Research

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Research Interests

The Falke lab lab employs an array of approaches including single molecule and other biophysical methods, in vitro reconstitution of membrane signaling pathways, protein biochemistry, live cell imaging, and molecular biology to elucidate the molecular mechanisms of cellular signaling on membrane surfaces. ÌýThe main focus is on lipid signaling pathwaysÌýthat control macrophage chemotaxis, phagocytosis, and autophagy in the innate immune response. Macrophages and other white blood cells possess a remarkable chemosensory pathway that enables these first respondersÌýto follow chemical trails to sites of infection, inflammation, and tissue damage. Upon arrival, the phagocytosis pathway triggers the engulfmentÌýand destruction of invading bacteria, viruses, and damaged cells. All cells also possess an autophagy pathway that grows a large, double-walled membrane to trap pathogens and damaged cell components in a sealed compartment for destruction and recycling. ÌýThe regulatory hubs of these pathways are lipid kinases (PI-3-kinases or PI3Ks) that phosphorylate substrate phosphatidylinositol (PI) lipids at the 3-position of the inositol sugar headgroup, yielding the essential signaling lipids PI-3,4,5-trisphosphate (PIP3) in the chemosensory pathway, and PI-3-phosphate (PI3P) in phagocytosis and autophagy. Dysregulation of PIP3Ìýand PI3P signals yields multiple pathologies including cancer, inflammatory disease and autoimmune defects. Understanding the molecular mechanisms ofÌýPIP3Ìýand PI3P signal in pathwaysÌýis crucial for signaling biology and medicine.

The general approach begins with single molecule TIRF studies of a reconstituted, multi-proteinÌýcircuit on a supported lipid bilayer mimicking the native membrane. ÌýThese single molecule studies elucidate the regulatory mechanisms underlying signal transduction. ÌýSubsequently, the hypothesized mechanisms are tested by fluorescenceÌýimaging studies in live cells, thereby revealing which mechanisms are most important in theÌýnative context. ÌýThe lab also employs a broadÌýarray of otherÌýbiophysical and biochemical tools as needed.

Summary of Falke Lab Accomplishments

Signal transduction mechanisms in macrophage chemotaxis

In the chemosensory signaling circuit that controls macrophage chemotaxis, attractant signals sensed by cell-surface receptors are amplified by a positive feedback loop at the leading edge of the cell. The feedback loop, in turn, controls second messenger signals that recruit dozens of proteins to the leading edge membrane, where these proteins form the signaling circuit that drives actin and membrane remodeling to push the leading edge up the attractant gradient.

The Falke group is investigating the molecular mechanisms underlying the assembly and operation of the chemosensory circuit on the leading edge membrane. Traditionally, the signaling lipid PIP3 has been considered the only relevant second messenger at the leading edge, but live cell studies by the group revealed that a localized Ca(II) signal is also an essential component of the leading edge postitive feedback loop. Together, these PIP3 and Ca(II) signals recruit PH- and C2-domain proteins, respectively, to the leading edge membrane, where they serve as upstream regulators or downstream effectors of the Class I PI3KÌýlipid kinase that serves as the regulatory hub of the leading edge chemosensory circuit.

Current work is targeting the molecular mechanisms underlying (i) the rapid recruitment of master kinases to the leading edge membrane, (ii) their activation on the membrane surface, (iii) their interactions with target and substrate lipids, (iv) their interactions with other membrane proteins to formÌýsignaling complexes, and (v) sequential information flow between the protein components of the membrane-based signalingÌýcircuit. The targeted master kinases include PKCalpha, PI3Kalpha, PDK1, and AKT1/PKB. An innovative single molecule fluorescence method developed by the group is revealing, for the first time, the surface diffusion,Ìýinteractions, and regulatory mechanismsÌýof the circuit components reconstituted on a supported lipid bilayer resembling the native membrane. Subsequent live cell imaging studies test the resulting mechanistic models in the native context of the macrophage leading edge. ÌýMany other biophysical and biochemical methods are also employed as needed to answer key questions. ÌýTogether, these diverse approaches are providing new insights into the molecular basis of macrophage chemosensing at the leading edge membrane during the primary immune response to infection, inflammation, and tissue damage. More broadly, each of the master kinases plays central roles in other signaling pathways and in multiple human cancers.

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Signal transduction mechanisms in phagocytosis and autophagy

In the signaling circuit that initiates phagocytosis, cell-surface receptors trigger phagocytosis when theyÌýrecognize and bind motifs characteristic of pathogens, or the antibodies coating pathogens, or damaged tissue. ÌýPhagocytosis and engulfment yields an internalizedÌýphagosome, which then undergoes three stages of development. ÌýThe early stage isÌýcharacterized by simultaneous Class I and Class III PI3-kinase lipid signals (PIP3 and PI3P, respectively) present on the phagosome membrane, which recruit specific signaling proteins to the membrane surface. ÌýNext, during the middle stage of phagosome development the phagosome Class III PI3-kinase is stronglyÌýactivated and the resulting intense PI3P signal activates the production of reactive oxygen species (ROS) that kill the trapped pathogens within the phagosome. ÌýFinally, during the late stage of phagosome development the Class III PI3-kinase activity decreases and the phagosome is prepared for fusion with the lysosome, which breaks down pathogens into fragments used to guide theÌýdevelopment of specific antibodies against the pathogen via adaptive immunity. ÌýÌýÌý

Autophagy is initiated by internal cell signals arising from cell invasion or starvation, which trigger activation of the autophagy Class III PI3-kinase localized to autophagosome membranes. ÌýThe resulting PI3P lipid signal stimulates rapid growth of the autophagosome membrane, the fastest growing membrane in the cell with the highest lipid/protein ratio.

The Falke group is currently investigating the molecular mechanisms of Class III PI3-kinase regulation by reconstituting both the phagosome and autophagy lipid kinases with their activating G-proteins Rab5A and Rab1A, respectively, on supported lipiid bilayers containing the relevant endosomal lipids. ÌýMolecular mechanisms being studied include (i)Ìýregulation of the Class III PI3K-kinases and PI3P production by their specific G proteins, (ii) activation of downstream effectors of each lipid kinase, and (iii) downregulation of the lipid kinase and PI3P signaling in the late stage phagosome.ÌýÌýAs described for studies of the chemotaxis pathway, the lab elucidates molecular mechanisms of regulation using single molecule TIRFM studies of reconstituted signaling reactions in vitro, then employs live-cell imaging studies to test the resulting mechanistic models in the native macrophage context, and also incorporates otherÌýbiophysical and biochemical tools as needed to answer key biological questions.Ìý

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Signaling reactions on the macrophage leading edge membrane (PMID 17911247, 29715315)
Signaling reactions on the macrophage phagosome membrane (Falke Lab, unpublished)
Single molecule assay for Class I PI3-kinase and PIP3 production (PMID 27119641, 29211993)
Single molecule assay for Class III PI3-kinase and PI3P production (PMID 33137306)

Selected Falke Group Accomplishments

  • (2026) Autophagy Kinase Diffuses Faster than Lipids as it Uses an Electrostatic Search Mechanism to Scan the Surface of Its Target Membrane: ÌýSingle Molecule Studies (Lizardos, McCombs, Ohashi, Knight, Tremel, Williams & Falke)
  • (2025) COSMIC-Linked Ras Mutations on the Docking Surface for PI3-Kinase Frequently Generate Affinity Increases (Mead, Batz, Shih, Fleming, Tesdahl, Lizardos, Armendariz, Hannan, Hickey, Leyk, Erbse & Falke)Ìý
  • (2023) Direct Detection and Kinetic Analysis of PDK1:PKCα Heterodimer Association-Dissociation Events Between Single Molecules on a Target Membrane Surface (Gordon, Ziemba & Falke)
  • (2023) A Quantitative Assay for Measuring the Binding of Active Ras to the Ras Binding Domain of PI-3-Kinase gamma (Fleming, Hannan, Swisher, Tesdahl, Martyr, Cordaro, Erbse & Falke)
  • (2021) Development of an HPLC Method to Resolve and Quantify Guanine Nucleotides Bound to Ras Family G Proteins (Hannan, Swisher, Martyr, Cordaro, Erbse & Falke)
  • (2021) Discovery that Conventional PKC Can CompetitivelyÌýInhibit PDK1 Phosphoactivation of AKT1 on a Target Membrane, As Revealed by Single Molecule Analysis (Gordon, Ziemba & Falke)
  • (2021) Development of a UV Deconvolution Method to Analyze theÌýProtein Concentration, Nucleotide Stoichiometry, and Purity of Ras-Guanine Nucleotide Complexes (Swisher, Hannan, Cordaro, Erbse, & Falke)
  • (2020)ÌýElucidation via Single Molecule Analysis of a Novel DualÌýMolecular Mechanism by which the Small GTPase Rab5 Recruits and Allosterically Activates Class III PI3K and PI3P Production, (Buckles, Ziemba, Masson, Williams & Falke)
  • (2020) Development of the First Single Molecule Assay for Class III PI3K Lipid Kinase Activity and PI3P Production on a Reconstituted Phagosome-Like Bilayer. Ìý(Buckles, Burke, Ohashi, Tremmel, Gordon, Williams & Falke)
  • (2018) Hypothesis Testing in Live Macrophages Reveals that Ca-PKC, but not Ca-Calmodulin, Regulates the MARCKS-PI3K-PIP3 Circuit at the Leading Edge MembraneÌýÌý(Buckles, Ziemba, Masson, Williams & Falke)
  • (2017) Discovery via Single Molecule Analysis that Ca-Calmodulin (Ca-CaM)ÌýStimulates PIP3 Lipid Signaling In VitroÌývia a Ca-CaM-MARCKS-PI3K-PIP3 Activation Module (Buckles, Ziemba, Masson, Williams & Falke)
  • (2017) Elucidation via Single Molecule Analysis of the Molecular Mechanism by which the Oncogenic Small GTPase Ras Activates the Oncogenic Lipd Kinase PI3K and thereby Amplifies PIP3 Signals, (Buckles, Ziemba, Masson, Williams & Falke)
  • (2016) Discovery Via Single Molecule Analysis in vitroÌýthat Ca Signals Stimulate PIP3 Lipid Signaling via a Ca-PKC-MARCKS-PI3K-PIP3 Activation ModuleÌýÌý(Ziemba, Swisher, Burke, Masson, Williams & Falke)
  • (2016) Development of the First Single Molecule Assay for Class I PI3K Lipid Kinase Activity and PIP3 Production on a Reconstituted Plasma-Menbrane-Like Bilayer. Ìý(Ziemba, Swisher, Burke, Masson, Williams & Falke)
  • (2014) Engineered Disulfide Bonds that Further Enhance the Kinetic Stability of the Bacterial Chemosensory Array (Ziemba, Pilling, Calleja, Larijani & Falke)
  • (2014) Discovery of a New, Predominant Intermediate in the Activation Mechanism of Protein Kinase C (PKC) Bound to its Target Membrane (Ziemba, Li, Landgraf, Knight, Voth & Falke)
  • (2013) Elucidation of a Novel Dimer-to-Monomer Activation Mechanism for the PH domain of PDK1 (Ziemba, Pilling, Calleja, Larijani & Falke)
  • (2013) Discovery that Bound Lipid and Protein Keels In the Bilayer Make Additive Contributions to the Total Friction of Peripheral Proteins Undergoing Lateral Diffusion (Ziemba & Falke)
  • (2013) Elucidation of the Structure and Function of Two Essential Protein-Protein Contacts in the Functional, Bacterial Chemosensory Array (Piasta, Natale, Duplantis, Ulliman, Slivka, Crane & Falke)
  • (2012) Initial Evidence that the Ultrastability of the Bacterial Chemosensory Array Requires a High Degree of Array Order (Slivka & Falke)
  • (2012) First Experimental Determination of a PH Domain Membrane Docking Geometry by EPR Depth Parameter Measurements (Chen, Ziemba & Falke)
  • (2012) Development of a Single-Molecule Method for Detecting the Formation of Signaling Protein Complexes on Membrane Surfaces (Ziemba, Knight & Falke)
  • (2011) Demonstration that the Sentry Glutamate is a Widespread Feature of PIP3-Specific Binding Sites in PH domains (Pilling, Landgraf & Falke)
  • (2011) Development of One-Sample Method for Bulk Fret Measurements, Known As OSFRET (Erbse & Falke)
  • (2010) First systematic study showing that tightly bound lipids make additive contributions to the bilayer friction of peripheral membrane proteins during lateral diffusion (Knight, Lerner, Velazquez, Pastor & Falke)
  • (2009) Discovery that the conserved cytoplasmic domain of bacterial chemoreceptors transmits signals through its long four-helix bundle via a novel yin-yang mechanism (Swain & Falke)
  • (2009) Discovery that the bacterial chemosensory signaling complex is ultrastable (Erbse & Falke)
  • (2009) Development of a novel single-molecule method to probe the protein-lipid interactions and surface dynamics of membrane-bound proteins (Knight & Falke)
  • (2008) Elucidation of the molecular mechanism underlying a highly oncogenic mutation in AKT1 PH domain known to cause multiple human cancers (Landgraf, Pilling & Falke)
  • (2008) Determination of the distinct membrane docking geometries of PKC-alpha C2 domain in two different lipid binding states (Landgraf, Malmberg & Falke)
  • (2007) Discovery that a localized Ca(II) influx is an essential component of the positive feedback loop at the macrophage leading edge (Evans & Falke)
  • (2007) Chemical structure determination that the conserved HAMP signal conversion domain of bacterial chemoreceptors is a parallel 4-helix bundle (Swain & Falke)
  • (2007, 2006) Demonstration that PIP2 is a third essential target lipid of PKC-alpha (Evans, Corbin, Landgraf & Falke)
  • (2006) Chemical mapping of four protein interactions sites on the surface of the bacterial chemosensory kinase CheA (Miller, Kohout & Falke)
  • (2005) Discovery of a conserved, essential Gly hinge in the cytoplasmic 4-helix bundle of bacterial chemoreceptors (Coleman, Bass & Falke)
  • (2005) Elucidation of the electrostatic mechanism underlying adaptation site signaling in bacterial chemoreceptors (Starrettt & Falke)
  • (2004) EPR determination of the highest resolution membrane docking geometry currently available Ã� the C2 domain of cytosolic phospholipase A2 (Malmberg & Falke)
  • (2004) Development of an electrostatic method to drive piston displacements of transmembrane helices (Miller & Falke)
  • (2004) Discovery that GRP1 PH domain uses an electrostatic search mechanism to rapidly find its rare target lipid PIP3 (Corbin & Falke)
  • (2003) Chemical mapping of the protein interaction sites on the surface of bacterial chemoreceptors (Mehan & Falke)
  • (2003) Demonstration that covalent adaptation introduces multiple sub-states into the on-off switching behavior of the receptor-CheA signaling complex (Bornhorst & Falke)
  • (1999) Chemical determination of the 4-helix bundle architecture of bacterial chemoreceptor cytoplasmic domains (Bass, Butler, Danielson & Falke)
  • (1997) Elucidation of the Ca(II)-signaling cycle for the membrane-docking C2 domain of cytosolic phospholipase A2, the Ca(II) sensor of inflammation (Nalefski & Falke)
  • (1997) Development of a novel FRET assay for monitoring the equilibrium and kinetic parameters of protein-membrane docking reactions (Nalefski & Falke)
  • (1996) Discovery that the amino acid at the gateway position of EF-hand sites controls the Ca(II) on-off kinetics (Drake & Falke)
  • (1996) Determination of the effects of protein stabilizing agents on long-range backbone motions in proteins via disulfide trapping (Butler & Falke)
  • (1996) Discovery that the transmembrane signal of bacterial chemoreceptors is transmitted by a piston displacement of the signaling helix (Chervitz & Falke)
  • (1995) Engineering reversible, lock-on and lock-off disulfide bonds that covalently trap the signaling states of bacterial chemoreceptors (Chervitz & Falke)
  • (1994) Use of 19F NMR to probe conformational changes in a receptor (Danielson & Falke)
  • (1993) Use of 19F NMR to probe conformational changes in a signaling protein (Drake & Falke)
  • (1992) Detection and trajectory analysis of thermal backbone motions in a folded, aqueous protein by a novel disulfide trapping method (Careaga & Falke)
  • (1991) Use of 19F NMR to probe conformational changes in a binding protein (Luck & Falke)