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Prof. Christian Betzel
University Hamburg

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0 structure based drug discovery
0 Bio Fuel
0 bio imaging
0 protein cyrstallization

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Journal article
Published: 31 August 2021 in International Journal of Molecular Sciences
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Plant U-box armadillo repeat (PUB-ARM) ubiquitin (Ub) ligases have important functions in plant defense through the ubiquitination of target proteins. Defense against pathogens involves vesicle trafficking and the formation of extracellular vesicles. The PUB-ARM protein SENESCENCE ASSOCIATED UBIQUITIN E3 LIGASE1 (SAUL1) can form patches at the plasma membrane related to tethering multi-vesicular bodies (MVBs) to the plasma membrane. We uncovered the structure of a full-length plant ubiquitin ligase and the structural requirements of SAUL1, which are crucial for its function in patch formation. We resolved the structure of SAUL1 monomers by small-angle X-ray scattering (SAXS). The SAUL1 model showed that SAUL1 consists of two domains: a domain containing the N-terminal U-box and armadillo (ARM) repeats and the C-terminal ARM repeat domain, which includes a positively charged groove. We showed that all C-terminal ARM repeats are essential for patch formation and that this function requires arginine residue at position 736. By applying SAXS to polydisperse SAUL1 systems, the oligomerization of SAUL1 is detectable, with SAUL1 tetramers being the most prominent oligomers at higher concentrations. The oligomerization domain consists of the N-terminal U-box and some N-terminal ARM repeats. Deleting the U-box resulted in the promotion of the SAUL1 tethering function. Our findings indicate that structural changes in SAUL1 may be fundamental to its function in forming patches at the plasma membrane.

ACS Style

Jan Knop; Tim Lienemann; Haifa El-Kilani; Sven Falke; Catharina Krings; Maria Sindalovskaya; Johannes Bergler; Christian Betzel; Stefan Hoth. Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane. International Journal of Molecular Sciences 2021, 22, 9455 .

AMA Style

Jan Knop, Tim Lienemann, Haifa El-Kilani, Sven Falke, Catharina Krings, Maria Sindalovskaya, Johannes Bergler, Christian Betzel, Stefan Hoth. Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane. International Journal of Molecular Sciences. 2021; 22 (17):9455.

Chicago/Turabian Style

Jan Knop; Tim Lienemann; Haifa El-Kilani; Sven Falke; Catharina Krings; Maria Sindalovskaya; Johannes Bergler; Christian Betzel; Stefan Hoth. 2021. "Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane." International Journal of Molecular Sciences 22, no. 17: 9455.

Journal article
Published: 25 July 2021 in Microorganisms
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Staphylotrichum longicolleum FW57 (DSM105789) is a prolific chitinolytic fungus isolated from wood, with a chitinase activity of 0.11 ± 0.01 U/mg. We selected this strain for genome sequencing and annotation, and compiled its growth characteristics on four different chitinous substrates as well as two agro-industrial waste products. We found that the enzymatic mixture secreted by FW57 was not only able to digest pre-treated sugarcane bagasse, but also untreated sugarcane bagasse and maize leaves. The efficiency was comparable to a commercial enzymatic cocktail, highlighting the potential of the S. longicolleum enzyme mixture as an alternative pretreatment method. To further characterize the enzymes, which efficiently digested polymers such as cellulose, hemicellulose, pectin, starch, and lignin, we performed in-depth mass spectrometry-based secretome analysis using tryptic peptides from in-gel and in-solution digestions. Depending on the growth conditions, we were able to detect from 442 to 1092 proteins, which were annotated to identify from 134 to 224 putative carbohydrate-active enzymes (CAZymes) in five different families: glycoside hydrolases, auxiliary activities, carbohydrate esterases, polysaccharide lyases, glycosyl transferases, and proteins containing a carbohydrate-binding module, as well as combinations thereof. The FW57 enzyme mixture could be used to replace commercial enzyme cocktails for the digestion of agro-residual substrates.

ACS Style

Arslan Ali; Bernhard Ellinger; Sophie C. Brandt; Christian Betzel; Martin Rühl; Carsten Wrenger; Hartmut Schlüter; Wilhelm Schäfer; Hévila Brognaro; Martin Gand. Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms 2021, 9, 1581 .

AMA Style

Arslan Ali, Bernhard Ellinger, Sophie C. Brandt, Christian Betzel, Martin Rühl, Carsten Wrenger, Hartmut Schlüter, Wilhelm Schäfer, Hévila Brognaro, Martin Gand. Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms. 2021; 9 (8):1581.

Chicago/Turabian Style

Arslan Ali; Bernhard Ellinger; Sophie C. Brandt; Christian Betzel; Martin Rühl; Carsten Wrenger; Hartmut Schlüter; Wilhelm Schäfer; Hévila Brognaro; Martin Gand. 2021. "Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass." Microorganisms 9, no. 8: 1581.

Review
Published: 13 July 2021 in Frontiers in Cellular and Infection Microbiology
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Malaria is still today one of the most concerning diseases, with 219 million infections in 2019, most of them in Sub-Saharan Africa and Latin America, causing approx. 409,000 deaths per year. Despite the tremendous advances in malaria treatment and prevention, there is still no vaccine for this disease yet available and the increasing parasite resistance to already existing drugs is becoming an alarming issue globally. In this context, several potential targets for the development of new drug candidates have been proposed and, among those, the de novo biosynthesis pathway for the B6 vitamin was identified to be a promising candidate. The reason behind its significance is the absence of the pathway in humans and its essential presence in the metabolism of major pathogenic organisms. The pathway consists of two enzymes i.e. Pdx1 (PLP synthase domain) and Pdx2 (glutaminase domain), the last constituting a transient and dynamic complex with Pdx1 as the prime player and harboring the catalytic center. In this review, we discuss the structural biology of Pdx1 and Pdx2, together with and the understanding of the PLP biosynthesis provided by the crystallographic data. We also highlight the existing evidence of the effect of PLP synthesis inhibition on parasite proliferation. The existing data provide a flourishing environment for the structure-based design and optimization of new substrate analogs that could serve as inhibitors or even suicide inhibitors.

ACS Style

Angélica Luana C Barra; Najeeb Ullah; Luana G Morão; Carsten Wrenger; Christian Betzel; Alessandro S Nascimento. Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions. Frontiers in Cellular and Infection Microbiology 2021, 11, 688380 .

AMA Style

Angélica Luana C Barra, Najeeb Ullah, Luana G Morão, Carsten Wrenger, Christian Betzel, Alessandro S Nascimento. Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions. Frontiers in Cellular and Infection Microbiology. 2021; 11 ():688380.

Chicago/Turabian Style

Angélica Luana C Barra; Najeeb Ullah; Luana G Morão; Carsten Wrenger; Christian Betzel; Alessandro S Nascimento. 2021. "Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions." Frontiers in Cellular and Infection Microbiology 11, no. : 688380.

Journal article
Published: 10 June 2021 in Scientific Reports
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Previously, we reported the isolation of a quorum quenching protein (QQ), designated GqqA, from Komagataeibacter europaeus CECT 8546 that is highly homologous to prephenate dehydratases (PDT) (Valera et al. in Microb Cell Fact 15, 88. 10.1186/s12934-016-0482-y, 2016). GqqA strongly interfered with N-acyl-homoserine lactone (AHL) quorum sensing signals from Gram-negative bacteria and affected biofilm formation in its native host strain Komagataeibacter europaeus. Here we present and discuss data identifying GqqA as a novel acylase. ESI–MS–MS data showed unambiguously that GqqA hydrolyzes the amide bond of the acyl side-chain of AHL molecules, but not the lactone ring. Consistent with this observation the protein sequence does not carry a conserved Zn2+ binding motif, known to be essential for metal-dependent lactonases, but in fact harboring the typical periplasmatic binding protein domain (PBP domain), acting as catalytic domain. We report structural details for the native structure at 2.5 Å resolution and for a truncated GqqA structure at 1.7 Å. The structures obtained highlight that GqqA acts as a dimer and complementary docking studies indicate that the lactone ring of the substrate binds within a cleft of the PBP domain and interacts with polar residues Y16, S17 and T174. The biochemical and phylogenetic analyses imply that GqqA represents the first member of a novel type of QQ family enzymes.

ACS Style

Nadine Werner; Katrin Petersen; Christel Vollstedt; Pablo Perez Garcia; Jennifer Chow; Manuel Ferrer; Laura Fernandez-Lopez; Sven Falke; Markus Perbandt; Winfried Hinrichs; Christian Betzel; Wolfgang R. Streit. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. Scientific Reports 2021, 11, 1 -14.

AMA Style

Nadine Werner, Katrin Petersen, Christel Vollstedt, Pablo Perez Garcia, Jennifer Chow, Manuel Ferrer, Laura Fernandez-Lopez, Sven Falke, Markus Perbandt, Winfried Hinrichs, Christian Betzel, Wolfgang R. Streit. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. Scientific Reports. 2021; 11 (1):1-14.

Chicago/Turabian Style

Nadine Werner; Katrin Petersen; Christel Vollstedt; Pablo Perez Garcia; Jennifer Chow; Manuel Ferrer; Laura Fernandez-Lopez; Sven Falke; Markus Perbandt; Winfried Hinrichs; Christian Betzel; Wolfgang R. Streit. 2021. "The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity." Scientific Reports 11, no. 1: 1-14.

Preprint content
Published: 04 March 2021
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Previously, we reported the isolation of a quorum quenching protein (QQ), designated GqqA, from Komagataeibacter europaeus CECT 8546 that is highly homologous to prephenate dehydratases (PDT) 1. GqqA strongly interfered with N-acyl-homoserine lactone (AHL) quorum sensing signals from Gram-negative bacteria and affected biofilm formation in its native host strain Komagataeibacter europaeus. Here we present and discuss data identifying GqqA as a novel acylase. ESI-MS-MS data showed unambiguously that GqqA hydrolyzes the amide bond of the acyl side-chain of AHL molecules, but not the lactone ring. Consistent with this observation the protein sequence does not carry a conserved Zn2+ binding motif, known to be essential for metal-dependent lactonases, but in fact harboring the typical periplasmatic binding protein domain (PBP domain), acting as catalytic domain. We report structural details for the native structure at 2.5 Å resolution and for a truncated GqqA structure at 1.7 Å. The structures obtained highlight that GqqA acts as a dimer and complementary docking studies indicate that the lactone ring of the substrate binds within a cleft of the PBP domain and interacts with polar residues Y16, S17 and T174. The biochemical and phylogenetic analyses imply that GqqA represents the first member of a novel type of QQ family enzymes.

ACS Style

Nadine Werner; Katrin Petersen; Christel Vollstedt; Pablo Perez Garcia; Jennifer Chow; Manuel Ferrer; Laura Fernandes-Lopez; Sven Falke; Markus Perbandt; Winfried Hinrichs; Christian Betzel; Wolfgang R. Streit. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. 2021, 1 .

AMA Style

Nadine Werner, Katrin Petersen, Christel Vollstedt, Pablo Perez Garcia, Jennifer Chow, Manuel Ferrer, Laura Fernandes-Lopez, Sven Falke, Markus Perbandt, Winfried Hinrichs, Christian Betzel, Wolfgang R. Streit. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. . 2021; ():1.

Chicago/Turabian Style

Nadine Werner; Katrin Petersen; Christel Vollstedt; Pablo Perez Garcia; Jennifer Chow; Manuel Ferrer; Laura Fernandes-Lopez; Sven Falke; Markus Perbandt; Winfried Hinrichs; Christian Betzel; Wolfgang R. Streit. 2021. "The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity." , no. : 1.

Journal article
Published: 01 February 2021 in Journal of Applied Crystallography
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The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.

ACS Style

Huijong Han; Ekaterina Round; Robin Schubert; Yasmin Gül; Jana Makroczyová; Domingo Meza; Philipp Heuser; Martin Aepfelbacher; Imrich Barák; Christian Betzel; Petra Fromme; Inari Kursula; Poul Nissen; Elena Tereschenko; Joachim Schulz; Charlotte Uetrecht; Jozef Ulicný; Matthias Wilmanns; Janos Hajdu; Victor S. Lamzin; Kristina Lorenzen. The XBI BioLab for life science experiments at the European XFEL. Journal of Applied Crystallography 2021, 54, 7 -21.

AMA Style

Huijong Han, Ekaterina Round, Robin Schubert, Yasmin Gül, Jana Makroczyová, Domingo Meza, Philipp Heuser, Martin Aepfelbacher, Imrich Barák, Christian Betzel, Petra Fromme, Inari Kursula, Poul Nissen, Elena Tereschenko, Joachim Schulz, Charlotte Uetrecht, Jozef Ulicný, Matthias Wilmanns, Janos Hajdu, Victor S. Lamzin, Kristina Lorenzen. The XBI BioLab for life science experiments at the European XFEL. Journal of Applied Crystallography. 2021; 54 (1):7-21.

Chicago/Turabian Style

Huijong Han; Ekaterina Round; Robin Schubert; Yasmin Gül; Jana Makroczyová; Domingo Meza; Philipp Heuser; Martin Aepfelbacher; Imrich Barák; Christian Betzel; Petra Fromme; Inari Kursula; Poul Nissen; Elena Tereschenko; Joachim Schulz; Charlotte Uetrecht; Jozef Ulicný; Matthias Wilmanns; Janos Hajdu; Victor S. Lamzin; Kristina Lorenzen. 2021. "The XBI BioLab for life science experiments at the European XFEL." Journal of Applied Crystallography 54, no. 1: 7-21.

Reply
Published: 08 December 2020 in Toxins
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We appreciate the commentary on our article, and we would like to take the opportunity to address several points raised in the reviewers’ commentary

ACS Style

Aisha Munawar; Benjamin Dreyer; Hartmut Schlüter; Christian Betzel. Reply to Comments on Proteomic Investigations of Two Pakistani Naja Snake Venom Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins 2020, 12, 669. Toxins 2020, 12, 781 .

AMA Style

Aisha Munawar, Benjamin Dreyer, Hartmut Schlüter, Christian Betzel. Reply to Comments on Proteomic Investigations of Two Pakistani Naja Snake Venom Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins 2020, 12, 669. Toxins. 2020; 12 (12):781.

Chicago/Turabian Style

Aisha Munawar; Benjamin Dreyer; Hartmut Schlüter; Christian Betzel. 2020. "Reply to Comments on Proteomic Investigations of Two Pakistani Naja Snake Venom Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins 2020, 12, 669." Toxins 12, no. 12: 781.

Journal article
Published: 22 October 2020 in Toxins
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Latest advancement of omics technologies allows in-depth characterization of venom compositions. In the present work we present a proteomic study of two snake venoms of the genus Naja i.e., Naja naja (black cobra) and Naja oxiana (brown cobra) of Pakistani origin. The present study has shown that these snake venoms consist of a highly diversified proteome. Furthermore, the data also revealed variation among closely related species. High throughput mass spectrometric analysis of the venom proteome allowed to identify for the N. naja venom 34 protein families and for the N. oxiana 24 protein families. The comparative evaluation of the two venoms showed that N. naja consists of a more complex venom proteome than N. oxiana venom. Analysis also showed N-terminal acetylation (N-ace) of a few proteins in both venoms. To the best of our knowledge, this is the first study revealing this posttranslational modification in snake venom. N-ace can shed light on the mechanism of regulation of venom proteins inside the venom gland. Furthermore, our data showed the presence of other body proteins, e.g., ankyrin repeats, leucine repeats, zinc finger, cobra serum albumin, transferrin, insulin, deoxyribonuclease-2-alpha, and other regulatory proteins in these venoms. Interestingly, our data identified Ras-GTpase type of proteins, which indicate the presence of extracellular vesicles in the venom. The data can support the production of distinct and specific anti-venoms and also allow a better understanding of the envenomation and mechanism of distribution of toxins. Data are available via ProteomeXchange with identifier PXD018726.

ACS Style

Aisha Manuwar; Benjamin Dreyer; Andreas Böhmert; Anwar Ullah; Zia Mughal; Ahmed Akrem; Syed Abid Ali; Hartmut Schlüter; Christian Betzel. Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins 2020, 12, 669 .

AMA Style

Aisha Manuwar, Benjamin Dreyer, Andreas Böhmert, Anwar Ullah, Zia Mughal, Ahmed Akrem, Syed Abid Ali, Hartmut Schlüter, Christian Betzel. Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins. 2020; 12 (11):669.

Chicago/Turabian Style

Aisha Manuwar; Benjamin Dreyer; Andreas Böhmert; Anwar Ullah; Zia Mughal; Ahmed Akrem; Syed Abid Ali; Hartmut Schlüter; Christian Betzel. 2020. "Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles." Toxins 12, no. 11: 669.

Journal article
Published: 13 October 2020 in Communications Biology
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There is an increasing demand for rapid, effective methods to identify and detect protein micro- and nano-crystal suspensions for serial diffraction data collection at X-ray free-electron lasers or high-intensity micro-focus synchrotron radiation sources. Here, we demonstrate a compact multimodal, multiphoton microscope, driven by a fiber-based ultrafast laser, enabling excitation wavelengths at 775 nm and 1300 nm for nonlinear optical imaging, which simultaneously records second-harmonic generation, third-harmonic generation and three-photon excited ultraviolet fluorescence to identify and detect protein crystals with high sensitivity. The instrument serves as a valuable and important tool supporting sample scoring and sample optimization in biomolecular crystallography, which we hope will increase the capabilities and productivity of serial diffraction data collection in the future.

ACS Style

Qing-Di Cheng; Hsiang-Yu Chung; Robin Schubert; Shih-Hsuan Chia; Sven Falke; Celestin Nzanzu Mudogo; Franz X. Kärtner; Guoqing Chang; Christian Betzel. Protein-crystal detection with a compact multimodal multiphoton microscope. Communications Biology 2020, 3, 1 -7.

AMA Style

Qing-Di Cheng, Hsiang-Yu Chung, Robin Schubert, Shih-Hsuan Chia, Sven Falke, Celestin Nzanzu Mudogo, Franz X. Kärtner, Guoqing Chang, Christian Betzel. Protein-crystal detection with a compact multimodal multiphoton microscope. Communications Biology. 2020; 3 (1):1-7.

Chicago/Turabian Style

Qing-Di Cheng; Hsiang-Yu Chung; Robin Schubert; Shih-Hsuan Chia; Sven Falke; Celestin Nzanzu Mudogo; Franz X. Kärtner; Guoqing Chang; Christian Betzel. 2020. "Protein-crystal detection with a compact multimodal multiphoton microscope." Communications Biology 3, no. 1: 1-7.

Journal article
Published: 03 October 2020 in IUCrJ
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With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid spheroidene and a ubiquinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of spheroidene in its binding site.

ACS Style

Georgii Selikhanov; Tatiana Fufina; Lyudmila Vasilieva; Christian Betzel; Azat Gabdulkhakov. Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. IUCrJ 2020, 7, 1084 -1091.

AMA Style

Georgii Selikhanov, Tatiana Fufina, Lyudmila Vasilieva, Christian Betzel, Azat Gabdulkhakov. Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. IUCrJ. 2020; 7 (6):1084-1091.

Chicago/Turabian Style

Georgii Selikhanov; Tatiana Fufina; Lyudmila Vasilieva; Christian Betzel; Azat Gabdulkhakov. 2020. "Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center." IUCrJ 7, no. 6: 1084-1091.

Journal article
Published: 24 September 2020 in Scientific Reports
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Enzymatic degradation of vegetal biomass offers versatile procedures to improve the production of alternative fuels and other biomass-based products. Here we present the three-dimensional structure of a xylanase from Nectria haematococca (NhGH11) at 1.0 Å resolution and its functional properties. The atomic resolution structure provides details and insights about the complex hydrogen bonding network of the active site region and allowed a detailed comparison with homologous structures. Complementary biochemical studies showed that the xylanase can catalyze the hydrolysis of complex xylan into simple xylose aldopentose subunits of different lengths. NhGH11 can catalyze the efficient breakdown of beechwood xylan, xylan polysaccharide, and wheat arabinoxylan with turnover numbers of 1730.6 ± 318.1 min−1, 1648.2 ± 249.3 min−1 and 2410.8 ± 517.5 min−1 respectively. NhGH11 showed maximum catalytic activity at pH 6.0 and 45 °C. The mesophilic character of NhGH11 can be explained by distinct structural features in comparison to thermophilic GH11 enzymes, including the number of hydrogen bonds, side chain interactions and number of buried water molecules. The enzymatic activity of NhGH11 is not very sensitive to metal ions and chemical reagents that are typically present in associated industrial production processes. The data we present highlights the potential of NhGH11 to be applied in industrial biomass degradation processes.

ACS Style

Hina Andaleeb; Najeeb Ullah; Sven Falke; Markus Perbandt; Hévila Brognaro; Christian Betzel. High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. Scientific Reports 2020, 10, 1 -13.

AMA Style

Hina Andaleeb, Najeeb Ullah, Sven Falke, Markus Perbandt, Hévila Brognaro, Christian Betzel. High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. Scientific Reports. 2020; 10 (1):1-13.

Chicago/Turabian Style

Hina Andaleeb; Najeeb Ullah; Sven Falke; Markus Perbandt; Hévila Brognaro; Christian Betzel. 2020. "High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca." Scientific Reports 10, no. 1: 1-13.

Journal article
Published: 19 August 2020 in International Journal of Molecular Sciences
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Plasmodium species are protozoan parasites causing the deadly malaria disease. They have developed effective resistance mechanisms against most antimalarial medication, causing an urgent need to identify new antimalarial drug targets. Ideally, new drugs would be generated to specifically target the parasite with minimal or no toxicity to humans, requiring these drug targets to be distinctly different from the host’s metabolic processes or even absent in the host. In this context, the essential presence of vitamin B6 biosynthesis enzymes in Plasmodium, the pyridoxal phosphate (PLP) biosynthesis enzyme complex, and its absence in humans is recognized as a potential drug target. To characterize the PLP enzyme complex in terms of initial drug discovery investigations, we performed structural analysis of the Plasmodium vivax PLP synthase domain (Pdx1), glutaminase domain (Pdx2), and Pdx1–Pdx2 (Pdx) complex (PLP synthase complex) by utilizing complementary bioanalytical techniques, such as dynamic light scattering (DLS), X-ray solution scattering (SAXS), and electron microscopy (EM). Our investigations revealed a dodecameric Pdx1 and a monodispersed Pdx complex. Pdx2 was identified in monomeric and in different oligomeric states in solution. Interestingly, mixing oligomeric and polydisperse Pdx2 with dodecameric monodisperse Pdx1 resulted in a monodispersed Pdx complex. SAXS measurements revealed the low-resolution dodecameric structure of Pdx1, different oligomeric structures for Pdx2, and a ring-shaped dodecameric Pdx1 decorated with Pdx2, forming a heteromeric 24-meric Pdx complex.

ACS Style

Najeeb Ullah; Hina Andaleeb; Celestin Nzanzu Mudogo; Sven Falke; Christian Betzel; Carsten Wrenger. Solution Structures and Dynamic Assembly of the 24-Meric Plasmodial Pdx1–Pdx2 Complex. International Journal of Molecular Sciences 2020, 21, 5971 .

AMA Style

Najeeb Ullah, Hina Andaleeb, Celestin Nzanzu Mudogo, Sven Falke, Christian Betzel, Carsten Wrenger. Solution Structures and Dynamic Assembly of the 24-Meric Plasmodial Pdx1–Pdx2 Complex. International Journal of Molecular Sciences. 2020; 21 (17):5971.

Chicago/Turabian Style

Najeeb Ullah; Hina Andaleeb; Celestin Nzanzu Mudogo; Sven Falke; Christian Betzel; Carsten Wrenger. 2020. "Solution Structures and Dynamic Assembly of the 24-Meric Plasmodial Pdx1–Pdx2 Complex." International Journal of Molecular Sciences 21, no. 17: 5971.

Journal article
Published: 30 January 2020 in Nature Communications
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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 TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

ACS Style

Karol Nass; Lars Redecke; M. Perbandt; O. Yefanov; M. Klinge; R. Koopmann; F. Stellato; A. Gabdulkhakov; R. Schönherr; D. Rehders; J. M. Lahey-Rudolph; A. Aquila; A. Barty; S. Basu; R. B. Doak; R. Duden; M. Frank; R. Fromme; S. Kassemeyer; G. Katona; R. Kirian; H. Liu; I. Majoul; J. M. Martin-Garcia; M. Messerschmidt; R. L. Shoeman; U. Weierstall; S. Westenhoff; T. A. White; G. J. Williams; C. H. Yoon; N. Zatsepin; P. Fromme; M. Duszenko; H. N. Chapman; C. Betzel. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nature Communications 2020, 11, 1 -13.

AMA Style

Karol Nass, Lars Redecke, M. Perbandt, O. Yefanov, M. Klinge, R. Koopmann, F. Stellato, A. Gabdulkhakov, R. Schönherr, D. Rehders, J. M. Lahey-Rudolph, A. Aquila, A. Barty, S. Basu, R. B. Doak, R. Duden, M. Frank, R. Fromme, S. Kassemeyer, G. Katona, R. Kirian, H. Liu, I. Majoul, J. M. Martin-Garcia, M. Messerschmidt, R. L. Shoeman, U. Weierstall, S. Westenhoff, T. A. White, G. J. Williams, C. H. Yoon, N. Zatsepin, P. Fromme, M. Duszenko, H. N. Chapman, C. Betzel. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nature Communications. 2020; 11 (1):1-13.

Chicago/Turabian Style

Karol Nass; Lars Redecke; M. Perbandt; O. Yefanov; M. Klinge; R. Koopmann; F. Stellato; A. Gabdulkhakov; R. Schönherr; D. Rehders; J. M. Lahey-Rudolph; A. Aquila; A. Barty; S. Basu; R. B. Doak; R. Duden; M. Frank; R. Fromme; S. Kassemeyer; G. Katona; R. Kirian; H. Liu; I. Majoul; J. M. Martin-Garcia; M. Messerschmidt; R. L. Shoeman; U. Weierstall; S. Westenhoff; T. A. White; G. J. Williams; C. H. Yoon; N. Zatsepin; P. Fromme; M. Duszenko; H. N. Chapman; C. Betzel. 2020. "In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors." Nature Communications 11, no. 1: 1-13.

Journal article
Published: 13 December 2019 in Heliyon
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Liquid-liquid phase separation (LLPS) phenomena have been observed in vitro as well as in vivo and came in focus of interdisciplinary research activities particularly aiming at understanding the physico-chemical pathways of LLPS and its functionality in recent years. Dynamic light scattering (DLS) has been proven to be a most efficient method to analyze macromolecular clustering in solutions and suspensions with diverse applications in life sciences, material science and biotechnology. For spatially and time-resolved investigations of LLPS, i.e. formation of liquid dense protein clusters (LDCs) and aggregation, a novel eight-channel in situ DLS instrument was designed, constructed and applied. The real time formation of LDCs of glucose isomerase (GI) and bovine pancreatic trypsin inhibitor (BPTI) under different physico-chemical conditions was investigated in situ. Complex shifts in the particle size distributions indicated growth of LDCs up to the μm size regime. Additionally, near-UV circular dichroism spectroscopy was performed to monitor the folding state of the proteins in the process of LDC formation.

ACS Style

Sven Falke; Hévila Brognaro; Arayik Martirosyan; Karsten Dierks; Christian Betzel. A multi-channel in situ light scattering instrument utilized for monitoring protein aggregation and liquid dense cluster formation. Heliyon 2019, 5, e03016 .

AMA Style

Sven Falke, Hévila Brognaro, Arayik Martirosyan, Karsten Dierks, Christian Betzel. A multi-channel in situ light scattering instrument utilized for monitoring protein aggregation and liquid dense cluster formation. Heliyon. 2019; 5 (12):e03016.

Chicago/Turabian Style

Sven Falke; Hévila Brognaro; Arayik Martirosyan; Karsten Dierks; Christian Betzel. 2019. "A multi-channel in situ light scattering instrument utilized for monitoring protein aggregation and liquid dense cluster formation." Heliyon 5, no. 12: e03016.

Journal article
Published: 30 November 2019 in Journal of Molecular Structure
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The orexigenic peptide ghrelin is involved in various and vital physiological processes such as food uptake, regulation of body weight and glucose metabolism. At Ser3 ghrelin is modified with a fatty acid. This unique posttranslational modification renders ghrelin active to bind to the growth hormone secretagogue receptor (GHSR)1a whereas deacylated ghrelin is inactive. The L-aptamer NOX-B11 was identified to specifically bind and neutralize octanoylated, i.e. active ghrelin. L-aptamers (also termed Spiegelmers) are oligonucleotide binders built from non-natural L-nucleotides that confer resistance to nucleases. Dynamic light and X-ray scattering measurements were applied to learn more about the specific recognition of a fatty acid modification by an oligonucleotide. First data revealed that upon ghrelin binding NOX-B11 undergoes a conformational change resulting in a 1:1 Ghrelin•NOX-B11 complex. Furthermore, crystals of Ghrelin•NOX-B11 were obtained and optimized by multiple cycles of micro seeding. X-ray diffraction data were collected from a single crystal to a resolution of 2.65 Å and the space group was determined to be C2. The Matthews coefficient was calculated to be 2.75 Å3Da−1, corresponding to a solvent content of approx. 60%.

ACS Style

Christina Schmidt; Markus Perbandt; Sven Klussmann; Christian Betzel. Molecular characterization of a ghrelin-l-aptamer complex. Journal of Molecular Structure 2019, 1204, 127510 .

AMA Style

Christina Schmidt, Markus Perbandt, Sven Klussmann, Christian Betzel. Molecular characterization of a ghrelin-l-aptamer complex. Journal of Molecular Structure. 2019; 1204 ():127510.

Chicago/Turabian Style

Christina Schmidt; Markus Perbandt; Sven Klussmann; Christian Betzel. 2019. "Molecular characterization of a ghrelin-l-aptamer complex." Journal of Molecular Structure 1204, no. : 127510.

Journal article
Published: 26 November 2019 in Crystals
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Protein phase separation and protein liquid cluster formation have been observed and analysed in protein crystallization experiments and, in recent years, have been reported more frequently, especially in studies related to membraneless organelles and protein cluster formation in cells. A detailed understanding about the phase separation process preceding liquid dense cluster formation will elucidate what has, so far, been poorly understood—despite intracellular crowding and phase separation being very common processes—and will also provide more insights into the early events of in vitro protein crystallization. In this context, the phase separation and crystallization kinetics of concanavalin A were analysed in detail, which applies simultaneous dynamic light scattering and depolarized dynamic light scattering to obtain insights into metastable intermediate states between the soluble phase and the crystalline form. A multi-step mechanism was identified for ConA phase separation, according to the resultant ACF decay, acquired after an increase in the concentration of the crowding agent until a metastable ConA gel intermediate between the soluble and final crystalline phases was observed. The obtained results also revealed that ConA is trapped in a macromolecular network due to short-range intermolecular protein interactions and is unable to transform back into a non-ergodic solution.

ACS Style

Hévila Brognaro; Sven Falke; Celestin Nzanzu Mudogo; Christian Betzel. Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering. Crystals 2019, 9, 620 .

AMA Style

Hévila Brognaro, Sven Falke, Celestin Nzanzu Mudogo, Christian Betzel. Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering. Crystals. 2019; 9 (12):620.

Chicago/Turabian Style

Hévila Brognaro; Sven Falke; Celestin Nzanzu Mudogo; Christian Betzel. 2019. "Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering." Crystals 9, no. 12: 620.

Review
Published: 30 October 2019 in Traffic
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Liquid‐Liquid Phase Separation (LLPS) in cells is known as a complex physicochemical process causing the formation of membrane‐less organelles (MLOs). Cells have well‐defined different membrane‐surrounded organelles like mitochondria, endoplasmic reticulum, lysosomes, peroxisomes, etc., however, on demand they can create membrane‐less organelles as stress granules, nucleoli and P bodies to cover vital functions and regulatory activities. However, the mechanism of intracellular molecule assembly into functional compartments within a living cell remains till now not fully understood. (Soft Matter 2019, 15 (6):1135‐1154). In vitro and in vivo investigations unveiled that MLOs emerge after preceding liquid‐liquid, liquid‐gel, liquid‐semi‐crystalline, or liquid‐crystalline phase separations. Liquid‐liquid and liquid‐gel MLOs form the majority of cellular phase separation events, while the occurrence of micro‐sized crystals in cells was only rarely observed, however can be considered as a result of a preceding protein phase separation event. In vivo, also known and termed as in cellulo crystals, are reported since 1853 (Botanische Zeitung, 13, 881‐8 821 855; CR Mem. Soc. Biol. 5, 450‐454, 1853). In some cases, they have been linked to vital cellular functions, such as storage and detoxification. However, the occurrence of in cellulo crystals is also associated to diseases like cataract, hemoglobin C diseases etc. (Biology Chemistry De Gruyter 2018, 399 (7):751‐752). Therefore, better knowledge about the involved molecular processes will support drug discovery investigations to cure diseases related to in cellulo crystallization. We summarize physical and chemical determinants known today required for phase separation initiation and formation and in cellulo crystal growth. This article is protected by copyright. All rights reserved.

ACS Style

Celestin Nzanzu Mudogo; Sven Falke; Hévila Brognaro; Michael Duszenko; Christian Betzel. Protein phase separation and determinants of in cell crystallization. Traffic 2019, 21, 220 -230.

AMA Style

Celestin Nzanzu Mudogo, Sven Falke, Hévila Brognaro, Michael Duszenko, Christian Betzel. Protein phase separation and determinants of in cell crystallization. Traffic. 2019; 21 (2):220-230.

Chicago/Turabian Style

Celestin Nzanzu Mudogo; Sven Falke; Hévila Brognaro; Michael Duszenko; Christian Betzel. 2019. "Protein phase separation and determinants of in cell crystallization." Traffic 21, no. 2: 220-230.

Journal article
Published: 28 October 2019 in Toxins
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(1) Background. Snake venom phosphodiesterases (SVPDEs) are among the least studied venom enzymes. In envenomation, they display various pathological effects, including induction of hypotension, inhibition of platelet aggregation, edema, and paralysis. Until now, there have been no 3D structural studies of these enzymes, thereby preventing structure–function analysis. To enable such investigations, the present work describes the model-based structural and functional characterization of a phosphodiesterase from Crotalus adamanteus venom, named PDE_Ca. (2) Methods. The PDE_Ca structure model was produced and validated using various software (model building: I-TESSER, MODELLER 9v19, Swiss-Model, and validation tools: PROCHECK, ERRAT, Molecular Dynamic Simulation, and Verif3D). (3) Results. The proposed model of the enzyme indicates that the 3D structure of PDE_Ca comprises four domains, a somatomedin B domain, a somatomedin B-like domain, an ectonucleotide pyrophosphatase domain, and a DNA/RNA non-specific domain. Sequence and structural analyses suggest that differences in length and composition among homologous snake venom sequences may account for their differences in substrate specificity. Other properties that may influence substrate specificity are the average volume and depth of the active site cavity. (4) Conclusion. Sequence comparisons indicate that SVPDEs exhibit high sequence identity but comparatively low identity with mammalian and bacterial PDEs.

ACS Style

Anwar Ullah; Kifayat Ullah; Hamid Ali; Christian Betzel; Shafiq Ur Rehman. The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases. Toxins 2019, 11, 625 .

AMA Style

Anwar Ullah, Kifayat Ullah, Hamid Ali, Christian Betzel, Shafiq Ur Rehman. The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases. Toxins. 2019; 11 (11):625.

Chicago/Turabian Style

Anwar Ullah; Kifayat Ullah; Hamid Ali; Christian Betzel; Shafiq Ur Rehman. 2019. "The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases." Toxins 11, no. 11: 625.

Chapter
Published: 22 September 2019 in Biomedical and Resonance Optics
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Focus a laser on dissolved particles and analyze the scattered light to reveal their size. This well established principle is used in dynamic light scattering (DLS), or also called photon-correlation spectroscopy, which is a widely popular and highly adaptable analytical method applied in different fields of life and material sciences, as well as in industrial quality control processes.

ACS Style

Sven Falke; Christian Betzel. Dynamic Light Scattering (DLS). Biomedical and Resonance Optics 2019, 8, 173 -193.

AMA Style

Sven Falke, Christian Betzel. Dynamic Light Scattering (DLS). Biomedical and Resonance Optics. 2019; 8 ():173-193.

Chicago/Turabian Style

Sven Falke; Christian Betzel. 2019. "Dynamic Light Scattering (DLS)." Biomedical and Resonance Optics 8, no. : 173-193.

Paper
Published: 07 August 2019 in Physical Chemistry Chemical Physics
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Trivalent lanthanide and actinide can strongly bind to calmodulin (CaM). The global structure of Ln/An-bound CaM were found to be similar to Ca-CaM but the local environment around Ln/An is distorted giving less structural rigidity to Ln/An-CaM.

ACS Style

Björn Drobot; Moritz Schmidt; Yuji Mochizuki; Takaya Abe; Koji Okuwaki; Florian Brulfert; Sven Falke; Sergey A. Samsonov; Yuto Komeiji; Christian Betzel; Thorsten Stumpf; Johannes Raff; Satoru Tsushima. Cm3+/Eu3+induced structural, mechanistic and functional implications for calmodulin. Physical Chemistry Chemical Physics 2019, 21, 21213 -21222.

AMA Style

Björn Drobot, Moritz Schmidt, Yuji Mochizuki, Takaya Abe, Koji Okuwaki, Florian Brulfert, Sven Falke, Sergey A. Samsonov, Yuto Komeiji, Christian Betzel, Thorsten Stumpf, Johannes Raff, Satoru Tsushima. Cm3+/Eu3+induced structural, mechanistic and functional implications for calmodulin. Physical Chemistry Chemical Physics. 2019; 21 (38):21213-21222.

Chicago/Turabian Style

Björn Drobot; Moritz Schmidt; Yuji Mochizuki; Takaya Abe; Koji Okuwaki; Florian Brulfert; Sven Falke; Sergey A. Samsonov; Yuto Komeiji; Christian Betzel; Thorsten Stumpf; Johannes Raff; Satoru Tsushima. 2019. "Cm3+/Eu3+induced structural, mechanistic and functional implications for calmodulin." Physical Chemistry Chemical Physics 21, no. 38: 21213-21222.