¶¶Òõapp University Protein Institute
¶¶Òõapp the Institute
The ¶¶Òõapp University Protein Institute (YUPI) is a multidisciplinary research center committed to advancing the understanding of protein structure, function, and dynamics. By studying structural biology, biochemistry, proteomics, biology of diseases and computational modeling, YUPI utilizes cutting-edge research into the molecular mechanisms that affect health, disease and biotechnological innovation. The Institute serves as a collaborative hub, providing access to advanced instrumentation and training for students and researchers.
YUPI plays a pivotal role in identifying therapeutic targets, engineering novel proteins, and driving innovation in biotechnology and medicine. By cultivating academic and industry partnerships, the Institute supports translational science with meaningful societal impact.
Institute Members
Spermatogenesis is regulated by various protein posttranslational modifications. Sumoylation, a covalent addition of small ubiquitin-like modifiers (SUMO) to target proteins, is essential for developmental processes such as reproduction. SUMO proteins are highly expressed in all testicular cells, where they bind many proteins necessary for spermatogenesis; however, the cell-specific function of sumoylation during spermatogenesis has not been characterized. We use cell lines, primary cells freshly purified from mouse testes, and mouse models to address the role of sumoylation in testicular cells and male fertility. We have shown that inhibition of sumoylation ex vivo arrested the completion of meiosis in purified mouse spermatocytes, and the activity of several kinases regulating meiosis has been downregulated. Inhibition of sumoylation also affected the secretion of the primary mouse Sertoli cells and activated their apoptotic response. To address the role of sumoylation in vivo we are generating transgenic LoxP-Cre mouse models to inactivate sumoylation in specific testicular cell types. Various proliferation, differentiation, apoptotic markers, proteomic, phosphoproteomic, and transcriptomic analyses are being employed to better characterize the molecular pathways regulated by sumoylation during spermatogenesis.
The temporally and spatially regulated association between messenger RNAs (mRNA) and proteins to form messenger ribonucleic protein complexes (mRNP) is essential for proper gene expression. In multicellular model systems like the fruit fly egg chamber, the composition of mRNPs is continuously edited during long-range transport. Our goal is to understand how protein-RNA interactions influence the dynamic processes of RNA transport and localization. We aim to develop tools for efficient, inexpensive detection and visualization of RNA and proteins in mRNPs under physiological conditions, without limitations from common constraints such as target inaccessibility or toxic reagents.
Cells are bounded by a plasma membrane, which is composed of bilayer forming phospholipids. Although phospholipids are integral structural components of cells, they are not inert or static. Membrane phospholipids are dynamically reorganized and biochemically remodeled in response to signaling pathways and changing cellular behaviors. Recently, technological advances in mass spectrometry have shed new light on the detailed molecular composition of membrane phospholipids, revealing hundreds of different phospholipid species per cell, which differ in their headgroups, length of their fatty acid chains, and degree of unsaturation. It is not clear why cells require so many different phospholipid species. Perhaps different species play subtly different physiological roles in the lives of cells. Phospholipids also can be cleaved to release potent lipid signaling molecules (mediators), which can initiate signal transduction cascades. Perhaps the variety of phospholipid species is due to the variety of stored mediator precursors. There is still much to be discovered about phospholipid metabolism and remodeling in vivo. My research focuses on the Lands Cycle, a phospholipid metabolism pathway important both for lipid signal release and for phospholipid molecular remodeling, in the fruit fly Drosophila melanogaster.
Ice has an enormous effect on our life and the life of smaller organisms around us. We are interested in studying how ice grows in the presence of different additives, aiming to develop new ways to inhibit and to control ice growth. Specifically, we study the interaction between ice crystals and natural/synthetic molecules that inhibit ice growth. Natural molecules such as ice-binding proteins (IBPs), or antifreeze proteins (AFPs), are able to inhibit ice growth and to protect organisms such as fish, insects, plants and fungi from freezing injury. We apply this knowledge on efforts to improving the quality of frozen foods using thermal imaging.
The Oliveira Lab investigates how bioluminescent organisms produce light and explores direct applications of the chemicals and enzymes involved to create brighter, more stable reporters for bioimaging, diagnostics, and environmental sensing.
Current research areas are image reconstruction with scanning probe microscopes, atomistic modeling of materials, quantum optics, and mathematical optimization.
Quantum Transport - Theoretical studies of electronic transport through quantum structures.
Friction - Experimental studies of stick-slip and its relationship to Self Organized Criticality.
Defects in Solids - Generalizing Equivalent Crystal Theory to evaluate defect formation energies.
Colloids - Theoretical studies to obtain interactions between particles and surfaces in aqueous solutions.
Viscosity - Reconstruction algorithms to extract oil viscosity from Atomic Force spectroscopy.
Identifying protein interfaces in general, and antigen epitopes, in particular, is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes.
Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable. We have reported an improved interface prediction method for proteins (ISPIP) and have applied this to predict multiple epitopes in antigens (ISPIPab). We are currently working to extend this methodology to identify small molecular glues (MG) that can function as novel drug molecules by aiding in the degradation of non-druggable proteins, protein of interest (POI), by facilitating their binding to the effector protein (EP). We will use the methodology previously developed to identify interfacial regions in POI and EF and use target docking to these regions to predict the effectiveness of MG to enhance the binding between POI and EF.
Prof. Viswanathan's lab website
Spermatogenesis is regulated by various protein posttranslational modifications. Sumoylation, a covalent addition of small ubiquitin-like modifiers (SUMO) to target proteins, is essential for developmental processes such as reproduction. SUMO proteins are highly expressed in all testicular cells, where they bind many proteins necessary for spermatogenesis; however, the cell-specific function of sumoylation during spermatogenesis has not been characterized. We use cell lines, primary cells freshly purified from mouse testes, and mouse models to address the role of sumoylation in testicular cells and male fertility. We have shown that inhibition of sumoylation ex vivo arrested the completion of meiosis in purified mouse spermatocytes, and the activity of several kinases regulating meiosis has been downregulated. Inhibition of sumoylation also affected the secretion of the primary mouse Sertoli cells and activated their apoptotic response. To address the role of sumoylation in vivo we are generating transgenic LoxP-Cre mouse models to inactivate sumoylation in specific testicular cell types. Various proliferation, differentiation, apoptotic markers, proteomic, phosphoproteomic, and transcriptomic analyses are being employed to better characterize the molecular pathways regulated by sumoylation during spermatogenesis.
The temporally and spatially regulated association between messenger RNAs (mRNA) and proteins to form messenger ribonucleic protein complexes (mRNP) is essential for proper gene expression. In multicellular model systems like the fruit fly egg chamber, the composition of mRNPs is continuously edited during long-range transport. Our goal is to understand how protein-RNA interactions influence the dynamic processes of RNA transport and localization. We aim to develop tools for efficient, inexpensive detection and visualization of RNA and proteins in mRNPs under physiological conditions, without limitations from common constraints such as target inaccessibility or toxic reagents.
Cells are bounded by a plasma membrane, which is composed of bilayer forming phospholipids. Although phospholipids are integral structural components of cells, they are not inert or static. Membrane phospholipids are dynamically reorganized and biochemically remodeled in response to signaling pathways and changing cellular behaviors. Recently, technological advances in mass spectrometry have shed new light on the detailed molecular composition of membrane phospholipids, revealing hundreds of different phospholipid species per cell, which differ in their headgroups, length of their fatty acid chains, and degree of unsaturation. It is not clear why cells require so many different phospholipid species. Perhaps different species play subtly different physiological roles in the lives of cells. Phospholipids also can be cleaved to release potent lipid signaling molecules (mediators), which can initiate signal transduction cascades. Perhaps the variety of phospholipid species is due to the variety of stored mediator precursors. There is still much to be discovered about phospholipid metabolism and remodeling in vivo. My research focuses on the Lands Cycle, a phospholipid metabolism pathway important both for lipid signal release and for phospholipid molecular remodeling, in the fruit fly Drosophila melanogaster.
Ice has an enormous effect on our life and the life of smaller organisms around us. We are interested in studying how ice grows in the presence of different additives, aiming to develop new ways to inhibit and to control ice growth. Specifically, we study the interaction between ice crystals and natural/synthetic molecules that inhibit ice growth. Natural molecules such as ice-binding proteins (IBPs), or antifreeze proteins (AFPs), are able to inhibit ice growth and to protect organisms such as fish, insects, plants and fungi from freezing injury. We apply this knowledge on efforts to improving the quality of frozen foods using thermal imaging.
The Oliveira Lab investigates how bioluminescent organisms produce light and explores direct applications of the chemicals and enzymes involved to create brighter, more stable reporters for bioimaging, diagnostics, and environmental sensing.
Current research areas are image reconstruction with scanning probe microscopes, atomistic modeling of materials, quantum optics, and mathematical optimization.
Quantum Transport - Theoretical studies of electronic transport through quantum structures.
Friction - Experimental studies of stick-slip and its relationship to Self Organized Criticality.
Defects in Solids - Generalizing Equivalent Crystal Theory to evaluate defect formation energies.
Colloids - Theoretical studies to obtain interactions between particles and surfaces in aqueous solutions.
Viscosity - Reconstruction algorithms to extract oil viscosity from Atomic Force spectroscopy.
Identifying protein interfaces in general, and antigen epitopes, in particular, is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes.
Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable. We have reported an improved interface prediction method for proteins (ISPIP) and have applied this to predict multiple epitopes in antigens (ISPIPab). We are currently working to extend this methodology to identify small molecular glues (MG) that can function as novel drug molecules by aiding in the degradation of non-druggable proteins, protein of interest (POI), by facilitating their binding to the effector protein (EP). We will use the methodology previously developed to identify interfacial regions in POI and EF and use target docking to these regions to predict the effectiveness of MG to enhance the binding between POI and EF.
Prof. Viswanathan's lab website
Spermatogenesis is regulated by various protein posttranslational modifications. Sumoylation, a covalent addition of small ubiquitin-like modifiers (SUMO) to target proteins, is essential for developmental processes such as reproduction. SUMO proteins are highly expressed in all testicular cells, where they bind many proteins necessary for spermatogenesis; however, the cell-specific function of sumoylation during spermatogenesis has not been characterized. We use cell lines, primary cells freshly purified from mouse testes, and mouse models to address the role of sumoylation in testicular cells and male fertility. We have shown that inhibition of sumoylation ex vivo arrested the completion of meiosis in purified mouse spermatocytes, and the activity of several kinases regulating meiosis has been downregulated. Inhibition of sumoylation also affected the secretion of the primary mouse Sertoli cells and activated their apoptotic response. To address the role of sumoylation in vivo we are generating transgenic LoxP-Cre mouse models to inactivate sumoylation in specific testicular cell types. Various proliferation, differentiation, apoptotic markers, proteomic, phosphoproteomic, and transcriptomic analyses are being employed to better characterize the molecular pathways regulated by sumoylation during spermatogenesis.
The temporally and spatially regulated association between messenger RNAs (mRNA) and proteins to form messenger ribonucleic protein complexes (mRNP) is essential for proper gene expression. In multicellular model systems like the fruit fly egg chamber, the composition of mRNPs is continuously edited during long-range transport. Our goal is to understand how protein-RNA interactions influence the dynamic processes of RNA transport and localization. We aim to develop tools for efficient, inexpensive detection and visualization of RNA and proteins in mRNPs under physiological conditions, without limitations from common constraints such as target inaccessibility or toxic reagents.
Cells are bounded by a plasma membrane, which is composed of bilayer forming phospholipids. Although phospholipids are integral structural components of cells, they are not inert or static. Membrane phospholipids are dynamically reorganized and biochemically remodeled in response to signaling pathways and changing cellular behaviors. Recently, technological advances in mass spectrometry have shed new light on the detailed molecular composition of membrane phospholipids, revealing hundreds of different phospholipid species per cell, which differ in their headgroups, length of their fatty acid chains, and degree of unsaturation. It is not clear why cells require so many different phospholipid species. Perhaps different species play subtly different physiological roles in the lives of cells. Phospholipids also can be cleaved to release potent lipid signaling molecules (mediators), which can initiate signal transduction cascades. Perhaps the variety of phospholipid species is due to the variety of stored mediator precursors. There is still much to be discovered about phospholipid metabolism and remodeling in vivo. My research focuses on the Lands Cycle, a phospholipid metabolism pathway important both for lipid signal release and for phospholipid molecular remodeling, in the fruit fly Drosophila melanogaster.
Ice has an enormous effect on our life and the life of smaller organisms around us. We are interested in studying how ice grows in the presence of different additives, aiming to develop new ways to inhibit and to control ice growth. Specifically, we study the interaction between ice crystals and natural/synthetic molecules that inhibit ice growth. Natural molecules such as ice-binding proteins (IBPs), or antifreeze proteins (AFPs), are able to inhibit ice growth and to protect organisms such as fish, insects, plants and fungi from freezing injury. We apply this knowledge on efforts to improving the quality of frozen foods using thermal imaging.
The Oliveira Lab investigates how bioluminescent organisms produce light and explores direct applications of the chemicals and enzymes involved to create brighter, more stable reporters for bioimaging, diagnostics, and environmental sensing.
Current research areas are image reconstruction with scanning probe microscopes, atomistic modeling of materials, quantum optics, and mathematical optimization.
Quantum Transport - Theoretical studies of electronic transport through quantum structures.
Friction - Experimental studies of stick-slip and its relationship to Self Organized Criticality.
Defects in Solids - Generalizing Equivalent Crystal Theory to evaluate defect formation energies.
Colloids - Theoretical studies to obtain interactions between particles and surfaces in aqueous solutions.
Viscosity - Reconstruction algorithms to extract oil viscosity from Atomic Force spectroscopy.
Identifying protein interfaces in general, and antigen epitopes, in particular, is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes.
Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable. We have reported an improved interface prediction method for proteins (ISPIP) and have applied this to predict multiple epitopes in antigens (ISPIPab). We are currently working to extend this methodology to identify small molecular glues (MG) that can function as novel drug molecules by aiding in the degradation of non-druggable proteins, protein of interest (POI), by facilitating their binding to the effector protein (EP). We will use the methodology previously developed to identify interfacial regions in POI and EF and use target docking to these regions to predict the effectiveness of MG to enhance the binding between POI and EF.
Prof. Viswanathan's lab website