phenotype of IFNγ-producing T cells acting through the transcriptional control of glucose utilization. High expression of survivin in CD4⁺T cells was associated with IFNγ-dependent phenotype and anaerobic glycolysis. Transcriptome of CD4⁺ cells and sequencing of surv...

Background Bivalent chromatin (BvCR) is characterized by the presence of simultaneous active and repressive modifications on histone H3 proteins. Influencing expression of the genes, BvCR determine cell fate and direct differentiation and lineage commitment in primary T cells and contribute to autoimmunity. Survivin is highly expressed during cell...

Survivin is a small protein that belongs to the inhibitor of apoptosis protein family and participates in cell division and apoptosis. It was actively studied in human cancers, inflammatory diseases and in autoimmune diseases. Here, we reveal that survivin takes part in epigenetic gene silencing by interaction with the polycomb repressive complex 2...

MicroScale Thermophoresis (MST) follows the movement of fluorescent-labelled biomolecules with different sizes along a temperature gradient. The presence of a “contrary trend” pattern, that is, the trend of fluorescence change reversing at higher titrant concentrations, is a well-known problem with uncertain cause. Conventionally, binding curves an...

Proper physiological functioning of any cell type requires ordered chromatin organization. In this context, cohesin complex performs important functions preventing premature separation of sister chromatids after DNA replication. In partnership with CCCTC-binding factor, it ensures insulator activity to organize enhancers and promoters within regula...

This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We observed differential expression of PRC2 subunits in CD4+ T cells with varying levels of survivin e...

Upon activation, CD4 ⁺ T cells adapt metabolically to fulfill their effector function in autoimmunity. Here we show that nuclear survivin is essential for transcriptional regulation of glucose utilization. We found that the glycolytic switch in interferon (IFN) g–producing CD4 ⁺ cells is dependent on a complex of survivin with interferon regulatory...

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔCP‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions...

Interferon-gamma (IFNγ) producing T cells develop metabolic adaptation required for their effector functions in tumour biology, autoimmunity and antiviral defence. Using sorted CD4 ⁺ cells we demonstrated that glycolytic switch and high glucose uptake in IFNγ-producing cells was associated with survivin expression. Inhibition of survivin restored g...

High-resolution diffraction studies of macromolecules incorporate the tensor form of the anisotropic displacement parameter (ADP) of atoms from their mean position. The comparison of these parameters requires a statistical framework that can handle the experimental and modeling errors linked to structure determination. Here, a Bayesian machine lear...

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis can reveal links between the protein free energy landscape, global protein dynamics and enzyme turnover, suggesting that subtle changes molecular interactions at the act...

Background Survivin, coded by BIRC5 gene, is a multitasking protein essential for cell renewal and homeostasis. In autoimmune conditions as rheumatoid and psoriasis arthritis, survivin was associated with inflammation severity and joint damage. Importantly, inhibition of survivin alleviated experimental arthritis in mice. We have recently shown sur...

Background Survivin is an integral part of the Chromosomal Passenger Complex (CPC) which plays a vital role in mitosis. Experiments have demonstrated that survivin can physically bind to DNA. Crystallographic studies show that survivin binds to Threonine-3 of histone H3. In patients with autoimmune diseases, increased survivin expression contribute...

Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals u...

Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle...

Background The oncogenic protein survivin is a marker of severe rheumatoid arthritis (RA). High serum levels of Survivin predict progressive joint damage ¹ and poor treatment response ² . Objectives To study the role of survivin in the transcriptional regulation of phenotype in CD4 ⁺ T cells. Methods CD4 ⁺ T cells of RA female patients were isola...

Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools...

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMP...

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography...

Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been...

The high-brilliance beamline P12 of the EMBL at PETRA III (DESY) is dedicated to biological small-angle X-ray scattering (SAXS) and is optimized for scattering experiments on macromolecular solutions. P12 offers automated sample delivery with on-line data processing capabilities but also tailored sample environments. In addition, the recent develop...

Vibrational oscillations in amide and side chain groups are well studied in proteins, but these are not occupied at ambient temperatures and they have a short lifespan when infrared radiation is present. Active vibrational modes in proteins lie in the terahertz (THz) range at physiological temperatures, and their experimental descriptions of them i...

Background Oncoprotein survivin emerged as an important player in the pathogenesis of rheumatoid arthritis (RA). Results of genome-wide study suggest that survivin may take part in transcription stimulation of the RA-specific genes. Objectives To identify and describe survivin-dependent differences in transcription pattern between CD4⁺ T-cells of...

A biomolecular ensemble exhibits different responses to a temperature gradient depending on its diffusion properties. MicroScale Thermophoresis technique exploits this effect and is becoming a popular technique for analyzing interactions of biomolecules in solution. When comparing affinities of related compounds, the reliability of the determined t...

Annexin A2 (ANXA2) has a versatile role in membrane-associated functions including membrane aggregation, endo- and exocytosis, and it is regulated by post-translational modifications and protein-protein interactions through the unstructured N-terminal domain (NTD). Our sequence analysis revealed a short motif responsible for clamping the NTD to the...

Survivin is a protein functionally important for cell division, apoptosis, and possibly, for micro-RNA biogenesis. It is an established marker of malignant cell transformation. In non-malignant conditions, the unique properties of survivin make it indispensable for homeostasis of the immune system. Indeed, it is required for the innate and adaptive...

Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which al...

Significance The small lectin-like protein ZG16 (zymogen granulae protein 16) aggregates bacteria and by that works together with the inner colon mucus layer to maintain bacteria at a safe distance from the epithelial cell surface. In the absence of Zg16, more bacteria penetrate the epithelium, enter the regional lymph nodes and spleen, trigger the...

We have periodically (25ms on −25ms off) illuminated lysozyme crystals with 0.4 THz radiation and simultaneously monitored their X-ray diffraction intensity in order to study non-thermal structural changes in the protein. In this work we analyze the X-ray scaled and unmerged diffraction intensity observations using a multivariate Bayesian model in...

In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for imp...

Mitogen-activated protein kinases (MAPK) promote MAPK activated protein kinase (MAPKAPK) activation. In the MAPK pathway responsible to cell growth, ERK2 initiates the first phosphorylation event on RSK1, which is inhibited by calcium-binding S100 proteins in malignant melanomas. Here we present a detailed in vitro biochemical and structural charac...

Follicular T helper (Tfh) cells are recognized by the expression of CXCR5 and the transcriptional regulator Bcl-6. Tfh cells control B cell maturation and antibody production, and if deregulated, may lead to autoimmunity. Here, we study the role of the proto-oncogene survivin in the formation of Tfh cells. We show that blood Tfh cells of patients w...

Serine proteases and their natural inhibitors have long been served as excellent models for studying (primary, secondary and tertiary) structure - activity relationships of biologically interacting proteins. As protein flexibility has been accepted as a "fourth dimension" of the protein structure, its contribution to the binding process has gained...

S100A4 or metastasin plays a central role in the progression of metastatic diseases. Like many other examples, the protein S100A4 contains ordered and disordered regions. The aim of this study was to determine how the disordered C‐terminal region influences the binding to Ca2+ and in turn how Ca ²⁺ binding alters the dynamics of the C‐terminal rand...

Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an...

LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2 bound form by us...

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picosecon...

Photosynthetic reaction centers develop a stable charge separated state upon illumination. To investigate the molecular vibrations associated with the illuminated state of a reaction center we recorded terahertz absorption spectra of the photosynthetic reaction center from Rhodobacter sphaeroides in the dark and upon illumination and observed a sma...

S100A4 interacts with many binding partners upon Ca2+ activation and is strongly associated with increased metastasis formation. In order to understand the role of the C-terminal random coil for the protein function we examined how small angle X-ray scattering of the wild-type S100A4 and its C-terminal deletion mutant (residues 1-88, Δ13) changes u...

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femto...

This paper provides evidence for the extremely high resistance of a complex of crayfish trypsin ( CFT ) and bovine pancreatic trypsin inhibitor ( BPTI ) against heating and chemical denaturing agents such as sodium dodecyl sulfate ( SDS ) and urea. To dissociate this complex, 15 min boiling in SDS was necessary, compared to a complex of bovine tryp...

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 o...

Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from th...

Schematic representation of the compounds used in the DFT simulations. Cartesian coordinates of atoms marked with red were fixed during optimization. (TIF)

Data and refinement statistics of the additional crystal structures provided in the Supporting information. (DOC)

UV/visible spectrum of Bv Bfr crystals. (A) UV/visible spectrum of native as isolated Bv Bfr crystals before (black) and after (red) 100 s X-ray exposure at beamline ID29, ESRF (5% transmission, X-ray flux: 9.6×1010 ph/s). (B) Crystal spectrum of Fe(II) soaked Bv Bfr before (black) and after (red) 1 s X-ray exposure at beamline ID29, ESRF (5% trans...

Superposition of the pore forming residues in the 3-fold and 4-fold pore. (A) 3-fold pore (B) 4-fold pore. The native ‘as isolated’ structure, the Fe(II) soaked and double soaked structures are marked with green, blue and yellow respectively. (TIF)

Identified peptides of protease digested Bv Bfr fragments. (DOC)

Coordinate and structure factor files of the additional crystal structure named in Table S2 as Dataset S3. (ZIP)

Method description of de novo sequencing by tandem mass spectrometry and DFT calculations. (DOC)

Total energy, charge and spin distributions derived from the DFT calculations. (DOC)

Coordinate and structure factor files of the additional crystal structure named in Table S2 as Dataset S1. (ZIP)