The Kossiakoff Group’s research interests are to provide a molecular understanding of how molecular recognition governs virtually all aspects of biological function. To study these issues our group employs a combination of X-ray crystallography and cryo-EM, site-directed mutagenesis, phage display and biophysical analysis. The Kossiakoff group has also pioneered a new technology called “chaperone-assisted” crystallography, which has facilitated the structural analyses of protein systems that had been totally recalcitrant to other approaches. The group has also been at the forefront of developing synthetic antibodies. These synthetic antibodies are much more powerful than traditional monoclonal antibodies and have the potential to completely replace them for uses in live cell imaging and proteomics.
Latest Publications
Romane K; Peteani G; Mukherjee S; Kowal J; Rossi L; Hou J; Kossiakoff A A; Lemmin T; Locher K P
Structural basis of drug recognition by human MATE1 transporter Journal Article
In: Nat Commun, vol. 16, no. 1, pp. 9444, 2025, ISSN: 2041-1723.
@article{pmid41145429,
title = {Structural basis of drug recognition by human MATE1 transporter},
author = {Ksenija Romane and Giulia Peteani and Somnath Mukherjee and Julia Kowal and Lorenzo Rossi and Jingkai Hou and Anthony A Kossiakoff and Thomas Lemmin and Kaspar P Locher},
doi = {10.1038/s41467-025-64490-z},
issn = {2041-1723},
year = {2025},
date = {2025-10-28},
urldate = {2025-10-01},
journal = {Nat Commun},
volume = {16},
number = {1},
pages = {9444},
abstract = {Human MATE1 (multidrug and toxin extrusion protein 1) is highly expressed in the kidney and liver, where it mediates the final step in the excretion of a broad range of cationic drugs, including the antidiabetic drug metformin, into the urine and bile. This transport process is essential for drug clearance and also affects therapeutic efficacy. To understand the molecular basis of drug recognition by hMATE1, we determined cryo-electron microscopy structures of the transporter in complex with the substrates 1-methyl-4-phenylpyridinium (MPP) and metformin and with the inhibitor cimetidine. The structures reveal a shared binding site located in a negatively charged pocket in the C-lobe of the protein. We functionally validated key interactions using radioactivity-based cellular uptake assays using hMATE1 mutants. Molecular dynamics simulations provide insights into the different binding modes and dynamic behaviour of the ligands within the pocket. Collectively, these findings define the structural basis of hMATE1 substrate specificity and shed light on its role in drug transport and drug-drug interactions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Human MATE1 (multidrug and toxin extrusion protein 1) is highly expressed in the kidney and liver, where it mediates the final step in the excretion of a broad range of cationic drugs, including the antidiabetic drug metformin, into the urine and bile. This transport process is essential for drug clearance and also affects therapeutic efficacy. To understand the molecular basis of drug recognition by hMATE1, we determined cryo-electron microscopy structures of the transporter in complex with the substrates 1-methyl-4-phenylpyridinium (MPP) and metformin and with the inhibitor cimetidine. The structures reveal a shared binding site located in a negatively charged pocket in the C-lobe of the protein. We functionally validated key interactions using radioactivity-based cellular uptake assays using hMATE1 mutants. Molecular dynamics simulations provide insights into the different binding modes and dynamic behaviour of the ligands within the pocket. Collectively, these findings define the structural basis of hMATE1 substrate specificity and shed light on its role in drug transport and drug-drug interactions.
Cottom C O; Heinz E; Erramilli S; Kossiakoff A; Slade D J; Noinaj N
Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum Journal Article
In: Structure, iss. 33, pp. 1-15, 2025, ISSN: 1878-4186.
@article{pmid40897170,
title = {Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum},
author = {Claire Overly Cottom and Eva Heinz and Satchal Erramilli and Anthony Kossiakoff and Daniel J Slade and Nicholas Noinaj},
doi = {10.1016/j.str.2025.08.008},
issn = {1878-4186},
year = {2025},
date = {2025-08-01},
urldate = {2025-08-01},
journal = {Structure},
issue = {33},
pages = {1-15},
abstract = {F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.
Lodwick J E; Shen R; Erramilli S; Xie Y; Roganowicz K; Kossiakoff A A; Zhao M
Structural Insights into the Roles of PARP4 and NAD in the Human Vault Cage Journal Article
In: Nature Communications, iss. 16, no. 6724, 2025, ISSN: 2692-8205.
@article{pmid38979142,
title = {Structural Insights into the Roles of PARP4 and NAD in the Human Vault Cage},
author = {Jane E Lodwick and Rong Shen and Satchal Erramilli and Yuan Xie and Karolina Roganowicz and Anthony A Kossiakoff and Minglei Zhao},
doi = {10.1038/s41467-025-61981-x},
issn = {2692-8205},
year = {2025},
date = {2025-07-21},
urldate = {2024-06-01},
journal = {Nature Communications},
number = {6724},
issue = {16},
abstract = {Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD -binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD -binding sites could support its enzymatic function within the vault.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD -binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD -binding sites could support its enzymatic function within the vault.
Arina A; Arauz E; Masoumi E; Warzecha K W; Sääf A; Widło Ł; Slezak T; Zieminska A; Dudek K; Schaefer Z P; Lecka M; Usatyuk S; Weichselbaum R R; Kossiakoff A A
A universal chimeric antigen receptor (CAR)-fragment antibody binder (FAB) split system for cancer immunotherapy Journal Article
In: Sci Adv, vol. 11, no. 27, pp. eadv4937, 2025, ISSN: 2375-2548.
@article{pmid40614208,
title = {A universal chimeric antigen receptor (CAR)-fragment antibody binder (FAB) split system for cancer immunotherapy},
author = {Ainhoa Arina and Edwin Arauz and Elham Masoumi and Karolina W Warzecha and Annika Sääf and Łukasz Widło and Tomasz Slezak and Aleksandra Zieminska and Karolina Dudek and Zachary P Schaefer and Maria Lecka and Svitlana Usatyuk and Ralph R Weichselbaum and Anthony A Kossiakoff},
doi = {10.1126/sciadv.adv4937},
issn = {2375-2548},
year = {2025},
date = {2025-07-01},
urldate = {2025-07-01},
journal = {Sci Adv},
volume = {11},
number = {27},
pages = {eadv4937},
abstract = {Chimeric antigen receptor (CAR) T cell therapy has shown extraordinary results in treating hematological cancer but faces challenges like antigen loss, toxicity, and complex manufacturing. Universal and modular CAR constructs offer improved flexibility, safety, and cost-effectiveness over conventional CAR constructs. We present a CAR-fragment antibody binder (Fab) platform on the basis of an engineered protein G variant (GA1) and Fab scaffolds. Expression of GA1CAR on human CD8 T cells leads to antigen recognition and T cell effector function that can be modulated according to the affinity of the CAR for the Fab and of the Fab for the target. GA1CAR T cells can recognize multiple Fab-antigen pairs on breast and ovarian cancer cell lines. Adoptively transferred GA1CAR T cells control tumors in breast cancer xenograft models, and their targeting can be quickly redirected using different Fabs. This versatile "plug-and-play" CAR T platform has potential for application in personalized therapy, preventing antigen loss variant escape, decreasing toxicity, and increasing access.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chimeric antigen receptor (CAR) T cell therapy has shown extraordinary results in treating hematological cancer but faces challenges like antigen loss, toxicity, and complex manufacturing. Universal and modular CAR constructs offer improved flexibility, safety, and cost-effectiveness over conventional CAR constructs. We present a CAR-fragment antibody binder (Fab) platform on the basis of an engineered protein G variant (GA1) and Fab scaffolds. Expression of GA1CAR on human CD8 T cells leads to antigen recognition and T cell effector function that can be modulated according to the affinity of the CAR for the Fab and of the Fab for the target. GA1CAR T cells can recognize multiple Fab-antigen pairs on breast and ovarian cancer cell lines. Adoptively transferred GA1CAR T cells control tumors in breast cancer xenograft models, and their targeting can be quickly redirected using different Fabs. This versatile "plug-and-play" CAR T platform has potential for application in personalized therapy, preventing antigen loss variant escape, decreasing toxicity, and increasing access.
Ogbu C P; de Las Alas M; Mandriota A M; Liu X; Kapoor S; Choudhury J; Ruma Y N; Goodman M C; Sanders C R; Gonen T; Kossiakoff A A; Duffey M E; Vecchio A J
Biophysical basis of tight junction barrier modulation by a pan-claudin-binding molecule Journal Article
In: PNAS Nexus, vol. 4, no. 6, pp. pgaf189, 2025, ISSN: 2752-6542.
@article{pmid40575703,
title = {Biophysical basis of tight junction barrier modulation by a pan-claudin-binding molecule},
author = {Chinemerem P Ogbu and Mason de Las Alas and Alexandria M Mandriota and Xiangdong Liu and Srajan Kapoor and Jagrity Choudhury and Yasmeen N Ruma and Michael C Goodman and Charles R Sanders and Tamir Gonen and Anthony A Kossiakoff and Michael E Duffey and Alex J Vecchio},
doi = {10.1093/pnasnexus/pgaf189},
issn = {2752-6542},
year = {2025},
date = {2025-06-01},
urldate = {2025-06-01},
journal = {PNAS Nexus},
volume = {4},
number = {6},
pages = {pgaf189},
abstract = {Claudins are a 27-member family of membrane proteins that form and fortify specialized cell contacts in endothelium and epithelium called tight junctions. Tight junctions restrict paracellular transport through tissues by forming molecular barriers between cells. Claudin-binding molecules thus hold promise for modulating tight junction permeability to deliver drugs or as therapeutics to treat tight junction-linked disease. The development of claudin-binding molecules, however, is hindered by their physicochemical intractability and small targetable surfaces. Here, we determine that a synthetic antibody fragment (sFab) that we developed binds with nanomolar affinity directly to 10 claudin subtypes and other distantly related claudin family members but not to other tight junction-localized membrane proteins. It does so by targeting the extracellular surfaces of claudins, which we verify by applying this sFab to a model intestinal epithelium and observe that it opens paracellular barriers comparable to a known, but application limited, tight junction modulating protein. This pan-claudin-binding molecule holds potential for both basic and translational applications as it is a probe of claudin and tight junction structure in vitro and in vivo and a tool to modulate the permeability of tight junctions broadly across tissue barriers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Claudins are a 27-member family of membrane proteins that form and fortify specialized cell contacts in endothelium and epithelium called tight junctions. Tight junctions restrict paracellular transport through tissues by forming molecular barriers between cells. Claudin-binding molecules thus hold promise for modulating tight junction permeability to deliver drugs or as therapeutics to treat tight junction-linked disease. The development of claudin-binding molecules, however, is hindered by their physicochemical intractability and small targetable surfaces. Here, we determine that a synthetic antibody fragment (sFab) that we developed binds with nanomolar affinity directly to 10 claudin subtypes and other distantly related claudin family members but not to other tight junction-localized membrane proteins. It does so by targeting the extracellular surfaces of claudins, which we verify by applying this sFab to a model intestinal epithelium and observe that it opens paracellular barriers comparable to a known, but application limited, tight junction modulating protein. This pan-claudin-binding molecule holds potential for both basic and translational applications as it is a probe of claudin and tight junction structure in vitro and in vivo and a tool to modulate the permeability of tight junctions broadly across tissue barriers.
O'Leary K M; Slezak T; Kossiakoff A A
Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution Journal Article
In: Proc Natl Acad Sci U S A, vol. 122, no. 24, pp. e2424679122, 2025, ISSN: 1091-6490.
@article{pmid40489625,
title = {Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution},
author = {Kelly M O'Leary and Tomasz Slezak and Anthony A Kossiakoff},
doi = {10.1073/pnas.2424679122},
issn = {1091-6490},
year = {2025},
date = {2025-06-01},
urldate = {2025-06-01},
journal = {Proc Natl Acad Sci U S A},
volume = {122},
number = {24},
pages = {e2424679122},
abstract = {Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to decouple. Here, we engineered synthetic intracellular antibodies (intrabodies) that are capable of modulating mTOR signaling with genetically programmable spatial resolution. Epitope-directed phage display was exploited to generate high affinity synthetic antibody fragments (Fabs) against the FKBP12-Rapamycin binding site of mTOR (mTOR). We determined high-resolution crystal structures of two unique Fabs that discriminate distinct conformational states of mTOR through recognition of its substrate recruitment interface. By leveraging these conformation-specific binders as intracellular probes, we uncovered the structural basis for an allosteric mechanism governing mTOR complex 1 (mTORC1) stability mediated by subtle structural adjustments within mTOR. Furthermore, our results demonstrated that synthetic binders emulate natural substrates by employing divergent yet complementary hydrophobic residues at defined positions, underscoring the broad molecular recognition capability of mTOR. Intracellular signaling studies showed differential time-dependent inhibition of S6 kinase 1 and Akt phosphorylation by genetically encoded intrabodies, thus supporting a mechanism of inhibition analogous to the natural product rapamycin. Finally, we implemented a feasible approach to selectively modulate mTOR signaling in the nucleus through spatially programmed intrabody expression. These findings establish intrabodies as versatile tools for dissecting the conformational regulation of mTORC1 and should be useful to explore how location-specific mTOR signaling influences disease progression.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to decouple. Here, we engineered synthetic intracellular antibodies (intrabodies) that are capable of modulating mTOR signaling with genetically programmable spatial resolution. Epitope-directed phage display was exploited to generate high affinity synthetic antibody fragments (Fabs) against the FKBP12-Rapamycin binding site of mTOR (mTOR). We determined high-resolution crystal structures of two unique Fabs that discriminate distinct conformational states of mTOR through recognition of its substrate recruitment interface. By leveraging these conformation-specific binders as intracellular probes, we uncovered the structural basis for an allosteric mechanism governing mTOR complex 1 (mTORC1) stability mediated by subtle structural adjustments within mTOR. Furthermore, our results demonstrated that synthetic binders emulate natural substrates by employing divergent yet complementary hydrophobic residues at defined positions, underscoring the broad molecular recognition capability of mTOR. Intracellular signaling studies showed differential time-dependent inhibition of S6 kinase 1 and Akt phosphorylation by genetically encoded intrabodies, thus supporting a mechanism of inhibition analogous to the natural product rapamycin. Finally, we implemented a feasible approach to selectively modulate mTOR signaling in the nucleus through spatially programmed intrabody expression. These findings establish intrabodies as versatile tools for dissecting the conformational regulation of mTORC1 and should be useful to explore how location-specific mTOR signaling influences disease progression.