LP3 Annual Report 2024

The “new” LP3 was created as a center in June 2016 by the Faculty of Science, the Faculty of Medicine and LTH (Faculty of Engineering) by combining the “old” LP3, specialized in protein production, with LU’s protein crystallization facility. As part of the research infrastructure Protein Production Sweden (PPS, external link) since 2022, parts of LP3 are hosting and staffing the PPS Lund University node. In 2024, The Vice-Chancellor of LU named three of the university’s large research infrastructures as University Platforms including LP3. The designation signals that such research infrastructure has a high strategic significance for the entire university. 
LP3’s part in PPS is described in the PPS annual report to the Swedish research council. This report here will mainly focus on LP3 activities outside of PPS and try to highlight LP3’s local role for Lund University.
Outside PPS, LP3 continued to offer crystallization and protein crystal screening at the BioMAX beamline at MAX IV laboratory to its users. This enables non-experts in protein crystallography to use X-ray crystallography at MAX IV and pursue structure determination, as well as LP3 continued to offer services within biophysical characterization of proteins. LP3 continued the support to the DEMAX platform of ESS and the FragMAX platform of MAX IV and LP3 is associated with the SciLifeLab Lund node as a local research infrastructure.
LP3 staff were involved in teaching, as well as national and international conferences and networks of interest. 
In general, both within and outside PPS, LP3 continued in 2024 to deliver projects to its users at the maximum of its capacities.
 

Wolfgang Knecht
Manager, LP3
April 2025

Introduction

Lund Protein Production Platform (LP3) is a center at Lund University (LU) that offers services and equipment in the areas of recombinant protein production, protein crystallization, biophysical characterization, and structure determination as illustrated in Figure 1. 

The center was established by the Faculties of Science (FoS), Medicine (FoM) and Engineering (LTH) in 2016 (STYR 2023/2145). LP3 serves as the LU node of the distributed national research infrastructure Protein Production Sweden (PPS, external link) since 2022 and is a part of the MAX IV laboratory X-ray-aided fragment screening platform (FragMAX)  that was established by a Swedish research council (VR) grant with LP3 as co-applicant since 2019. In 2024, The Vice-Chancellor of LU named three of the university’s large research infrastructures as University Platforms including LP3. The designation signals that such research infrastructure has a high strategic significance for the entire university.

LP3 provides labs and services for and collaborates with the Deuteration and Macromolecular Crystallization platform (DEMAX) , of the European Spallation Source ERIC (ESS), currently as a Swedish in kind contribution to ESS . The labs managed by LP3 serve as a meeting point for all these platforms. LP3 has staff equivalent to 6 full-time employees. Of this workforce roughly 50 % support the operations of the LU node of PPS (also referred to as LP3-PPS), 10 % support FragMAX, 10 % deliver the Swedish in-kind contributions to ESS and 30 % support crystallization and structure determination operations of LP3, as well as all other local support. Both FragMAX and DEMAX also have their own staff placed in the labs provided by LP3. Those parts outside LP3-PPS are also in summary referred to as LP3-local. Just LP3 means in the following parts LP3-PPS and LP3-local.

The crystallization and structure determination operations of LP3 in LP3-local, as well as the FragMAX platform have been selected to be included in the SciLifeLab platform plans for evaluation during 2024, with the possibility to become a part of the Integrated Structural Biology (ISB) platform from 2025 on. However, a decision was not taken by SciLifeLab in 2024. LP3 is already associated as a local research infrastructure with the Lund SciLifeLab node and as a LU infrastructure of national importance, as well as listed in Lucris by LU as such . Additionally, LP3 is part of LU thematic collaboration initiative: Pandemics and Alertness .

LP3’s mission (STYR 2023/2145) is to: 
•    offer open service and support, primarily to researchers at LU, with protein production, characterization and crystallization for their research projects.
•    be responsible for a common and open infrastructure for protein production and crystallization, as well as to contribute actively to the interaction of LU with MAX IV, ESS and other relevant major research facilities, networks and initiatives.
•    act as Lund University's node for the national research infrastructure PPS
•    develop competence and methods in the area of protein sciences.
•    serve the surrounding community (e.g. closely located large infrastructures, small biotech etc.).

User access is given on a first come basis and technical feasibility. In 2024, LP3 services were fully subscripted, yet sufficient to meet the demand with limited waiting times for users. Extensive work requests, however filling up all available capacity, are divided into smaller parts or rejected in order not to delay delivery times unproportionally for many other users. In general, at LP3-local, LU researchers and LP3-local’s commitments to FragMAX and DEMAX (ESS) are prioritized while for LP3-PPS this is obviously not the case and in case of lacking capacity at PPS, scientific quality of the project application is assessed for prioritization by the management group of PPS.
 

Organisation

LP3 was run in 2024 by a manager (60 % FTE, senior lecturer) and 5 research engineers. In 2024, the staffing also included 2 experts (10 %) in microbial protein production and crystallization as well as hosting Dr. Z. Fisher (Head of DEMAX (ESS), assoc. lecturer at LU with 20 %). 
6 visitors were associated with LP3 in 2023, not counting the staffing of the FragMAX project or DEMAX staff. Additionally, LP3-local and the wet-labs of FragMAX facility have a lot of users (e.g. in 2024, 22 users) coming to LP3’s labs to use certain equipment themselves or doing short experiments on one or several occasions.

LP3 is fully equipped for protein production in E. coli and insect cells (Baculovirus Expression Vector System, BEVS). This includes flow hoods for sterile handling of cells, temperature-controlled shakers for culturing of cells (including access to temperature-controlled rooms), centrifuges, cell homogenization equipment (e.g., French Press and sonicators). In 2024, a new bioreactor for up to 2 L working volume was procured funded by the “Swedish in-kind contributions to ESS”. For purification there are several chromatography systems, including one Äkta Avant, two Äkta Pure Systems, and an Äkta Flux for diafiltration. Equipment for SDS PAGE, Western blotting and other standard equipment for protein characterization and enzymatic activity assays is available at the center or within close proximity. All documentation is captured using electronic lab notebooks. 

For crystallization the facility is equipped with state-of-the-art nanoliter pipetting equipment with the capability to handle lipidic cubic phases for membrane proteins, as well as “plate hotels” with the capacity to store and automatically image plates. Tecan and a TTP (Dragonfly) liquid handling systems for the preparation of crystallization screens are also available. 

For characterization of proteins LP3 can provide differential scanning fluorimetry (nanoDSF), dynamic light scattering system (DLS) and a size exclusion chromatography (SEC) system (with integrated multi-detector module) for the measurement of absolute molecular weight, molecular size and sample composition (OMNISEC).

For more specifics on the capabilities and services of LP3 please see our homepage: www.lp3.lu.se.
 

Placement of the infrastructure

LP3 is placed at the Biology Department (Biology Building A, Sölvegatan 35, 22362 Lund), within the Faculty of Science (FoS) at LU. LP3 is a separate entity within the existing administrative structure of the Department of Biology and follows the working and delegation principles of the FoS.

Leadership of the infrastructure

LP3 is governed by a board of one chairman (Prof. Susanna Horsefield) and 6 members (Prof. Ingemar André, Dr. Kajsa Paulsson, Prof. Mats Ohlin, Dr. Kajsa Sigfridsson Clauss, Dr. Sindra Petersson Årsköld), one each from Faculty of Science (FoS), Faculty of Medicine (FoM), LTH, MAX IV laboratory and ESS (external member) and one student (vacant during 2024). The daily business of the center is led by a manager (60 % FTE) (Dr. Wolfgang Knecht). The manager is supported in his function by additional experts (10 % FTE) (Currently Dr. Claes von Wachenfeldt (microbiological protein production and deputy manager LP3) and Prof. Derek Logan (crystallization and structural biology). 

PPS – Summary from the annual report 2024

Protein Production Sweden (PPS) has in its third year consolidated its position as a national infrastructure. Project applications are entered through the common web application form into our project database and are then discussed in the management group and distributed to the different labs. In this third year, 145 PIs applied for 206 different projects (corresponding to 12 and 5% increase respectively compared to 2023), a smaller increase than from 2022 to 2023. Nevertheless, this shows the continued high demand for recombinant proteins from the Swedish scientific community. During 2024, 212 projects were completed, resulting in the delivery of 373 protein batches (15 % increase compared to 2023) showing that our infrastructure has gained momentum, but also bringing us to the edge of our capacities. To continue spreading the information about PPS among Swedish researchers, we have presented our capabilities at different conferences and meetings on 22 different occasions. New users have come, but the third year has also seen many returning users from previous years, and PPS received again very favorable user survey results. We have fully established and implemented consensus quality analyses of our proteins. Moreover, we have worked on several activities to develop our services. 

FragMAX (BioMAX Fragment Screening platform)

The FragMAX platform of MAX IV is a Swedish Research Council financed project, with LP3, AstraZeneca AB and Saromics Biostructures AB as co-applicants. The project aims at setting up high throughput X-ray fragment screening (XFS) at the BioMAX beamline with LP3 as the partner for crystallization and sample preparation. FragMAX ,  has become a permanent platform within MAX IV laboratories with its “wet labs” firmly established at LP3.
LP3 supported 10 (7 academic, 3 industry) FragMAX campaigns in 2024.
 

Deuteration and Macromolecular Crystallization (DEMAX)

The DEMAX platform of the European Spallation Source ERIC (ESS) has been co-localized with LP3 since 2016. The under an agreement for this was renewed for the period 2021–2025.

DEMAX and LP3 are collaborating to coordinate their efforts to develop cost-effective production of deuterated biomaterials (lipids and proteins) for neutron-based methods such as protein crystallography, neutron reflectometry, and small angle neutron scattering. In 2024, we have together published a methodology for protein perdeuteration (Algal Research (2024) DOI: 10.1016/j.algal.2024.103459) that reduces deuteration costs significantly making protein perdeuteration more cost-efficient.

Dr. Knecht on behalf of LP3 applied within the first VR call for in-kind contributions to ESS for providing deuteration lab services. This proposal was accepted by VR and ESS. LP3 is thereby among the very first Swedish in-kind contributions to ESS.

Besides the internal development activities of DEMAX, LP3 supported 3 DEMAX user projects in 2024.
 

Long term strategy

The full-length strategic plan  for LP3 can be found in the annual report 2021 (available at www.lu.se/lp3) and the strategic plan for PPS can be found on the PPS webpage (external link). These strategic documents (LP3 and PPS) do govern the long-term strategic work, as well as the short-term plans that are formulated in the respective operational plans for PPS and LP3 for each year established by the respective steering committees. 

In short, LP3 has the ambition within PPS (LP3-PPS) to become and remain:

a) Preferred supplier of (per)deuterated biomolecules for neutron scattering experiments

b) Preferred supplier of specialty protein reagents for X-ray crystallography 

c) Preferred supplier of protein expression in insect cells with the Baculovirus Expression Vector System (BEVS). 

This aligns with the overall long-term strategy aim of PPS: 

“PPS shall become and remain the preferred provider of proteins for research purposes for Swedish researchers from academia, public sector and commercial entities”. 

Outside of PPS (LP3-local), LP3s strategic plan points towards protein characterization, protein structure determination for non-experts (non-crystallographers) and to support the FragMAX at MAX IV and the DEMAX platform of ESS. This aligns well with the strategic LU goal:

 “The potential of MAX IV and ESS is to be fully exploited”.

Services

LP3 offers services for the entire process chain of production, purification, characterization, protein crystallization and protein structure determination and structure refinement or each individual step in the chain (Figure 1).

For details of current services and updates, please see LP3 homepage.

Users and projects

Some overall user statistics will be reported here. LP3-PPS part within PPS is described in the annual PPS report to VR. LP3-local’s activities outside PPS, will be described in more detail in this report below. 
 

Overall

56 groups used LP3 in 2024 both through PPS and as a local infrastructure. Of these, 34 principal investigators came from LU and 22 were external. The distribution to different faculties and external users is presented in Figure 2. The development of user groups in numbers at LP3 since 2016 is shown in Figure 3. The principal investigators in the external user group come from the ESS, other Swedish and international universities (for example in 2024: UU, GU, KI, LinU, University of Amsterdam (Netherlands), Marburg (Germany), Turku (Estonia), Helsinki (Finland), College de France (France), UCL (UK) and industry/biotech (in 2024: five companies).

Figure 4 presents the total distribution of 161 unique users at LP3 in the timeframe of 2016 - 2024. Compared to 2023 when this number was 146, this is an increase of 15 unique new users.

The distribution of users between LP3-PPS and LP3-local (all LP3 activities like crystallization, structure determination, biophysics, local support (e.g. for protein production of previous LP3 projects)) is shown in Figure 5 for 2022 to 2024. Here, the external users are separated into other Swedish universities, international academics and other users (e.g. from industry, public sector and infrastructures like ESS ERIC).

Not included in the numbers above are the “indirect” users that LP3-local served due to supporting all FragMAX campaigns and delivering “Deuteration Lab Services” (DLS) as Swedish in kind contribution to DEMAX (ESS). Those numbers have been given above in the introduction under the descriptions of FragMAX and DEMAX.

LP3-local

In the two areas crystallization and biophysics, LP3-local, had 26 user groups. A total of 244 crystallisation plates were processed in 2024. LP3-local had 4 projects with the aim of structure X-ray crystallography managed by LP3-local for non-expert users.

The distribution of user groups in crystallization and biophysics and the development of the number of user groups since 2016 are shown in Figures 6 and 7. 

12 of the user groups above also used LP3 or PPS for protein production 2024. In 2023, 10 user groups (4 FoS, 2 FoM, 1 LTH, 1 MAX IV, 2 Extern) used other support by LP3-local ranging from production of biomass, production of new batches in previous LP3 projects to technical assistance with Western blotting and production of reagents for undergraduate teaching.

The number of crystallization plates is presented in Figure 8, separated after projects that LP3 runs on behalf of users (non-experts in structural biology), FragMAX projects and projects at which the user sets up the plates themselves.

Crystal screening at the BioMAX Beamline

In 2024, 263 crystals from 8 projects were sent by LP3 staff to BioMAX on 10 occasions. 4 of these projects were managed by LP3 for non-expert users and resulted in 123 crystals and 105 datasets. For the other 4 projects with crystals, LP3 helped expert users to fish 140 crystals to be measured at the BioMAX beamline.

FragMAX project (BioMAX Fragment Screening platform)

LP3 supported 10 (7 academic, 3 industry) FragMAX campaigns in 2024.

DEMAX projects

For DEMAX, LP3-local delivered in all 3 areas of the DLS agreed services: 
•    Development of methods for the production of protiated and deuterated yeast cell paste suitable for lipid extraction.
•    Development of production of deuterated biomass and/or proteins and/or DNA.
•    Support for neutron protein crystallography

Additional in 2024 was the procurement and installation of a bioreactor for the DLS.
Besides above, LP3 supported 3 DEMAX user projects in 2024.

Visibility, access, outreach

LP3 presents its services, capabilities and new developments through Lund University-based homepages (www.lp3.lu.se) and the LUCRIS infrastructure pages , as well as at meetings (see below).

LP3 is featured in EUGLOHRIA Talks and EUGLOHRIA Virtual Tours approaching audiences with interactive and innovative content strengthening the collaboration potential by featuring model core facilities. LP3 was identified as one of those infrastructures available to the Alliance. On the EUGLOHRIA Talks homepage, an interview with LP3’s head (external link), Dr. Wolfgang Knecht, can be found, and it is possible to take a virtual tour of LP3 on the EUGLOHRIA Virtual Tours website (external link).

LP3 participates in relevant national and international networks and societies, (e.g., Protein Production and Purification Partnership in Europe (P4EU) (p4eu.org, external link) and Core Technologies for Life Sciences (CTLS) (ctls-org.eu , external link)). Since 2019, LP3 is one of the LU infrastructures affiliated with EATRIS ERIC (European infrastructure for translational medicine (eatris.eu , external link)) in their small molecule platform. LP3 is also a member of the Deuteration Network DeuNet (deuteration.org , external link).

Above, engagements are for dissemination of LP3’s work as well as for the exchange and adoption of new methods and ideas into LP3.

As nearly every year, LP3 staff  was contributing to undergraduate education.

In 2024, DEMAX together with LP3 published a methodology for protein perdeuteration (Algal Research (2024), DOI) that reduces deuteration costs, making protein perdeuteration more cost-efficient.

Presentations of LP3 and/or PPS by LP3 staff were provided on the following occasions in 2024:

Oral presentations

LP3 and PPS

• Seminar at the Division of Applied Biochemistry, LU, Lund, October 2024
• Presentation for the Department of Chemistry, Department Day, LU, Lund, November 2024
• SciLifeLab Lund retreat, Lund, November 2024
• DeuNet meeting, digital, December 2024

LP3 only

• SFBBM/KVA PI-meeting, Gothenburg, November 2024

These presentations supported continued dissemination and engagement with both local and international research communities, highlighting LP3’s services, expertise, and collaborative projects.

Poster presentations

LP3 only

In 2023, LP3 contributed to scientific outreach and collaboration by presenting posters at several high-profile conferences:

• MAX IV User Days, Lund, January 2024
• 27th Swedish Conference on Macromolecular Structure and Function, Tällberg, June 2024

These events offered opportunities to highlight LP3’s capabilities, research collaborations, and recent developments to national and international audiences.

Attendance

LP3 and PPS

• P4EU 20th Meeting, Braunschweig, Germany, July 2024

Results and/or proteins produced at the facility were used in the following 2024 publications (in the time 2016 – 2024, the total number of publications has thereby reached 126):

Publications

1. Ebenwaldner, C., García Saura, A.G., Ekström, S., Bernfur, K. and Schüler, H. (2024) Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15. bioRxiv, 2024.2004.2004.588081.DOI: 10.1101/2024.04.04.588081
2. Izadi, A., Karami, Y., Bratanis, E., Wrighton, S., Khakzad, H., Nyblom, M., Olofsson, B., Happonen, L., Tang, D., Sundwall, M. et al. (2024) The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies. Nature communications, 15, 3600. DOI: 10.1038/s41467-024-47928-8
3. Kalabekova, R., Quinn, C.M., Movellan, K.T., Gronenborn, A.M., Akke, M. and Polenova, T. (2024) 19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3. Biochemistry, 63, 2207-2216. DOI: 10.1021/acs.biochem.4c00232
4. Kondratieva, A., Palica, K., Frøhlich, C., Hovd, R.R., Leiros, H.-K.S., Erdelyi, M. and Bayer, A. (2024) Fluorinated captopril analogues inhibit metallo-β-lactamases and facilitate structure determination of NDM-1 binding pose. European Journal of Medicinal Chemistry, 266, 116140. DOI: 10.1016/j.ejmech.2024.116140
5. Koruza, K., Krupinska, E., Sele, C., Végvári, Á., Knecht, W. and Fisher, S.Z. (2024) Botryococcus braunii autolysate for the production of deuterium-labeled recombinant protein. Algal Research, 79, 103459. DOI: 10.1016/j.algal.2024.103459
6. Mero, I.L., Orozco Rodriguez, J.M., Bjørgo, K., Hankin, R.A., Krupinska, E., Kulseth, M.A., Rossow, M.A. and Knecht, W. (2024) A mild skeletal phenotype with overlapping features of Miller syndrome and functional characterisation of two new variants of human dihydroorotate dehydrogenase. Heliyon, 10, e38659. DOI: 10.1016/j.heliyon.2024.e38659
7. Saamarthy, K., Ahlqvist, K., Daams, R., Balagunaseelan, N., Rinaldo-Matthis, A., Kazi, J.U., Sime, W. and Massoumi, R. (2024) Discovery of a small molecule that inhibits Bcl-3-mediated cyclin D1 expression in melanoma cells. BMC Cancer, 24, 103. DOI: 10.1186/s12885-023-11663-y
8. Sele, C., Krupinska, E., Andersson Rasmussen, A., Ekström, S., Hultgren, L., Lou, J., Kozielski, F., Fisher, S.Z. and Knecht, W. (2024) New insights into complex formation by SARS-CoV-2 nsp10 and nsp14. Nucleosides, nucleotides & nucleic acids, 43, 798-812. DOI: 10.1080/15257770.2024.2321600
9. Tang, D., Gueto-Tettay, C., Hjortswang, E., Ströbaek, J., Ekström, S., Happonen, L., Malmström, L. and Malmström, J. (2024) Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O. Analytical chemistry. 96, 9060-9068. DOI: 10.1021/acs.analchem.4c00596
10. Tang, D., Khakzad, H., Hjortswang, E., Malmström, L., Ekström, S., Happonen, L. and Malmström, J. (2024) Streptolysin O accelerates the conversion of plasminogen to plasmin. Nature communications, 15, 10212. DOI: 10.1038/s41467-024-54173-6
11. Torres-Sangiao, E., Happonen, L., Heusel, M., Palm, F., Gueto-Tettay, C., Malmström, L., Shannon, O. and Malmström, J. (2024) Quantification of Adaptive Immune Responses Against Protein-Binding Interfaces in the Streptococcal M1 Protein. Mol Cell Proteomics, 23, 100753. DOI: 10.1038/s41467-019-10583-5
12. van Klaveren, S., Hassan, M., Håkansson, M., Johnsson, R.E., Larsson, J., Jakopin, Ž., Anderluh, M., Leffler, H., Tomašič, T. and Nilsson, U.J. (2024) Galectin-8N-Selective 4-Halophenylphthalazinone-Galactals Double π-Stack in a Unique Pocket. ACS Medicinal Chemistry Letters, 15, 1319-1324. DOI: 10.1021/acsmedchemlett.4c00212
13. Verteramo, M.L., Ignjatović, M.M., Kumar, R., Wernersson, S., Ekberg, V., Wallerstein, J., Carlström, G., Chadimová, V., Leffler, H., Zetterberg, F. et al. (2024) Interplay of halogen bonding and solvation in protein–ligand binding. iScience, 27, 109636. DOI: 10.1016/j.isci.2024.109636

Additionally in this PhD thesis:
Tang, D. (2025). Deciphering protective immunity by multimodal mass spectrometry: Towards epitope-focused streptococcal vaccines. [Doctoral Thesis (compilation), Department of Clinical Sciences, Lund]. Lund University, Faculty of Medicine. LU Internal Access to PDF

Collaboration

We collaborate in various ways with wider society and organizations within and outside LU. In 2024 LP3 hosted 6 visitors. LP3s efforts for visibility, access and outreach are described in the equally named chapter above. LP3 is part of PPS, which results in collaborations between the different nodes and platforms in PPS. LP3 became associated in late 2023 as a local research infrastructure with the Lund SciLifeLab node. Additionally, LP3 is part of LU thematic collaboration initiative: Pandemics and Alertness.