Jacobson
David received his Ph.D. in physics from the University of California, Santa Barbara, where he studied the electrostatics of single-stranded nucleic acids.
Thomas Perkins
Uyetake
Lyle earned his Bachelors in Chemistry and Biochemistry/Biophysics at Oregon State University. His early research was in organic synthesis and protein purification. Most of his research experience since then has been in the fields of Parasitology and Cancer Biology. His main focus here is using molecular biology techniques to design unique DNA constructs to be used in AFM and optical trapping.
Membrane proteins
We are studying the energetics that stabilize membrane proteins by folding and unfolding individual molecules using AFM. By using cantilevers optimized for 1-µs resolution, we can measure the unfolding of individual molecules of the model membrane protein bacteriorhodopsin (bR) at 100-fold higher time resolution and 10-fold higher force precision than prior studies. This improvement in instrumental performance has allowed us to identify the energy barriers between states and to distinguish among obligatory, non-obligatory, and off-pathway intermediates.
Protein folding and mechanobiology
Over the last 50 years, the search to understand the protein-folding process has blossomed into a large, interdisciplinary field. More recently, mechanobiology—the study of the mechanical forces exerted on molecules and cells—has also become an important and rapidly growing field. In both fields, the energy landscape provides the framework to describe the process of protein folding and how proteins respond to force. Local and global minima on this landscape represent intermediate and final states, respectively.
Advancing single-molecule assays
Single-molecule studies are a powerful means to study the dynamics and energetics of biological molecules and biomolecular complexes. These studies are limited by instrumentation resolution and assay efficiency. Historically, AFM was considered to have force resolution of ~5–20 pN and to suffer from significant instrumental drift. Over the last 15 years, we have substantially improved the precision, stability, and temporal resolution of bioAFM, culminating in studying membrane-protein unfolding with a 100-fold improvement in time resolution and a 10-fold improvement in force precision.
Nucleic-acid and protein-nucleic-acid interactions
We apply optical traps and AFM to yield mechanistic insight into how enzymes move along and bind to DNA as well as DNA’s fundamental mechanical properties. We developed an actively stabilized, optical-trapping microscope and applied it to study RecBCD, a helicase, at 1-bp resolution. More recently, we developed new techniques for AFM imaging of DNA in liquid and applied them to visualize the Polycomb repressive complex 2 (PRC2) bound to DNA.
The Physics Frontiers Centers (PFC) program supports university-based centers and institutes where the collective efforts of a larger group of individuals can enable transformational advances in the most promising research areas. The program is designed to foster major breakthroughs at the intellectual frontiers of physics by providing needed resources such as combinations of talents, skills, disciplines, and/or specialized infrastructure, not usually available to individual investigators or small groups, in an environment in which the collective efforts of the larger group can be shown to be seminal to promoting significant progress in the science and the education of students. PFCs also include creative, substantive activities aimed at enhancing education, broadening participation of traditionally underrepresented groups, and outreach to the scientific community and general public.