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Biomedical subjects

John A Cooper

Publications and source records attributed to John A Cooper.

At least 19 recordsLinked to original sources
PubMed2006

Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein: implications for how capping protein binds the actin filament.

The heterodimeric actin-capping protein (CP) can be inhibited by polyphosphoinositides, which may be important for actin polymerization at membranes in cells. Here, we have identified a conserved set of basic residues on the surface of CP that are important for the interaction with phosphatidylinositol 4,5-bisphosphate (PIP(2)). Computational docking studies predicted the identity of residues involved in this interaction, and functional and physical assays with site-directed mutants of CP confirmed the prediction. The PIP(2) binding site overlaps with the more important of the two known actin-binding sites of CP. Correspondingly, we observed that loss of PIP(2) binding correlated with loss of actin binding among the mutants. Using TIRF (total internal reflection fluorescence) microscopy, we observed that PIP(2) rapidly converted capped actin filaments to a growing state, consistent with uncapping. Together, these results extend our understanding of how CP binds to the barbed end of the actin filament, and they support the idea that CP can "wobble" when bound to the barbed end solely by the C-terminal "tentacle" of its beta-subunit.

Actin Capping Proteins↗
PubMed2006

The role of CKIP-1 in cell morphology depends on its interaction with actin-capping protein.

CKIP-1 is a pleckstrin homology domain-containing protein that induces alterations of the actin cytoskeleton and cell morphology when expressed in human osteosarcoma cells. CKIP-1 interacts with the heterodimeric actin-capping protein in cells, so we postulated that this interaction was responsible for the observed cytoskeletal and morphological effects of CKIP-1. To test this postulate, we used peptide "walking arrays" and alignments of CKIP-1 with CARMIL, another CP-binding protein, to identify Arg-155 and Arg-157 of CKIP-1 as residues potentially required for its interactions with CP. CKIP-1 mutants harboring Arg-155 and Arg-157 substitutions exhibited greatly decreased CP binding, while retaining wild-type localization, the ability to interact with protein kinase CK2, and self-association. To examine the phenotype associated with expression of these mutants, we generated tetracycline-inducible human osteosarcoma cells lines expressing R155E,R157E mutants of CKIP-1. Examination of these cell lines reveals that CKIP-1 R155E,R157E did not induce the distinct changes in cell morphology and the actin cytoskeleton that are characteristic of wild-type CKIP-1 demonstrating that the interaction between CKIP-1 and CP is required for these cellular effects.

Actins↗
PubMed2006

Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end.

The heterodimeric actin-capping protein (CP) regulates actin assembly and cell motility by binding tightly to the barbed end of the actin filament. Here we demonstrate that myotrophin/V-1 binds directly to CP in a 1:1 molar ratio with a Kd of 10-50 nm. V-1 binding inhibited the ability of CP to cap the barbed ends of actin filaments. The actin-binding COOH-terminal region, the "tentacle," of the CP beta subunit was important for binding V-1, with lesser contributions from the alpha subunit COOH-terminal region and the body of the protein. V-1 appears to be unable to bind to CP that is on the barbed end, based on the observations that V-1 had no activity in an uncapping assay and that the V-1.CP complex had no capping activity. Two loops of V-1, which extend out from the alpha-helical backbone of this ankyrin repeat protein, were necessary for V-1 to bind CP. Parallel computational studies determined a bound conformation of the beta tentacle with V-1 that is consistent with these findings, and they offered insight into experimentally observed differences between the alpha1 and alpha2 isoforms as well as the mutant lacking the alpha tentacle. These results support and extend our "wobble" model for CP binding to the actin filament, in which the two COOH-terminal regions of CP bind independently to the actin filament, and bound CP is able to wobble when attached only via its mobile beta-subunit tentacle. This model is also supported by molecular dynamics simulations of CP reported here. The existence of the wobble state may be important for actin dynamics in cells.

Actin Capping Proteins↗
PubMed2006

Identification of a novel inhibitory actin-capping protein binding motif in CD2-associated protein.

CD2-associated protein (CD2AP) is a scaffold molecule that plays a critical role in the maintenance of the kidney filtration barrier. Little, however, is understood about its mechanism of function. We used mass spectrometry to identify CD2AP-interacting proteins. Many of the proteins that we identified suggest a role for CD2AP in endocytosis and actin regulation. To address the role of CD2AP in regulation of the actin cytoskeleton, we focused on characterizing the interaction of CD2AP with actin-capping protein CP. We identified a novel binding motif LXHXTXXRPK(X)6P present in CD2AP that is also found in its homolog Cin85 and other capping protein-associated proteins such as CARMIL and CKIP-1. CD2AP inhibits the function of capping protein in vitro. Therefore, our results support a role of CD2AP in the regulation of the actin cytoskeleton.

Actins↗
PubMed2006

Cortactin has an essential and specific role in osteoclast actin assembly.

Osteoclasts are essential for bone dynamics and calcium homeostasis. The cells form a tight seal on the bone surface, onto which they secrete acid and proteases to resorb bone. The seal is associated with a ring of actin filaments. Cortactin, a c-Src substrate known to promote Arp2/3-mediated actin assembly in vitro, is expressed in osteoclasts and localizes to the sealing ring. To address the role of cortactin and actin assembly in osteoclasts, we depleted cortactin by RNA interference. Cortactin-depleted osteoclasts displayed a complete loss of bone resorption with no formation of sealing zones. On nonosteoid surfaces, osteoclasts flatten with a dynamic, actin-rich peripheral edge that contains podosomes, filopodia, and lamellipodia. Cortactin depletion led to a specific loss of podosomes, revealing a tight spatial compartmentalization of actin assembly. Podosome formation was restored in cortactin-depleted cells by expression of wild-type cortactin or a Src homology 3 point mutant of cortactin. In contrast, expression of a cortactin mutant lacking tyrosine residues phosphorylated by Src did not restore podosome formation. Cortactin was found to be an early component of the nascent podosome belt, along with dynamin, supporting a role for cortactin in actin assembly.

Actin-Related Protein 2↗
PubMed2006

Checkpoint control of mitotic exit--do budding yeast mind the GAP?

Cell cycle checkpoints can delay mitotic exit in budding yeast. The master controller is the small GTPase Tem1, with inputs from a proposed guanine nucleotide exchange factor (GEF), Lte1, and a GTPase-activating protein (GAP), Bub2/Bfa1. In this issue, Fraschini et al. (p. 335) show that GAP activity of Bub2/Bfa1 appears to be dispensable for inactivation of Tem1 in cells. Their results call into question the GTP/GDP switch model for Tem1 activity, as have other results in the past. The paper also focuses attention on the two spindle pole bodies as potential sites for regulation of Tem1.

Cell Cycle Proteins↗
PubMed2006

Actin-based motility during endocytosis in budding yeast.

Actin assembly nucleated by Arp2/3 complex has been implicated in the formation and movement of endocytic vesicles. The dendritic nucleation model has been proposed to account for Arp2/3-mediated actin assembly and movement. Here, we explored the model by examining the role of capping protein in vivo, with quantitative tracking analysis of fluorescence markers for different stages of endocytosis in yeast. Capping protein was most important for the initial movement of endocytic vesicles away from the plasma membrane, which presumably corresponds to vesicle scission and release. The next phase of endosome movement away from the plasma membrane was also affected, but less so. The results are consistent with the dendritic nucleation model's prediction of capping protein as important for efficient actin assembly and force production. In contrast, the movement of late-stage endocytic vesicles, traveling through the cytoplasm en route to the vacuole, did not depend on capping protein. The movement of these vesicles was found previously to depend on Lsb6, a WASp interactor, whereas Lsb6 was found here to be dispensable for early endosome movement. Thus, the molecular requirements for Arp2/3-based actin assembly differ in early versus later stages of endocytosis. Finally, acute loss of actin cables led to increased patch motility.

Actin Capping Proteins↗
PubMed2006

Relative accuracy testing of an X-ray fluorescence-based mercury monitor at coal-fired boilers.

The relative accuracy (RA) of a newly developed mercury continuous emissions monitor, based on X-ray fluorescence, was determined by comparing analysis results at coal-fired plants with two certified reference methods (American Society for Testing and Materials [ASTM] Method D6784-02 and U.S. Environment Protection Agency [EPA] Method 29). During the first determination, the monitor had an RA of 25% compared with ASTM Method D6784-02 (Ontario Hydro Method). However, the Ontario Hydro Method performed poorly, because the mercury concentrations were near the detection limit of the reference method. The mercury in this exhaust stream was primarily elemental. The second test was performed at a U.S. Army boiler against EPA Reference Method 29. Mercury and arsenic were spiked because of expected low mercury concentrations. The monitor had an RA of 16% for arsenic and 17% for mercury, meeting RA requirements of EPA Performance Specification 12a. The results suggest that the sampling stream contained significant percentages of both elemental and oxidized mercury. The monitor was successful at measuring total mercury in particulate and vapor forms.

Air Pollutants↗
PubMed2006

Validation of three new methods for determination of metal emissions using a modified Environmental Protection Agency Method 301.

Three new methods applicable to the determination of hazardous metal concentrations in stationary source emissions were developed and evaluated for use in U.S. Environmental Protection Agency (EPA) compliance applications. Two of the three independent methods, a continuous emissions monitor-based method (Xact) and an X-ray-based filter method (XFM), are used to measure metal emissions. The third method involves a quantitative aerosol generator (QAG), which produces a reference aerosol used to evaluate the measurement methods. A modification of EPA Method 301 was used to validate the three methods for As, Cd, Cr, Pb, and Hg, representing three hazardous waste combustor Maximum Achievable Control Technology (MACT) metal categories (low volatile, semivolatile, and volatile). The modified procedure tested the methods using more stringent criteria than EPA Method 301; these criteria included accuracy, precision, and linearity. The aerosol generation method was evaluated in the laboratory by comparing actual with theoretical aerosol concentrations. The measurement methods were evaluated at a hazardous waste combustor (HWC) by comparing measured with reference aerosol concentrations. The QAG, Xact, and XFM met the modified Method 301 validation criteria. All three of the methods demonstrated precisions and accuracies on the order of 5%. In addition, correlation coefficients for each method were on the order of 0.99, confirming the methods' linear response and high precision over a wide range of concentrations. The measurement methods should be applicable to emissions from a wide range of sources, and the reference aerosol generator should be applicable to additional analytes. EPA recently approved an alternative monitoring petition for an HWC at Eli Lilly's Tippecanoe site in Lafayette, IN, in which the Xact is used for demonstrating compliance with the HWC MACT metal emissions (low volatile, semivolatile, and volatile). The QAG reference aerosol generator was approved as a method for providing a quantitative reference aerosol, which is required for certification and continuing quality assurance of the Xact.

Aerosols↗
PubMed2005

NudEL targets dynein to microtubule ends through LIS1.

Dynein is a minus-end-directed microtubule motor with critical roles in mitosis, membrane transport and intracellular transport. Several proteins regulate dynein activity, including dynactin, LIS1 (refs 2, 3) and NudEL (NudE-like). Here, we identify a NUDEL homologue in budding yeast and name it Ndl1. The ndl1delta null mutant shows decreased targeting of dynein to microtubule plus ends, an essential element of the model for dynein function. We find that Ndl1 regulates dynein targeting through LIS1, with which it interacts biochemically, but not through CLIP170, another plus-end protein involved in dynein targeting. Ndl1 is found at far fewer microtubule ends than are LIS1 and dynein. However, when Ndl1 is present at a plus end, the molar amount of Ndl1 approaches that of LIS1 and dynein. We propose a model in which Ndl1 binds transiently to the plus end to promote targeting of LIS1, which cooperatively recruits dynein.

Cell Cycle Proteins↗
PubMed2005

The offloading model for dynein function: differential function of motor subunits.

During mitosis in budding yeast, dynein moves the mitotic spindle into the mother-bud neck. We have proposed an offloading model to explain how dynein works. Dynein is targeted to the dynamic plus end of a cytoplasmic microtubule, offloads to the cortex, becomes anchored and activated, and then pulls on the microtubule. Here, we perform functional studies of dynein intermediate chain (IC) and light intermediate chain (LIC). IC/Pac11 and LIC/Dyn3 are both essential for dynein function, similar to the heavy chain (HC/Dyn1). IC and LIC are targeted to the distal plus ends of dynamic cytoplasmic microtubules, as is HC, and their targeting depends on HC. Targeting of HC to the plus end depends on IC, but not LIC. IC also localizes as stationary dots at the cell cortex, the presumed result of offloading in our model, as does HC, but not LIC. Localization of HC to cortical dots depends on both IC and LIC. Thus, the IC and LIC accessory chains have different but essential roles in dynein function, providing new insight into the offloading model.

Blotting, Western↗
PubMed2005

Mammalian CARMIL inhibits actin filament capping by capping protein.

Actin polymerization in cells occurs via filament elongation at the barbed end. Proteins that cap the barbed end terminate this elongation. Heterodimeric capping protein (CP) is an abundant and ubiquitous protein that caps the barbed end. We find that the mouse homolog of the adaptor protein CARMIL (mCARMIL) binds CP with high affinity and decreases its affinity for the barbed end. Addition of mCARMIL to cell extracts increases the rate and extent of Arp2/3 or spectrin-actin seed-induced polymerization. In cells, GFP-mCARMIL concentrates in lamellipodia and increases the fraction of cells with large lamellipodia. Decreasing mCARMIL levels by siRNA transfection lowers the F-actin level and slows cell migration through a mechanism that includes decreased lamellipodia protrusion. This phenotype is reversed by full-length mCARMIL but not mCARMIL lacking the domain that binds CP. Thus, mCARMIL is a key regulator of CP and has profound effects on cell behavior.

Actin Cytoskeleton↗
PubMed2005

The pleckstrin homology domain-containing protein CKIP-1 is involved in regulation of cell morphology and the actin cytoskeleton and interaction with actin capping protein.

CKIP-1 is a pleckstrin homology domain-containing protein that interacts with protein kinase CK2. To elucidate the functions of CKIP-1, we generated human osteosarcoma cell lines with tetracycline-regulated expression of Flag-CKIP-1. Flag-CKIP-1 expression resulted in distinct changes in cellular morphology. Therefore, we examined the actin profile by immunofluorescence, quantitative measurement of phalloidin binding, and immunoblot analysis. These studies demonstrate that Flag-CKIP-1 expression resulted in increases in F-actin staining and protein levels of beta-actin. To elucidate the mechanisms behind the observed phenotype, we utilized tandem affinity purification to isolate CKIP-1 interacting proteins. Mass spectrometry analysis led to the identification of the actin capping protein subunits, CPalpha and CPbeta, as novel CKIP-1 interaction partners. Interactions were confirmed by coimmunoprecipitation and by colocalization. Furthermore, we demonstrate that Ser9 of CPalpha is phosphorylated by protein kinase CK2 in vitro, that CPalpha is phosphorylated in vivo, and that treatment with a CK2-specific inhibitor results in a decrease in CPalpha phosphorylation. Finally, we demonstrate that CKIP-1 and CK2 inhibit the activity of actin capping protein at the barbed ends of actin filaments. Overall, our results are consistent with CKIP-1 playing a role in the regulation of the actin cytoskeleton through its interactions with actin capping protein.

Actin Capping Proteins↗
PubMed2004

Yeast actin patches are networks of branched actin filaments.

Cortical actin patches are the most prominent actin structure in budding and fission yeast. Patches assemble, move, and disassemble rapidly. We investigated the mechanisms underlying patch actin assembly and motility by studying actin filament ultrastructure within a patch. Actin patches were partially purified from Saccharomyces cerevisiae and examined by negative-stain electron microscopy (EM). To identify patches in the EM, we correlated fluorescence and EM images of GFP-labeled patches. Patches contained a network of actin filaments with branches characteristic of Arp2/3 complex. An average patch contained 85 filaments. The average filament was only 50-nm (20 actin subunits) long, and the filament to branch ratio was 3:1. Patches lacking Sac6/fimbrin were unstable, and patches lacking capping protein were relatively normal. Our results are consistent with Arp2/3 complex-mediated actin polymerization driving yeast actin patch assembly and motility, as described by a variation of the dendritic nucleation model.

Actin Cytoskeleton↗
PubMed2004

Biological role and structural mechanism of twinfilin-capping protein interaction.

Twinfilin and capping protein (CP) are highly conserved actin-binding proteins that regulate cytoskeletal dynamics in organisms from yeast to mammals. Twinfilin binds actin monomer, while CP binds the barbed end of the actin filament. Remarkably, twinfilin and CP also bind directly to each other, but the mechanism and role of this interaction in actin dynamics are not defined. Here, we found that the binding of twinfilin to CP does not affect the binding of either protein to actin. Furthermore, site-directed mutagenesis studies revealed that the CP-binding site resides in the conserved C-terminal tail region of twinfilin. The solution structure of the twinfilin-CP complex supports these conclusions. In vivo, twinfilin's binding to both CP and actin monomer was found to be necessary for twinfilin's role in actin assembly dynamics, based on genetic studies with mutants that have defined biochemical functions. Our results support a novel model for how sequential interactions between actin monomers, twinfilin, CP, and actin filaments promote cytoskeletal dynamics.

Actin Depolymerizing Factors↗
PubMed2004

Effect of Fgd1 on cortactin in Arp2/3 complex-mediated actin assembly.

Mutations in faciogenital dysplasia protein (Fgd1) result in the human disease faciogenital dysplasia (FGDY). Fgd1 contains a RhoGEF domain specific for Cdc42. Fgd1 also contains a Src homology (SH3) binding domain (SH3-BD) that binds directly to the SH3 domain of cortactin, which promotes actin assembly by actin-related protein (Arp)2/3 complex. Here, we report the effect of ligation of cortactin's SH3 domain by the Fgd1 SH3-BD on actin polymerization in vitro. Glutathione S-transferase (GST)-fused Fgd1 SH3-BD enhanced the ability of cortactin to stimulate Arp2/3-mediated actin polymerization. However, a synthetic peptide containing only the SH3-BD sequence had no effect. The SH3-BD peptide bound to cortactin and inhibited the effect of GST-Fgd1 SH3-BD, suggesting that GST dimerization was responsible for the stimulating effect of GST-Fgd1 SH3-BD. When GST-Fgd1 SH3-BD was prepared as a heterodimer with a control GST fusion protein (GST-Pac1), no stimulatory effect on actin polymerization was observed. In addition, when cortactin was dimerized via its N-terminus, away from the C-terminal SH3 domain, actin polymerization with Arp2/3 complex increased markedly, compared to free cortactin. Thus, cortactin ligated by Fgd1 is fully active, indicating that the cell can use Fgd1 to target actin assembly. Moreover, if Fgd1 is multimerized, then cortactin's activity should be enhanced. Fgd1 and cortactin may participate as scaffolds and signal transducers in a positive feedback cycle to promote actin assembly at the cell cortex.

Actin-Related Protein 2↗
PubMed2004

Capping protein binding to actin in yeast: biochemical mechanism and physiological relevance.

The mechanism by which capping protein (CP) binds barbed ends of actin filaments is not understood, and the physiological significance of CP binding to actin is not defined. The CP crystal structure suggests that the COOH-terminal regions of the CP alpha and beta subunits bind to the barbed end. Using purified recombinant mutant yeast CP, we tested this model. CP lacking both COOH-terminal regions did not bind actin. The alpha COOH-terminal region was more important than that of beta. The significance of CP's actin-binding activity in vivo was tested by determining how well CP actin-binding mutants rescued null mutant phenotypes. Rescue correlated well with capping activity, as did localization of CP to actin patches, indicating that capping is a physiological function for CP. Actin filaments of patches appear to be nucleated first, then capped with CP. The binding constants of yeast CP for actin suggest that actin capping in yeast is more dynamic than in vertebrates.

Actin Capping Proteins↗