logo ipb
logo ipb mobile
x
  • Deutsch
  • English
Login
  • Research
    • Research Mission and Profile

    • Molecular Signal Processing

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Nutrient Sensing
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Symbiosis Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Jasmonate Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Bioorganic Chemistry

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Bioactives
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Natural Products & Metabolomics
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Biotechnology
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Biofunctional Synthesis
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Computational Chemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Data & Resources
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Biochemistry of Plant Interactions

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Calcium-dependent Protein Kinases
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Cellular Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Nuclear Processes in Plant Defense
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Cell and Metabolic Biology

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Glandular Trichomes and Isoprenoid Biosynthesis
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Jasmonate Function & Mycorrhiza
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Phenylpropanoid Metabolism
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Synthetic Biology
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Independent Junior Research Groups

      • Research Groups
        • Receptor Biochemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Program Center MetaCom

      • Secretariat & All staff
      • Publikationen
      • Our Equipment
      • Research Groups
        • Metabolomics Facility
          • Projects
          • Staff
          • Publications
          • Methods
        • MetaCom Analytical Laboratory
          • Projects
          • Staff
          • Publications
          • Methods
        • Computational Plant Biochemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Biochemical Genetics of Metabolic Plasticity
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Publications

    • Good Scientific Practice

    • Research Funding

    • Networks and Collaborative Projects

      • Collaborative Projects as Coordinator
        • Completed Projects as Coordinator
      • Collaborative Projects as Partner
        • Completed Projects as Partner
      • Networks
    • Symposia and Colloquia

      • Lectures
        • IPB Seminars
      • Leibniz Plant Biochemistry Symposia
    • Alumni Research Groups

      • Research Groups
        • Auxin Signaling
          • Projects
          • Publications
        • Bioorganic Chemistry
          • Projects
          • Publications
        • Designer Glycans
          • Projects
          • Publications
        • Jasmonate Mode of Action
          • Publications
        • Protein Recognition and Degradation
          • Projects
          • Publications
        • Regulatory RNAs (MLU-associated group)
          • Projects
          • Publications
        • Signal Integration
          • Projects
          • Publications
        • Ubiquitination in Immunity
          • Projects
          • Publications
        • Cellular Coordination
          • Projects
          • Publications
  • Infrastructure
    • Databases and Tools

      • XCMS
      • Rdisop
      • CAMERA
      • MetShot
      • MassBank
      • MetFrag
      • MetFamily
      • PaCeQuant
      • CytoskeletonAnalyzer
      • GoldenMutagenesis
      • cisHighlight
      • FlagScreen
      • RootDetection
    • Technical Resources

    • Imaging Unit

    • Greenhouses and Phytochambers

    • Library Services

      • OPAC
      • Electronic Journals Library
      • Service for Employees
  • Institute
    • Organizational Chart

    • Management and Boards

      • Board of Trustees
      • Scientific Advisory Board
      • IPB Management / Board of Directors
      • Scientific Council
      • Authorized Representatives of the IPB
      • Staff Council
      • Statutes
    • Administration and Infrastructure

      • Secretariat & All Staff
      • Working Groups
        • Human Resources
        • Finance & Accounting
        • Purchasing
        • IT & Technical Support
        • Experimental Nursery
        • Facility Management
        • Library
        • Digitalization
    • Energy Management

      • Objectives and Measures
      • Energy Management Team
    • Diversity, Family and Equality

    • Public Tendering

    • Patents and Licensing

    • The IPB Welcoming Culture

    • Guest Houses

    • IPB Site Map

    • Brief IPB History

      • Bildergalerie zur Historie
      • Alte Filmsequenzen zum Institut
      • Historischer Massenspektrograph
    • Alumni Network

      • The IPB as a career launching pad
  • Career
    • Data protection information for applicants

    • PhD Program

      • PhD Student Representatives
      • DoCou - Doctoral Training Courses
      • PSSC
    • Postdocs

    • Berufsausbildung

  • Public Relations
    • News

      • 2024
      • 2023
      • 2022
      • Archiv Aktuelles
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2016
        • 2015
        • 2014
        • vor 2014
    • News Ticker Science

      • News Ticker 2024
      • News Ticker 2023
      • News Ticker 2022
      • News Ticker Archive
        • News Ticker 2021
        • News Ticker 2020
        • News Ticker 2019
    • Press Releases

      • 2024
      • 2023
      • 2022
      • Archive Press Releases
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2016
        • 2015
        • 2014
        • 2013
        • 2012
        • 2011
        • 2010
        • 2009
        • 2008
        • 2007
        • 2006
        • 2005
        • 2004
        • 2003
        • 2002
    • IPB Pressespiegel

    • Lange Nacht, die Wissen schafft

      • 2024 Long Night of Sciences
      • 2022 Long Night of Sciences
    • IPB Newsletter

    • Printed / Information Material

    • Scientific Reports / Research Highlights

    • Events

      • 2024 Leibniz Plant Biochemistry Symposium
    • Cover Art

    • Citizen Science: Pilzberatung

      • Das Reich der Pilze
      • Pilzberatung
      • Forschung an Pilzen
  • Contact
    • Directions for Visitors

    • Staff Directory

    • Imprint

    • Data Protection

    • Accessibility

  1. IPB Halle
  2. Research
  3. Publications

    • Research Mission and Profile
    • Trenner 0
    • Molecular Signal Processing
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Nutrient Sensing
        • Symbiosis Signaling
        • Jasmonate Signaling
    • Bioorganic Chemistry
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Bioactives
        • Natural Products & Metabolomics
        • Biotechnology
        • Biofunctional Synthesis
        • Computational Chemistry
        • Data & Resources
    • Biochemistry of Plant Interactions
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Calcium-dependent Protein Kinases
        • Cellular Signaling
        • Nuclear Processes in Plant Defense
    • Cell and Metabolic Biology
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Glandular Trichomes and Isoprenoid Biosynthesis
        • Jasmonate Function & Mycorrhiza
        • Phenylpropanoid Metabolism
        • Synthetic Biology
    • Independent Junior Research Groups
      • Research Groups
        • Receptor Biochemistry
    • Program Center MetaCom
      • Secretariat & All staff
      • Publikationen
      • Our Equipment
      • Research Groups
        • Metabolomics Facility
        • MetaCom Analytical Laboratory
        • Computational Plant Biochemistry
        • Biochemical Genetics of Metabolic Plasticity
    • Trenner 1
    • Publications
    • Good Scientific Practice
    • Research Funding
    • Trenner
    • Networks and Collaborative Projects
      • Collaborative Projects as Coordinator
        • Completed Projects as Coordinator
      • Collaborative Projects as Partner
        • Completed Projects as Partner
      • Networks
    • Symposia and Colloquia
      • Lectures
        • IPB Seminars
      • Leibniz Plant Biochemistry Symposia
    • Trenner
    • Alumni Research Groups
      • Research Groups
        • Auxin Signaling
        • Bioorganic Chemistry
        • Designer Glycans
        • Jasmonate Mode of Action
        • Protein Recognition and Degradation
        • Regulatory RNAs (MLU-associated group)
        • Signal Integration
        • Ubiquitination in Immunity
        • Cellular Coordination

Advanced Search

  • Type of publication
    • Publication 4
  • Year
    • 2013 2
      2021 1
      2022 14
      2023 4
      2024 2
      2025 2
  • Journal / Volume / Preprint Server Sorted by frequency and by alphabetical order
    • Applied Microbiology and Biotechnology 1
      Catalysts 1
      Chin. J. Catal. 1
      JACS Au 1
  • Author Sorted by frequency and by alphabetical order
    • Wessjohann, L. A. 14
      Davari, M. D. 10
      Franke, K. 10
      Bürstenbinder, K. 8
      Neumann, S. 8
      Brunoni, F. 7
      Floková, K. 7
      Hause, B. 7
      Mik, V. 7
      Novák, O. 7
      Strnad, M. 7
      Wasternack, C. 7
      Ziegler, J. 7
      Široká, J. 7
      Peters, K. 6
      Farag, M. A. 5
      Hussain, H. 5
      Schuster, M. 5
      Buhl, J. 4
      Dahiya, P. 4
      Dam, N. M. 4
      Grúz, J. 4
      Kaiser, M. 4
      Miersch, O. 4
      Nožková, V. 4
      Porzel, A. 4
      Pospíšil, T. 4
      Proksch, C. 4
      Rizzo, P. 4
      Schwaneberg, U. 4
      Stamm, G. 4
      Thieme, D. 4
      Tissier, A. 4
      Wirthmueller, L. 4
      van der Hoorn, R. A. L. 4
      Ament, A. 3
      Armas-Egas, L. 3
      Brandt, W. 3
      Colby, T. 3
      D’Auria, J. 3
      Eisele, S. 3
      Fernández-Niño, M. 3
      Fuchs, J. 3
      Haluška, S. 3
      Htitich, M. 3
      Karady, M. 3
      Kaur, S. 3
      Kessenbrock, T. 3
      Kourelis, J. 3
      Kralová, M. 3
      Kölling, M. 3
      Machalett, K. 3
      Matić, I. 3
      Matschi, S. 3
      Morgan, I. 3
      Papsdorf, S. 3
      Pernisová, M. 3
      Pfeiffer, P. 3
      Poslíšil, T. 3
      Potocký, M. 3
      Ravindran, B. M. 3
      Ueda, M. 3
      Voiniciuc, C. 3
      Zehnich, D. 3
      Abel, S. 2
      Arnold, N. 2
      Barrios, A. F. G. 2
      Blatt-Janmaat, K. L. 2
      Cala, M. P. 2
      Dube, M. 2
      Frolov, A. 2
      Gerothanassis, I. P. 2
      Gorbach, D. 2
      Gorzolka, K. 2
      Homann, D. 2
      Hsieh, Y.-F. 2
      Ji, Y. 2
      Kaluđerović, G. N. 2
      Lee Erickson, J. 2
      Leonova, T. 2
      Li, Z. 2
      Liu, L. 2
      Manurung, J. 2
      Marx, J. 2
      Meng, S. 2
      Miroshnichenko, D. 2
      Münch, J. 2
      Paponov, I. A. 2
      Paponov, M. 2
      Poirier, Y. 2
      Pushin, A. S. 2
      Rajakumara, E. 2
      Rennert, R. 2
      Rivera, D. G. 2
      Rosahl, S. 2
      Saoud, M. 2
      Schrank, P. 2
      Siddiqui, H. 2
      Sorokina, M. 2
      Steinbeck, C. 2
  • Year
  • Type of publication
Search narrowed by: Year: 2023 Author Sorted by frequency and by alphabetical order: Schwaneberg, U. Remove all filters
Displaying results 1 to 4 of 4.
  • Results as:
  • Print view
  • Endnote (RIS)
  • BibTeX
  • Table: CSV | HTML
Results per page:
  • 1

Publications

Pourhassan, Z. N.; Cui, H.; Muckhoff, N.; Davari, M. D.; Smits, S. H. J.; Schwaneberg, U.; Schmitt, L.; A step forward to the optimized HlyA type 1 secretion system through directed evolution Applied Microbiology and Biotechnology 107 5131-5143 (2023) DOI: 10.1007/s00253-023-12653-7
  • Abstract
  • Internet
  • BibText
  • RIS

Secretion of proteins into the extracellular space has great advantages for the production of recombinant proteins. Type 1 secretion systems (T1SS) are attractive candidates to be optimized for biotechnological applications, as they have a relatively simple architecture compared to other classes of secretion systems. A paradigm of T1SS is the hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli harboring only three membrane proteins, which makes the plasmid-based expression of the system easy. Although for decades the HlyA T1SS has been successfully applied for secretion of a long list of heterologous proteins from different origins as well as peptides, but its utility at commercial scales is still limited mainly due to low secretion titers of the system. To address this drawback, we engineered the inner membrane complex of the system, consisting of HlyB and HlyD proteins, following KnowVolution strategy. The applied KnowVolution campaign in this study provided a novel HlyB variant containing four substitutions (T36L/F216W/S290C/V421I) with up to 2.5-fold improved secretion for two hydrolases, a lipase and a cutinase. Key points • An improvement in protein secretion via the use of T1SS • Reaching almost 400 mg/L of soluble lipase into the supernatant • A step forward to making E. coli cells more competitive for applying as a secretion host Graphical Abstract

Publications

Meng, S.; Li, Z.; Ji, Y.; Ruff, A. J.; Liu, L.; Davari, M. D.; Schwaneberg, U.; Introduction of aromatic amino acids in electron transfer pathways yielded improved catalytic performance of cytochrome P450s Chin. J. Catal. 49 81-90 (2023) DOI: 10.1016/s1872-2067(23)64445-6
  • Abstract
  • Internet
  • BibText
  • RIS

Cytochrome P450s are versatile catalysts for biosynthesis applications. In the P450 catalytic cycle, two electrons are required to reduce the heme iron and activate the subsequent reductions through proposed electron transfer pathways (eTPs), which often represent the rate-limiting step in reactions. Herein, the P450 BM3 from Bacillus megaterium was engineered for improved catalytic performance by redesigning proposed eTPs. By introducing aromatic amino acids on eTPs of P450 BM3, the “best” variant P2H02 (A399Y/Q403F) showed 13.9-fold improved catalytic efficiency (kcat/KM = 913.5 L mol−1 s−1) compared with P450 BM3 WT (kcat/KM = 65.8 L mol−1 s−1). Molecular dynamics simulations and electron hopping pathways analysis revealed that aromatic amino acid substitutions bridging the cofactor flavin mononucleotide and heme iron could increase electron transfer rates and improve catalytic performance. Moreover, the introduction of tyrosines showed positive effects on catalytic efficiency by potentially protecting P450 from oxidative damage. In essence, engineering of eTPs by aromatic amino acid substitutions represents a powerful approach to design catalytically efficient P450s (such as CYP116B3) and could be expanded to other oxidoreductases relying on long-range electron transfer pathways.

Publications

Liu, Y.; Li, Z.; Cao, C.; Zhang, X.; Meng, S.; Davari, M. D.; Xu, H.; Ji, Y.; Schwaneberg, U.; Liu, L.; Engineering of substrate tunnel of P450 CYP116B3 though machine learning Catalysts 13 1228 (2023) DOI: 10.3390/catal13081228
  • Abstract
  • Internet
  • BibText
  • RIS

The combinatorial complexity of the protein sequence space presents a significant challenge for recombination experiments targeting beneficial positions. To overcome these difficulties, a machine learning (ML) approach was employed, which was trained on a limited literature dataset and combined with iterative generation and experimental data implementation. The PyPEF method was utilized to identify existing variants and predict recombinant variants targeting the substrate channel of P450 CYP116B3. Through molecular dynamics simulations, eight multiple-substituted improved variants were successfully validated. Specifically, the RMSF of variant A86T/T91H/M108S/A109M/T111P was decreased from 3.06 Å (wild type) to 1.07 Å. Additionally, the average RMSF of the variant A86T/T91P/M108V/A109M/T111P decreased to 1.41 Å, compared to the wild type’s 1.53 Å. Of particular significance was the prediction that the variant A86T/T91H/M108G/A109M/T111P exhibited an activity approximately 15 times higher than that of the wild type. Furthermore, during the selection of the regression model, PLS and MLP regressions were compared. The effect of data size and data relevance on the two regression approaches has been summarized. The aforementioned conclusions provide evidence for the feasibility of the strategy that combines ML with experimental approaches. This integrated strategy proves effective in exploring potential variations within the protein sequence space. Furthermore, this method facilitates a deeper understanding of the substrate channel in P450 CYP116B3.

Publications

Hemmer, S.; Siedhoff, N. E.; Werner, S.; Ölçücü, G.; Schwaneberg, U.; Jaeger, K.-E.; Davari, M. D.; Krauss, U.; Machine learning-assisted engineering of light, oxygen, voltage photoreceptor adduct lifetime JACS Au 3 3311-3323 (2023) DOI: 10.1021/jacsau.3c00440
  • Abstract
  • Internet
  • BibText
  • RIS

Naturally occurring and engineered flavin-binding, blue-light-sensing, light, oxygen, voltage (LOV) photoreceptor domains have been used widely to design fluorescent reporters, optogenetic tools, and photosensitizers for the visualization and control of biological processes. In addition, natural LOV photoreceptors with engineered properties were recently employed for optimizing plant biomass production in the framework of a plant-based bioeconomy. Here, the understanding and fine-tuning of LOV photoreceptor (kinetic) properties is instrumental for application. In response to blue-light illumination, LOV domains undergo a cascade of photophysical and photochemical events that yield a transient covalent FMN-cysteine adduct, allowing for signaling. The rate-limiting step of the LOV photocycle is the darkrecovery process, which involves adduct scission and can take between seconds and days. Rational engineering of LOV domains with fine-tuned dark recovery has been challenging due to the lack of a mechanistic model, the long time scale of the process, which hampers atomistic simulations, and a gigantic protein sequence space covering known mutations (combinatorial challenge). To address these issues, we used machine learning (ML) trained on scarce literature data and iteratively generated and implemented experimental data to design LOV variants with faster and slower dark recovery. Over the three prediction−validation cycles, LOV domain variants were successfully predicted, whose adduct-state lifetimes spanned 7 orders of magnitude, yielding optimized tools for synthetic (opto)biology. In summary, our results demonstrate ML as a viable method to guide the design of proteins even with limited experimental data and when no mechanistic model of the underlying physical principles is available.

  • 1

Print

  • IPB Halle
  • News
  • Lectures
  • Publications
  • Public Tendering
  • IPB Remote & Mail
  • Imprint
  • Data Protection
  • Accessibility
  • Die Leibniz-Gemeinschaft
  • Wege zu einer pflanzenbasierten Wirtschaft
  • Martin-Luther Universität Halle
  • Erfolgsfaktor Familie
  • TOTAL E-QUALITY
  • Research
    • Research Mission and Profile

    • Molecular Signal Processing

    • Bioorganic Chemistry

    • Biochemistry of Plant Interactions

    • Cell and Metabolic Biology

    • Independent Junior Research Groups

    • Program Center MetaCom

    • Publications

    • Good Scientific Practice

    • Research Funding

    • Networks and Collaborative Projects

    • Symposia and Colloquia

    • Alumni Research Groups

  • Infrastructure
    • Databases and Tools

    • Technical Resources

    • Imaging Unit

    • Greenhouses and Phytochambers

    • Library Services

  • Institute
    • Organizational Chart

    • Management and Boards

    • Administration and Infrastructure

    • Energy Management

    • Diversity, Family and Equality

    • Public Tendering

    • Patents and Licensing

    • The IPB Welcoming Culture

    • Guest Houses

    • IPB Site Map

    • Brief IPB History

    • Alumni Network

  • Career
    • Data protection information for applicants

    • PhD Program

    • Postdocs

    • Berufsausbildung

  • Public Relations
    • News

    • News Ticker Science

    • Press Releases

    • IPB Pressespiegel

    • Lange Nacht, die Wissen schafft

    • IPB Newsletter

    • Printed / Information Material

    • Scientific Reports / Research Highlights

    • Events

    • Cover Art

    • Citizen Science: Pilzberatung

  • IPB Remote & Mail