Assistant Professor Daniel Schmidt

CBS Genetics, Cell Bio, Dev
College of Biological Sciences
Twin Cities
Project Title: 
Molecular Neurotechnologies

This group invents and applies protein engineering technologies to study fundamental functional principles of natural and artificial living systems at a cellular level. They are seeking mechanistic explanations for how cells sense, integrate and exchange information, how pathologic changes in these processes relate to health and disease, and provide insights into new therapies. They answer these questions by inventing methods to observe, delineate, and precisely control cellular physiology. Their approach employs techniques from multiple disciplines including optogenetics, electrophysiology, rational protein design, and, most recently, molecular dynamics. 

This group collaborates extensively to apply our technologies to diverse problems in human health. For example, they work to recapitulate misregulation of specific ion channels and receptors in models of cardiovascular disorders, to reveal how specific cell types contribute to the different neural circuits that underlie cognition and behavior, and to establish clear correlations between specific changes in regulated cell signaling networks and molecular signatures of tumors enabling tumor proliferation and migration.

The group is currently using MSI for a project that studies metazoan proteins, more that 80% of which are multidomain proteins. They are composed of quasi-independent structural domains, which are associated with a specific function and genetically mobile. It is these three properties exploited in protein engineering when domains are combined into synthetic proteins to study biological mechanisms (e.g., biosensors) or for biomedical applications (e.g., chimeric antigen receptors). Over much longer time scales, the same three properties have enabled functional diversification of natural proteins during evolution. Domain recombination is therefore also a window into the emergence of protein function, with inter-domain allosteric regulation being an essential feature of multi-domain proteins. However, due to technology constraints, domain recombination in the context of emerge of allostery and the ability to engineer multi-domain proteins has not been looked at in a systematic way.

These researchers recently described Differential Domain Insertion Permissibility through Sequencing (dDIPSEQ) as a scalable method that enables a systematic study of relationships between domain recombination and allosteric capacity. Their central hypothesis is that dDIPSEQ probes regional protein energetics, which is the mechanistic basis for how this method measures this allosteric potential that can be engineered for biomedical applications. Using human Kir3.2 as a representative member of the Inward Rectifier K+ channel family, the group will test this hypothesis by using molecular dynamics simulations. From this MD simulation they will extract metrics of protein dynamics (root mean square fluctuations, relative conformational entropy, compactness). They will use supervised machine learning to determine the explanatory power of MD-derived protein dynamics for experimentally measured differential permissibility of Kir3.2. They expect that dDIPSEQ and MD-derived protein dynamics will be in good agreement. Thus, completion of this preliminary study will establish the mechanistic basis of domain recombination (as implemented in dDIPSEQ) as a window into protein allostery and evolution. It will also pave the way for applying domain insertion in a broader sense; how to make proteins "druggable" and how to rationally engineer and endow them with new functions. 

 

Project Investigators

Vincenzo Carnevale
Willow Coyote-Maestas
David Nedrud
Assistant Professor Daniel Schmidt
Alina Zdechlik
 
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