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Physics of Biological Catalysis
Physics of Biological Catalysis
Understanding the remarkable efficiency of biological catalysis stands among the most long-standing challenges in science. Underlying the vast diversity of catalytic functions carried out by proteins and nucleic acids are a handful of fundamental principles, including conformational flexibility, preorganization, allosteric coupling, and rare fluctuations. Resolving these fundamental principles and connecting them with the broader action of catalysis requires novel experimental techniques coupled closely with computation and simulation. My lab leverages our expertise in spectroscopy and microscopy, soft matter physics, and biological macromolecule dynamics, coupled with collaborations in simulation, to generate explore the field of biological catalysis.
Excited State Catalysis
Excited State Catalysis
Biological macromolecules are known to adopt exotic, non-native conformations when forming the activated complex prior to catalysis. We are interested in identifying rare thermally excited conformations of proteins and nucleic acids and resolving their catalytic role. Using single-molecule 2D spectroscopy, we can observe exchange between the ground (duplexed) and excited (base flipped) conformations of DNA, and resolve what conformation is bound by enzymes.
coupling of fluctuation and reaction coordinates facilitates formation of activated complex
coupling of fluctuation and reaction coordinates facilitates formation of activated complex
single-molecule spectra resolving populations and exchange between multiple species
single-molecule spectra resolving populations and exchange between multiple species
combining non-canonical nucleotides for site-specific labelling of DNA with single-molecule spectroscopy, we are able to resolve rare dynamics involved in the formation of the activated complex.
we are able to resolve excited states traditionally hidden in ensemble measurements, and show they are biologically active.
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Nonequilibrium Thermodynamics of Proteins
Nonequilibrium Thermodynamics of Proteins
Many proteins, including motors, rotors, and pumps, operate under nonequilibrium conditions. Bacteriorhodopsin, found in Archaea, harnesses energy from sunlight to transport of ions across a membrane. The relaxation of this ion gradient drives the synthesis of ATP. In contrast to macroscopic motors, which operate orders of magnitude above the thermal energy floor, motor proteins must overcome randomizing thermal fluctuations to achieve directional action. Our group utilizes single-molecule spectroscopy to quantify the nonequilibrium thermodynamics associated with the reaction cycle of bacteriorhodopsin, with the goal of providing a general molecular framework from which we can understand the function of proteins operating under nonequilibrium conditions.
nanoscopic motors have to battle against thermal noise, yet are remarkably efficient
nanoscopic motors have to battle against thermal noise, yet are remarkably efficient
motors become less efficient at high temperatures as entropy production is lost
motors become less efficient at high temperatures as entropy production is lost
using single-molecule spectroscopy, we can identify reversible and irreversible steps in the catalytic cycle.
we can quantify key nonequilibrium thermodynamic parameters for each transition, including entropy production rate, heat dissipation, and step affinity, and see how these parameters respond to environmental conditions, or protein mutation.
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Technique Development
Technique Development
My lab is interested in developing the next wave of spectroscopy/microscopy tools. We have worked on technical aspects of both super-resolution microscopy and single-molecule spectroscopy in the past.
super-resolution microscopy to: resolve slip layer dynamics in flowing complex fluids
sm spectroscopy to: resolve equilibrium reaction kinetics on microsecond timescale
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