Dr. Kacper Rogala is Assistant Professor at Stanford University School of Medicine with a joint appointment between the Department of Structural Biology and the Department of Chemical & Systems Biology. He is also a Leader in the Stanford Cancer Institute.
Kacper was born and raised in Poland, and educated in three wonderful British cities: Oxford, London and Edinburgh, where he studied chemistry of living things, or simply — biochemistry. During his studies, Kacper developed a deep passion for proteins — how they work, what they look like, and how they interact with other proteins and small molecules. This passion led him to pursue a trans-Atlantic postdoc between two Cambridges: one in the UK and one in Massachusetts. As a researcher at MIT, the Whitehead Institute, the Broad Institute, and the MRC Laboratory of Molecular Biology, Kacper began unraveling the mechanisms of nutrient sensing on the surface of lysosomes.
Kacper joined Stanford as an assistant professor in 2022, and together with his team they are leading the charge towards mechanistic understanding of how cells control metabolism in response to nutrients and growth factors, and ways to modulate these activities with chemical probes — for the benefit of patients.
Leader, Stanford Cancer Institute (2022 - Present)
Honors & Awards
Maximizing Investigators' Research Award, National Institute of General Medical Sciences, MD (2023)
Career Development Award, United States Department of Defense, MD (2023)
Innovation and Collaboration Award, Lustgarten Foundation, NY (2023)
The NIH Pathway to Independence Award, National Cancer Institute, MD (2021)
Margaret and Herman Sokol Postdoctoral Award in Biomedical Research, Whitehead Institute, MA (2020)
Postdoctoral Research Fellowship Award, Charles A. King Trust, MA (2020)
Junior Fellowship, Tuberous Sclerosis Association, UK (2018)
Member, Royal Society of Chemistry, UK (2016)
College Research Associate, Sidney Sussex College, University of Cambridge, UK (2016)
Graduate Fellowship, Engineering and Physical Sciences Research Council, UK (2011)
Best Master of Research Student Prize, University College London, UK (2011)
Governor’s Award for Outstanding Students, Kraków, Poland (2006)
Postdoctoral Fellow, Massachusetts Institute of Technology, Structural and Chemical Biology (2022)
D.Phil., The University of Oxford, Structural Biology (2016)
M.Res., University College London, Biophysics (2011)
B.Sc. (Hons), The University of Edinburgh, Biochemistry (2010)
Current Research and Scholarly Interests
How are nutrients recognized by their protein sensors? How is their transport across cellular and intracellular membranes regulated? And, how is nutrient sensing integrated with other chemical signals, such as hormones, to determine cellular decisions, especially the decision: to grow or not to grow?
We are a team of structural and chemical biologists aiming to answer these fundamental questions at the level of ångstroms, nanometers, and micrometers. Many proteins in these pathways are deregulated in cancer, and our mission is to first reveal the mechanism of action of these proteins, and then use that knowledge to develop targeted chemical probes to modulate their activity in cells and organisms.
Structural mechanisms of the mTOR pathway.
Current opinion in structural biology
2023; 82: 102663
The mTOR signaling pathway is essential for regulating cell growth and mammalian metabolism. The mTOR kinase forms two complexes, mTORC1 and mTORC2, which respond to external stimuli and regulate differential downstream targets. Cellular membrane-associated translocation mediates function and assembly of the mTOR complexes, and recent structural studies have begun uncovering the molecular basis by which the mTOR pathway (1) regulates signaling inputs, (2) recruits substrates, (3) localizes to biological membranes, and (4) becomes activated. Moreover, indications of dysregulated mTOR signaling are implicated in a wide range of diseases and an increasingly comprehensive understanding of structural mechanisms is driving novel translational development.
View details for DOI 10.1016/j.sbi.2023.102663
View details for PubMedID 37572585
Structure of the nutrient-sensing hub GATOR2.
Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients1,2. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively3-5. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1 MDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 β-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and α-solenoids. Integration of SEH1L and SEC13 into the scaffold through β-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes6. The scaffold orients the WD40 β-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway.
View details for DOI 10.1038/s41586-022-04939-z
View details for PubMedID 35831510
Structural basis for the docking of mTORC1 on the lysosomal surface.
Science (New York, N.Y.)
2019; 366 (6464): 468-475
The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome.
View details for DOI 10.1126/science.aay0166
View details for PubMedID 31601708
Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
2019; 179 (6): 1319-1329.e8
mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
View details for DOI 10.1016/j.cell.2019.10.036
View details for PubMedID 31704029
View details for PubMedCentralID PMC7008705
Architecture of human Rag GTPase heterodimers and their complex with mTORC1.
Science (New York, N.Y.)
2019; 366 (6462): 203-210
The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
View details for DOI 10.1126/science.aax3939
View details for PubMedID 31601764
View details for PubMedCentralID PMC6795536
Interaction between the Caenorhabditis elegans centriolar protein SAS-5 and microtubules facilitates organelle assembly.
Molecular biology of the cell
2018; 29 (6): 722-735
Centrioles are microtubule-based organelles that organize the microtubule network and seed the formation of cilia and flagella. New centrioles assemble through a stepwise process dependent notably on the centriolar protein SAS-5 in Caenorhabditis elegans SAS-5 and its functional homologues in other species form oligomers that bind the centriolar proteins SAS-6 and SAS-4, thereby forming an evolutionarily conserved structural core at the onset of organelle assembly. Here, we report a novel interaction of SAS-5 with microtubules. Microtubule binding requires SAS-5 oligomerization and a disordered protein segment that overlaps with the SAS-4 binding site. Combined in vitro and in vivo analysis of select mutants reveals that the SAS-5-microtubule interaction facilitates centriole assembly in C. elegans embryos. Our findings lead us to propose that the interdependence of SAS-5 oligomerization and microtubule binding reflects an avidity mechanism, which also strengthens SAS-5 associations with other centriole components and, thus, promotes organelle assembly.
View details for DOI 10.1091/mbc.E17-06-0412
View details for PubMedID 29367435
View details for PubMedCentralID PMC6003225
Cross-linking mass spectrometry identifies new interfaces of Augmin required to localise the γ-tubulin ring complex to the mitotic spindle.
2017; 6 (5): 654-663
The hetero-octameric protein complex, Augmin, recruits γ-Tubulin ring complex (γ-TuRC) to pre-existing microtubules (MTs) to generate branched MTs during mitosis, facilitating robust spindle assembly. However, despite a recent partial reconstitution of the human Augmin complex in vitro, the molecular basis of this recruitment remains unclear. Here, we used immuno-affinity purification of in vivo Augmin from Drosophila and cross-linking/mass spectrometry to identify distance restraints between residues within the eight Augmin subunits in the absence of any other structural information. The results allowed us to predict potential interfaces between Augmin and γ-TuRC. We tested these predictions biochemically and in the Drosophila embryo, demonstrating that specific regions of the Augmin subunits, Dgt3, Dgt5 and Dgt6 all directly bind the γ-TuRC protein, Dgp71WD, and are required for the accumulation of γ-TuRC, but not Augmin, to the mitotic spindle. This study therefore substantially increases our understanding of the molecular mechanisms underpinning MT-dependent MT nucleation.
View details for DOI 10.1242/bio.022905
View details for PubMedID 28351835
View details for PubMedCentralID PMC5450317
Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit β by EPR Spectroscopy.
The Journal of biological chemistry
2015; 290 (27): 16539-49
Viral flice-interacting protein (vFLIP), encoded by the oncogenic Kaposi sarcoma-associated herpes virus (KSHV), constitutively activates the canonical nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) pathway. This is achieved through subversion of the IκB kinase (IKK) complex (or signalosome), which involves a physical interaction between vFLIP and the modulatory subunit IKKγ. Although this interaction has been examined both in vivo and in vitro, the mechanism by which vFLIP activates the kinase remains to be determined. Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/β subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation. To investigate this hypothesis we engineered a series of mutants along the length of the IKKγ molecule that could be individually modified with nitroxide spin labels. Subsequent distance measurements using electron paramagnetic resonance spectroscopy combined with molecular modeling and molecular dynamics simulations revealed that IKKγ is a parallel coiled-coil whose response to binding of vFLIP or IKKβ is localized twisting/stiffening and not large-scale rearrangements. The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway. In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.
View details for DOI 10.1074/jbc.M114.622928
View details for PubMedID 25979343
View details for PubMedCentralID PMC4505408
Misato Controls Mitotic Microtubule Generation by Stabilizing the TCP-1 Tubulin Chaperone Complex [corrected].
Current biology : CB
2015; 25 (13): 1777-83
Mitotic spindles are primarily composed of microtubules (MTs), generated by polymerization of α- and β-Tubulin hetero-dimers. Tubulins undergo a series of protein folding and post-translational modifications in order to fulfill their functions. Defects in Tubulin polymerization dramatically affect spindle formation and disrupt chromosome segregation. We recently described a role for the product of the conserved misato (mst) gene in regulating mitotic MT generation in flies, but the molecular function of Mst remains unknown. Here, we use affinity purification mass spectrometry (AP-MS) to identify interacting partners of Mst in the Drosophila embryo. We demonstrate that Mst associates stoichiometrically with the hetero-octameric Tubulin Chaperone Protein-1 (TCP-1) complex, with the hetero-hexameric Tubulin Prefoldin complex, and with proteins having conserved roles in generating MT-competent Tubulin. We show that RNAi-mediated in vivo depletion of any TCP-1 subunit phenocopies the effects of mutations in mst or the Prefoldin-encoding gene merry-go-round (mgr), leading to monopolar and disorganized mitotic spindles containing few MTs. Crucially, we demonstrate that Mst, but not Mgr, is required for TCP-1 complex stability and that both the efficiency of Tubulin polymerization and Tubulin stability are drastically compromised in mst mutants. Moreover, our structural bioinformatic analyses indicate that Mst resembles the three-dimensional structure of Tubulin monomers and might therefore occupy the TCP-1 complex central cavity. Collectively, our results suggest that Mst acts as a co-factor of the TCP-1 complex, playing an essential role in the Tubulin-folding processes required for proper assembly of spindle MTs.
View details for DOI 10.1016/j.cub.2015.05.033
View details for PubMedID 26096973
View details for PubMedCentralID PMC4510148
The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.
2015; 4: e07410
Centrioles are microtubule-based organelles crucial for cell division, sensing and motility. In Caenorhabditis elegans, the onset of centriole formation requires notably the proteins SAS-5 and SAS-6, which have functional equivalents across eukaryotic evolution. Whereas the molecular architecture of SAS-6 and its role in initiating centriole formation are well understood, the mechanisms by which SAS-5 and its relatives function is unclear. Here, we combine biophysical and structural analysis to uncover the architecture of SAS-5 and examine its functional implications in vivo. Our work reveals that two distinct self-associating domains are necessary to form higher-order oligomers of SAS-5: a trimeric coiled coil and a novel globular dimeric Implico domain. Disruption of either domain leads to centriole duplication failure in worm embryos, indicating that large SAS-5 assemblies are necessary for function in vivo.
View details for DOI 10.7554/eLife.07410
View details for PubMedID 26023830
View details for PubMedCentralID PMC4471805
Structural analysis of the G-box domain of the microcephaly protein CPAP suggests a role in centriole architecture.
Structure (London, England : 1993)
2013; 21 (11): 2069-77
Centrioles are evolutionarily conserved eukaryotic organelles composed of a protein scaffold surrounded by sets of microtubules organized with a 9-fold radial symmetry. CPAP, a centriolar protein essential for microtubule recruitment, features a C-terminal domain of unknown structure, the G-box. A missense mutation in the G-box reduces affinity for the centriolar shuttling protein STIL and causes primary microcephaly. Here, we characterize the molecular architecture of CPAP and determine the G-box structure alone and in complex with a STIL fragment. The G-box comprises a single elongated β sheet capable of forming supramolecular assemblies. Structural and biophysical studies highlight the conserved nature of the CPAP-STIL complex. We propose that CPAP acts as a horizontal "strut" that joins the centriolar scaffold with microtubules, whereas G-box domains form perpendicular connections.
View details for DOI 10.1016/j.str.2013.08.019
View details for PubMedID 24076405
View details for PubMedCentralID PMC3824074