Research Areas
1. Understanding Lipid Signaling by Protein Kinases C.
We are interested in integrating genetic, in vivo imaging, and a battery of biophysical, structural and computational approaches to a variety of questions that focus on cellular signaling. One major area of investigation is on how Protein Kinases C (PKC), essential enzymes in cellular signaling, is activated through interactions with lipids and other small molecules. Focusing on both mammalian and yeast PKCs, we use a combination of structural biology, biophysical assays, and cell biology-based studies to investigate how these interactions contribute to enzyme regulation and how these differ across isoforms and across species. Of particular interest are the mechanisms that underly lipid recognition by the C1B domain of protein kinases C (PKC) using X-ray crystallography, fluorescence-based binding measurements and all-atom unbiased molecular dynamics simulations. This domain binds diacylglycerol and related lipid second messengers to mediate signal-dependent membrane recruitment and activation. The study of the noncanonical role of the peptidyl prolyl isomerase Pin1, a cancer-associated regulator of protein kinases C and other enzymes, is included in these efforts.
2. Regulation of Phosphoinositide Signaling by Phosphatidylinositol Transfer Proteins.
A second major area of investigation focuses on the highly conserved phosphatidylinositol transfer proteins (PITPs) that are biologically critical potentiators of phosphoinositide signaling and whose activity is critical from single cell all eukaryotes to humans. These proteins couple biochemically fascinating lipid-binding/exchange activities to their various biological functions, and we seek to describe the protein and lipid conformational dynamics of fungal and mammalian PITPs associated with these activities at an atomistic level. A significant aspect of our interrogation of PITP function applies unbiased and GROMACS-based atomistic molecular dynamics (MD) simulations in membrane systems to this problem. These studies cover a wide menu of approaches that range from cell biological and physiological studies to protein biophysics and crystallography, and a wide variety of models that range from yeast to mammalian cells and from dense granule biogenesis in the obligate intracellular parasite Toxoplasma to engineered mouse models.
We are also pursuing a structural understanding of how protein–lipid interactions coordinate membrane trafficking and signal transduction with particular emphasis on structural studies using cryo-electron microscopy (Cryo-EM) to examine the phosphatidylinositol 4-OH kinase Pik1 and its calcium-sensing regulator Frq1 in yeast. These proteins are essential for Golgi function and membrane dynamics, and their activities are responsive to the actions of additional factors, including PITPs.
3. Mammalian PITPs, Neurodegeneration and Cancer Biology.
The peripheral membrane proteins of interest to our lab all have strong links to mammalian diseases such as neurodegeneration, diabetes, and cancer. We have produced genetically modified mice we are using to study the roles of mammalian PITPs in neurodegenerative diseases, Type II diabetes and cancer with a focus on melanoma. These studies are highly multidisciplinary that employ approaches ranging from animal models to cell models, tumor biology, biochemistry and structural biology, biophysics, with a strong emphasis on imaging, mitochondrial performance, and lipidomics.
We are also interested in elucidating the mechanisms by which lipid metabolism and signaling regulate mammalian brain development. This research direction currently focuses on two projects. The first project investigates how phosphatidylinositol transfer protein (PITP)-dependent lipid signaling regulates neural stem cell homeostasis, cell shape, cell proliferation, and cell migration in the embryonic mouse brain. The second project studies the roles of carnitine and fatty acid beta-oxidation and their involvement in the self-renewal and differentiation of neural stem cells during embryonic development, and in developmental brain disorders such as intellectual disabilities and autism.
4. Chemical Biology and Development of Next-Generation Anti-Fungal Compounds.
We are interested in applying chemical biology approaches to modulate signaling by peripheral membrane proteins. These studies fall into two general areas. The first involves the application of chemical biology to understand how PKC C1-domains are recruited to membranes to launch downstream signaling responses. In this project, we study how chemically diverse DAG-lactones (synthetic analogs of DAG) engage the PKC C1B domains by combining X-ray crystallography, binding/biophysical measurements, and in vivo imaging in yeast and mammalian systems. The goal is to connect molecular binding modes with membrane recruitment in cells. Together, these insights define structure–activity relationships and guide the rational design of next-generation, isoform-selective C1-domain probes for characterizing DAG-dependent signaling.
The second area of interest focuses on the development of lead compounds for next-generation anti-fungal drugs. Antimycotic-resistant fungi present a rising public health crisis due to the high mortality of invasive mycoses, a systemic consequence of inadequately treated infections. Thus, the identification and validation of novel antimycotic targets and their inhibitors is urgently needed. We have several projects that center around the structural and chemical biology of Sec14-like PITPs of virulent fungal pathogens. To this end, we deploy a combination of structural, biochemical, microbiological, genetic, and computational approaches to investigate how small-molecule inhibitors disrupt the function of these highly conserved PITPs. The latter includes fragment-based, structure-based drug design methods with pharmacophore screening and molecular docking coupled to deep learning models (e.g. graph neural networks; GNNs) and large language models (LLMs) for generating small molecule inhibitors de novo. We complement those studies with a combination of structural and biophysical approaches to investigate mechanisms for how small-molecule inhibitors displace the natural lipid ligands from Sec14 orthologs in pathogenic fungi.
5. Biology and Biophysics of Antagonists of Phosphoinositide Signaling.
Oxysterol-binding protein (OSBP) and its related proteins (ORPs) are a conserved family of functionally enigmatic lipid exchange proteins that regulate signal transduction processes and are garnering rapidly increasing interest in the cell biology/physiology arenas. A significant effort of the lab focuses on one member (Kes1/Osh4) of the seven-member yeast ORP family. This ORP is unique in its activity as an antagonist of Sec14-dependent phosphoinositide signaling. Our interest is to determine how Kes1/Osh4 utilizes its intrinsic lipid-binding properties to execute its in vivo function in regulating lipid signaling, membrane trafficking and cell cycle control. To that end, we couple in vitro biophysical approaches that include Förster resonance energy transfer (FRET)-based lipid binding and transfer assays with in vivo genetic and cell biological studies.
We are interested in integrating genetic, in vivo imaging, and a battery of biophysical, structural and computational approaches to a variety of questions that focus on cellular signaling. One major area of investigation is on how Protein Kinases C (PKC), essential enzymes in cellular signaling, is activated through interactions with lipids and other small molecules. Focusing on both mammalian and yeast PKCs, we use a combination of structural biology, biophysical assays, and cell biology-based studies to investigate how these interactions contribute to enzyme regulation and how these differ across isoforms and across species. Of particular interest are the mechanisms that underly lipid recognition by the C1B domain of protein kinases C (PKC) using X-ray crystallography, fluorescence-based binding measurements and all-atom unbiased molecular dynamics simulations. This domain binds diacylglycerol and related lipid second messengers to mediate signal-dependent membrane recruitment and activation. The study of the noncanonical role of the peptidyl prolyl isomerase Pin1, a cancer-associated regulator of protein kinases C and other enzymes, is included in these efforts.
2. Regulation of Phosphoinositide Signaling by Phosphatidylinositol Transfer Proteins.
A second major area of investigation focuses on the highly conserved phosphatidylinositol transfer proteins (PITPs) that are biologically critical potentiators of phosphoinositide signaling and whose activity is critical from single cell all eukaryotes to humans. These proteins couple biochemically fascinating lipid-binding/exchange activities to their various biological functions, and we seek to describe the protein and lipid conformational dynamics of fungal and mammalian PITPs associated with these activities at an atomistic level. A significant aspect of our interrogation of PITP function applies unbiased and GROMACS-based atomistic molecular dynamics (MD) simulations in membrane systems to this problem. These studies cover a wide menu of approaches that range from cell biological and physiological studies to protein biophysics and crystallography, and a wide variety of models that range from yeast to mammalian cells and from dense granule biogenesis in the obligate intracellular parasite Toxoplasma to engineered mouse models.
We are also pursuing a structural understanding of how protein–lipid interactions coordinate membrane trafficking and signal transduction with particular emphasis on structural studies using cryo-electron microscopy (Cryo-EM) to examine the phosphatidylinositol 4-OH kinase Pik1 and its calcium-sensing regulator Frq1 in yeast. These proteins are essential for Golgi function and membrane dynamics, and their activities are responsive to the actions of additional factors, including PITPs.
3. Mammalian PITPs, Neurodegeneration and Cancer Biology.
The peripheral membrane proteins of interest to our lab all have strong links to mammalian diseases such as neurodegeneration, diabetes, and cancer. We have produced genetically modified mice we are using to study the roles of mammalian PITPs in neurodegenerative diseases, Type II diabetes and cancer with a focus on melanoma. These studies are highly multidisciplinary that employ approaches ranging from animal models to cell models, tumor biology, biochemistry and structural biology, biophysics, with a strong emphasis on imaging, mitochondrial performance, and lipidomics.
We are also interested in elucidating the mechanisms by which lipid metabolism and signaling regulate mammalian brain development. This research direction currently focuses on two projects. The first project investigates how phosphatidylinositol transfer protein (PITP)-dependent lipid signaling regulates neural stem cell homeostasis, cell shape, cell proliferation, and cell migration in the embryonic mouse brain. The second project studies the roles of carnitine and fatty acid beta-oxidation and their involvement in the self-renewal and differentiation of neural stem cells during embryonic development, and in developmental brain disorders such as intellectual disabilities and autism.
4. Chemical Biology and Development of Next-Generation Anti-Fungal Compounds.
We are interested in applying chemical biology approaches to modulate signaling by peripheral membrane proteins. These studies fall into two general areas. The first involves the application of chemical biology to understand how PKC C1-domains are recruited to membranes to launch downstream signaling responses. In this project, we study how chemically diverse DAG-lactones (synthetic analogs of DAG) engage the PKC C1B domains by combining X-ray crystallography, binding/biophysical measurements, and in vivo imaging in yeast and mammalian systems. The goal is to connect molecular binding modes with membrane recruitment in cells. Together, these insights define structure–activity relationships and guide the rational design of next-generation, isoform-selective C1-domain probes for characterizing DAG-dependent signaling.
The second area of interest focuses on the development of lead compounds for next-generation anti-fungal drugs. Antimycotic-resistant fungi present a rising public health crisis due to the high mortality of invasive mycoses, a systemic consequence of inadequately treated infections. Thus, the identification and validation of novel antimycotic targets and their inhibitors is urgently needed. We have several projects that center around the structural and chemical biology of Sec14-like PITPs of virulent fungal pathogens. To this end, we deploy a combination of structural, biochemical, microbiological, genetic, and computational approaches to investigate how small-molecule inhibitors disrupt the function of these highly conserved PITPs. The latter includes fragment-based, structure-based drug design methods with pharmacophore screening and molecular docking coupled to deep learning models (e.g. graph neural networks; GNNs) and large language models (LLMs) for generating small molecule inhibitors de novo. We complement those studies with a combination of structural and biophysical approaches to investigate mechanisms for how small-molecule inhibitors displace the natural lipid ligands from Sec14 orthologs in pathogenic fungi.
5. Biology and Biophysics of Antagonists of Phosphoinositide Signaling.
Oxysterol-binding protein (OSBP) and its related proteins (ORPs) are a conserved family of functionally enigmatic lipid exchange proteins that regulate signal transduction processes and are garnering rapidly increasing interest in the cell biology/physiology arenas. A significant effort of the lab focuses on one member (Kes1/Osh4) of the seven-member yeast ORP family. This ORP is unique in its activity as an antagonist of Sec14-dependent phosphoinositide signaling. Our interest is to determine how Kes1/Osh4 utilizes its intrinsic lipid-binding properties to execute its in vivo function in regulating lipid signaling, membrane trafficking and cell cycle control. To that end, we couple in vitro biophysical approaches that include Förster resonance energy transfer (FRET)-based lipid binding and transfer assays with in vivo genetic and cell biological studies.