Biology subjects

Happonen, L.

Publications and source records attributed to Happonen, L..

13 recordsLinked to original sources

bioRxiv2026

Structural profiling of the pneumolysin epitope landscape uncovers a cross-species neutralising site across cholesterol-dependent cytolysins

Streptococcus pneumoniae remains a major public health concern, largely due to the limited serotype coverage and other constraints of pneumococcal conjugate vaccines, as well as the increasing antimicrobial resistance among circulating strains. In the pursuit of protein-based pneumococcal vaccines, pneumolysin (PLY), a secreted multifunctional cholesterol-dependent cytolysin, represents a promising target. To date, the relationship between the B-cell epitope landscape and neutralising PLY-specific antibody responses has remained elusive, hindering the rational design of effective PLY-based vaccines. Using a panel of PLY-specific monoclonal antibodies, functional assays, multimodal protein mass spectrometry and data-driven computational modelling, we mapped the structural epitope landscape of native PLY and linked epitope-paratope interactions to neutralising potency. We further refined and structurally characterised a protective cross-species epitope conserved among homologous cholesterol-dependent cytolysins (CDC). This epitope provides a promising foundation for rational, epitope-focused vaccine design, offering a pathway toward species-independent vaccines targeting the CDC protein superfamily.

immunology↗

bioRxiv2025

Design of a Streptolysin O Epitope-Centric Nanoparticle Vaccine Against Streptococcus pyogenes

Streptococcus pyogenes (Group A Streptococcus, GAS) is a significant human pathogen for which no licensed vaccine is currently available. Here, we report a de novo designed epitope-centric protein-based nanoparticle vaccine against GAS. By integrating structural mass spectrometry techniques and deep learning approaches, we re-engineered a protective epitope (D3m) present in domain 3 of streptolysin O, a prominent pore-forming toxin produced by GAS. D3m was displayed on the surface of a self-assembling icosahedral nanoparticle (D3m-NP) to enhance epitope presentation and immunogenicity. Mice immunised with D3m-NP mounted haemolysis-neutralising titres and displayed a more uniform, epitope-centric antibody response than those receiving the community-standard detoxified full-length streptolysin O. Our findings highlight a promising strategy for GAS vaccine development by combining multimodal protein mass spectrometry, protein design and a versatile protein-based nanoparticle vaccine platform.

immunology↗

bioRxiv2024

CDNF rescues human iPSCs-derived dopamine neurons through direct binding to unfolded protein response sensors PERK and IRE1α

Cerebral dopamine neurotrophic factor (CDNF) is an unconventional trophic factor that protects dopamine neurons in cellular and animal models of Parkinsons disease (PD). CDNF was safe and well tolerated in phase 1 clinical trials for PD treatment, and currently, its peptide analogue is under investigation in phase 1 clinical trials for PD. Despite prominent neuroprotective and neurorestorative activity, the receptors and exact mechanism of CDNF functioning have been obscure. Intracellularly acting CDNF exerts cytoprotection by attenuating endoplasmic reticulum (ER) stress and unfolded protein response (UPR). We demonstrated that this activity occurs through the direct binding of CDNF to ER transmembrane UPR sensors PERK and IRE1 for purified proteins and in cells. We identified CDNF mutants deficient for binding to UPR sensors. CDNF binding to PERK and IRE1 appeared to be crucial for the survival of mouse dopamine neurons in culture. Importantly for clinical translation, CDNF rescues human induced pluripotent stem cell-derived dopamine neurons and promotes their regeneration. CDNF binding to UPR sensors alleviated terminal UPR and promoted neurite outgrowth of human dopamine neurons through direct binding to PERK and IRE1. CDNF binding to BiP was dispensable for the neuroprotective and neurorestorative activity of CDNF. Therefore, CDNF, or small molecules mimicking its binding to UPR sensors and acting selectively on dopamine neurons with activated UPR, are promising drug candidates for PD treatment.

neuroscience↗

bioRxiv2024

Streptolysin O Accelerates the Conversion of Plasminogen to Plasmin

Streptococcus pyogenes is a human-specific bacterial pathogen that produces several proteins that exploit the plasminogen (PLG)-plasmin (PLM) fibrinolysis system to dismantle blood clots and to facilitate spread and survival within the host. In this study, we explored the interactions between streptolysin O (SLO), a key cytolytic toxin produced by S. pyogenes, and human plasma proteins using affinity-enrichment mass spectrometry. SLO binds specifically to PLG, and this interaction accelerates the conversion of PLG to PLM by tissue-type plasminogen activator (tPA). To further investigate the molecular detail of the PLG-SLO interaction, we employed hydrogen/deuterium exchange mass spectrometry combined with targeted cross-linking mass spectrometry, uncovering that SLO binding induces local conformational shifts in PLG. These changes lead to the formation of a stabilized intermediate PLG-SLO complex that becomes significantly more sensitive to proteolytic processing by tPA. Our findings reveal a conserved moonlighting pathomechanistic role for SLO extending beyond the well characterized cytolytic activity. Additionally, the work underscores the diversity of functional proteomics in identifying and clarifying new host-pathogen interactions.

molecular biology↗

bioRxiv2023

Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O

An important element of antibody-guided vaccine design is the use of neutralizing/opsonic monoclonal antibodies to define protective epitopes in their native three-dimensional conformation. Here, we demonstrate a multi-modal mass spectrometry-based strategy for in-depth characterization of antigen-antibody complexes to enable the identification of protective epitopes using the cytolytic exotoxin Streptolysin O (SLO) from Streptococcus pyogenes as a showcase. We first discovered a monoclonal antibody with an undisclosed sequence capable of neutralizing SLO-mediated cytolysis. The amino acid sequence of both the antibody light and the heavy chain was determined using mass spectrometry-based de novo sequencing, followed by chemical crosslinking mass spectrometry to generate distance constraints between the antibody fragment antigen-binding region and SLO. Subsequent integrative computational modeling revealed a discontinuous epitope located in Domain 3 of SLO that was experimentally validated by hydrogen-deuterium exchange mass spectrometry and reverse-engineering of the targeted epitope. The results show that the antibody inhibits SLO-mediated cytolysis by binding to a discontinuous epitope in Domain 3, likely preventing oligomerization and subsequent secondary structure changes critical for pore-formation. The epitope is highly conserved across >98% of the characterized S. pyogenes isolates, making it an attractive target for antibody-based therapy and vaccine design against severe streptococcal infections.

biochemistry↗

bioRxiv2023

The increased hinge flexibility of an IgG1-IgG3 hybrid monoclonal enhances Fc-mediated protection against group A streptococci

Antibodies are central to the immune response against microbes. We have previously generated a protective IgG1 monoclonal antibody targeting the M protein, a critical virulence factor of Streptococcus pyogenes. Here, we generated this antibody in all human IgG subclasses and evaluated their function. Despite significantly reduced binding, the IgG3 subclass antibody demonstrated remarkably enhanced opsonic function. We hypothesized that increased Fc flexibility could explain this improved efficacy. We engineered a hybrid IgG subclass antibody, IgGh, containing the backbone of IgG1 with the hinge of IgG3, leaving the Fabs unchanged. The IgGh maintained a similar binding ability as IgG1 while gaining the strong opsonic function seen with IgG3. Molecular dynamics simulations of the different antibodies showed altered IgG Fab-antigen interactions, reflecting the differences observed in affinity. More importantly, when the antibodies were bound to the antigen, the simulations showed that the Fc of both IgGh and IgG3 exhibited extensive movement in 3D space relative to the M protein. The increased flexibility of IgGh directly translated to enhanced opsonic function and significantly increased the protection against infection with Streptococcus pyogenes in mice. Our findings demonstrate how altering Fc flexibility can improve Fc-mediated opsonic function and how modifications in the constant domain can regulate Fab-antigen interactions. In addition, the enhanced in vivo function of a more flexible IgG provides new therapeutic opportunities for monoclonal antibodies. One sentence summaryAntibody Fc flexibility in 3D space correlates with efficient Fc-mediated phagocytosis of streptococci

immunology↗

bioRxiv2022

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon

Protein translocation across the endoplasmic reticulum (ER) membrane is an essential initial step in protein entry into the secretory pathway. The conserved Sec61 protein translocon facilitates polypeptide translocation and coordinates cotranslational polypeptide processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation or cotranslational modifications such as N-glycosylation remains unknown. Here, we demonstrate the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by Cryo-EM. The interactions with ribosome anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its the lumenal leaflet. We propose a model for how TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen by direct polypeptide interactions.

biochemistry↗

bioRxiv2022

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Generating and analyzing overlapping peptides through multienzymatic digestion is an efficient procedure for de novo protein using from bottom-up mass spectrometry (MS). Despite improved instrumentation and software, de novo MS data analysis remains challenging. In recent years, deep learning models have represented a performance breakthrough. Incorporating that technology into de novo protein sequencing workflows require machine-learning models capable of handling highly diverse MS data. In this study, we analyzed the requirements for assembling such generalizable deep learning models by systematically varying the composition and size of the training set. We assessed the generated models performances using two test sets composed of peptides originating from the multienzyme digestion of samples from various species. The peptide recall values on the test sets showed that the deep learning models generated from a collection of highly N- and C-termini diverse peptides generalized 76% more over the termini-restricted ones. Moreover, expanding the training sets size by adding peptides from the multienzymatic digestion with five proteases of several species samples led to a 2-3 fold generalizability gain. Furthermore, we tested the applicability of these multienzyme deep learning (MEM) models by fully de novo sequencing the heavy and light monomeric chains of five commercial antibodies (mAbs). MEM models extracted over 10000 matching and overlapped peptides across six different proteases mAb samples, achieving a 100% sequence coverage for 8 of the ten polypeptide chains. We foretell that the MEM models proven improvements to de novo analysis will positively impact several applications, such as analyzing samples of high complexity, unknown nature, or the peptidomics field.

bioinformatics↗

bioRxiv2021

Proteome-wide cross-linking mass spectrometry to identify specific virus capsid-host interactions between tick-borne encephalitis virus and neuroblastoma cells

Virus-host protein-protein interactions are central to viral infection, but are challenging to identify and characterise, especially in complex systems involving intact viruses and cells. In this work, we demonstrate a proteome-wide approach to identify virus-host interactions using chemical cross-linking coupled with mass spectrometry. We adsorbed tick-borne encephalitis virus onto metabolically-stalled neuroblastoma cells, covalently cross-linked interacting virus-host proteins, and performed limited proteolysis to release primarily the surface-exposed proteins for identification by mass spectrometry. Using the intraviral protein cross-links as an internal control to assess cross-link confidence levels, we identified 22 high confidence unique intraviral cross-links and 59 high confidence unique virus-host protein-protein interactions. The identified host proteins were shown to interact with eight distinct sites on the outer surface of the virus. Notably, we identified an interaction between the substrate-binding domain of heat shock protein family A member 5, an entry receptor for four related flaviviruses, and the hinge region of the viral envelope protein. We also identified host proteins involved in endocytosis, cytoskeletal rearrangement, or located in the cytoskeleton, suggesting that entry mechanisms for tick-borne encephalitis virus could include both clathrin-mediated endocytosis and macropinocytosis. Additionally, cross-linking of the viral proteins showed that the capsid protein forms dimers within tick-borne encephalitis virus, as previously observed with purified C proteins for other flaviviruses. This method enables the identification and mapping of transient virus-host interactions, under near-physiological conditions, without the need for genetic manipulation. Author summaryTick-borne encephalitis virus is an important human pathogen that can cause severe infection often resulting in life-long neurological complications or even death. As with other viruses, it fully relies on the host cells, and any successful infection starts with interactions between the viral structural proteins and cellular surface proteins. Mapping these interactions is essential both for the fundamental understanding of viral entry mechanisms, and for guiding the design of new antiviral drugs and vaccines. Here, we stabilise the interactions between tick-borne encephalitis virus and human proteins by chemical cross-linking. We then detect the interactions using mass spectrometry and analyse the data to identify protein-protein complexes. We demonstrate that we can visualise the protein interaction interfaces by mapping the cross-linked sites onto the host and viral protein structures. We reveal that there are eight distinct sites on the outer surface of the viral envelope protein that interact with host. Using this approach, we mapped interactions between the tick-borne encephalitis virus envelope protein, and 59 host proteins, identifying a possible new virus receptor. These results highlight the potential of chemical cross-linking coupled with mass spectrometry to identify and map interactions between viral and host proteins.

microbiology↗

bioRxiv2021

Opsonization by non-neutralizing antibodies can confer protection to SARS-CoV-2 despite Spike-dependent modulation of phagocytosis

Spike-specific antibodies are central to effective COVID19 immunity. Research efforts have focused on antibodies that neutralize the ACE2-Spike interaction but not on non-neutralizing antibodies. Antibody-dependent phagocytosis is an immune mechanism enhanced by opsonization, where typically, more bound antibodies trigger a stronger phagocyte response. Here, we show that Spike-specific antibodies, dependent on concentration, can either enhance or reduce Spike-bead phagocytosis by monocytes independently of the antibody neutralization potential. Surprisingly, we find that both convalescent patient plasma and patient-derived monoclonal antibodies lead to maximum opsonization already at low levels of bound antibodies and is reduced as antibody binding to Spike protein increases. Moreover, we show that this Spike-dependent modulation of opsonization seems to affect the outcome in an experimental SARS-CoV-2 infection model. These results suggest that the levels of anti-Spike antibodies could influence monocyte-mediated immune functions and propose that non-neutralizing antibodies could confer protection to SARS-CoV-2 infection by mediating phago-cytosis.

immunology↗

bioRxiv2021

Bacterial clearance caused by a single anti-M protein antibody simultaneously binding two separate epitopes

Group A streptococci have evolved multiple strategies to evade human antibodies, making it challenging to create effective vaccines or antibody treatments. Here, we have generated antibodies derived from the memory B cells of an individual who had successfully cleared a group A streptococcal infection. The antibodies bind with high affinity in the central region of the surface-bound M protein. Such antibodies are typically non-opsonic. However, one antibody could effectively promote vital immune functions, including phagocytosis and in vivo protection. Remarkably, this antibody primarily interacts through a bivalent dual-Fab cis mode, where the Fabs bind to two distinct epitopes in the M protein. The dual-Fab cis binding phenomenon is conserved across different groups of M types. In contrast, other antibodies binding with normal single-Fab mode to the same region can not bypass the M proteins virulent effects. A broadly binding, protective monoclonal antibody could be a candidate for anti-streptococcal therapy. Our findings highlight the concept of dual-Fab cis binding as a means to access conserved, and normally non-opsonic regions, for protective antibody targeting.

immunology↗

bioRxiv2021

Streptococcus pyogenes forms serotype and local environment-dependent inter-species protein complexes

Streptococcus pyogenes is known to cause both mucosal and systemic infections in humans. In this study, we used a combination of quantitative and structural mass spectrometry techniques to determine the composition and structure of the interaction network formed between human plasma proteins and the surface of different S. pyogenes serotypes. Quantitative network analysis revealed that S. pyogenes form serotype-specific interaction networks that are highly dependent on the domain arrangement of the surface-attached M protein. Subsequent structural mass spectrometry analysis and computational modelling on one of the M proteins, M28 revealed that the network structure changes across different host microenvironments. We report that M28 binds secretory IgA via two separate binding sites with high affinity in saliva. During vascular leakage mimicked by increasing plasma concentrations in saliva, the binding of secretory IgA was replaced by binding of monomeric IgA and C4BP. This indicates that an upsurge of C4BP in the local microenvironment due to damage of the mucosal membrane drives binding of C4BP and monomeric IgA to M28. The results suggest that S. pyogenes has evolved to form microenvironment-dependent host-pathogen protein complexes to combat the human immune surveillance during both mucosal and systemic infections.

microbiology↗

bioRxiv2020

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology

Streptococcus pyogenes (Group A streptococcus; GAS) is an important human pathogen responsible for mild to severe, life-threatening infections. GAS expresses a wide range of virulence factors, including the M family proteins. The M proteins allow the bacteria to evade parts of the human immune defenses by triggering the formation of a dense coat of plasma proteins surrounding the bacteria, including IgGs. However, the molecular level details of the M1-IgG interaction have remained unclear. Here, we characterized the structure and dynamics of this interaction interface in human plasma on the surface of live bacteria using integrative structural biology, combining cross-linking mass spectrometry and molecular dynamics (MD) simulations. We show that the primary interaction is formed between the S-domain of M1 and the conserved IgG Fc-domain. In addition, we show evidence for a so far uncharacterized interaction between the A-domain and the IgG Fc-domain. Both these interactions mimic the protein G-IgG interface of group C and G streptococcus. These findings underline a conserved scavenging mechanism used by GAS surface proteins that block the IgG-receptor (Fc{gamma}R) to inhibit phagocytic killing. We additionally show that we can capture Fab-bound IgGs in a complex background and identify the specific M1 epitopes targeted on live bacteria. Our results elucidate the M1-IgG interaction network involved in inhibition of phagocytosis and reveal important M1 peptides that can be further investigated as future vaccine targets.

molecular biology↗