Biophysical Chemistry Section
The Biophysical Chemistry Section focuses on fundamental aspects of the mechanism of protein folding. Researchers have developed a series of novel techniques to study the dynamics of fast processes in protein folding. These include the use of nanosecond pulsed lasers to trigger and monitor the folding reaction, as well as single molecule fluorescence measurements. Scientists use simple models to interpret the experimental results and expose the basic underlying physics of these processes. The experimental results and theoretical modeling are providing critical benchmarks for the construction of a detailed picture of the sequence of events as a protein forms its native conformation from the random structures of the unfolded polypeptide chain.
Research in this section for many years was concerned with the thermodynamics, kinetics, and mechanism of fiber formation of hemoglobin S, and its relation to the pathophysiology and therapy of sickle cell disease. The expertise developed in this research is now being used in a sensitive kinetic assay on sickle red cells to screen for compounds that could be used as a specific drug for sickle cell disease. The initial screen is being carried out on drugs already approved by the FDA for another disease, and, in collaboration with pharmaceutical companies, drugs that passed phase I clinical trials but were not sufficiently therapeutic to be marketed.
The Biophysical Nuclear Magnetic Resonance Spectroscopy Section develops new techniques and approaches for determining the structure and dynamics of bioactive molecules. Specific projects focus on developing methods for improving the accuracy of biomolecular structures determined by NMR data. Work in this area emphasizes the development of better measurement techniques for interproton distances and dihedral angles from NOEs and J couplings. We are also developing a quantitative relation between molecular structure and chemical shifts/chemical shift anisotropy.
The Protein Nuclear Magnetic Resonance Section studies the structure and dynamics of proteins, protein-protein complexes, and protein-nucleic acid complexes using multidimensional nuclear magnetic resonance (NMR) spectroscopy, and we develop and apply novel NMR and computational methods to aid in these studies. Special emphasis is placed on complexes involved in signal transduction and transcriptional regulation, and on AIDS and AIDS-related proteins. Recent focus has been on the development of novel NMR methods to detect, visualize, and characterize transient, sparsely populated states of macromolecules. Such states, which are invisible to conventional biophysical techniques, including crystallography, electron microscopy and single molecule spectroscopies, play a critical role in macromolecular recognition, allostery induced fit, conformational selection, and molecular assembly.
The Solid State Nuclear Magnetic Resonance & Biomolecular Physics Section, directed by Robert Tycko, develops solid-state NMR methods for structural studies of biopolymers and applies these methods to problems in biophysical chemistry and structural biology. Solid-state NMR methods provide structural information at atomic-level detail in systems that cannot be characterized by other structural methods, including x-ray diffraction and liquid state NMR.
Theoretical Biophysical Chemistry Section
Research in the Theoretical Biophysical Chemistry Section aims to bridge the gap between theory and experiment. We are developing the theories required to analyze and interpret both single-molecule optical (where the output is a sequence of photons with different colors) and mechanical (where the output is a force-extension curve) experiments. The goal of our work is to extract both kinetic and thermodynamic information. In addition, one of our long-term interests is to understand the role of diffusion in determining the rates of chemical reactions, including ligand binding and protein-protein association.
Ultrafast Biophysical Chemistry Section
The Ultrafast Biophysical Chemistry Section investigates the relationships between protein structure, dynamics, and function using ultrafast time-resolved laser spectroscopy and X-ray crystallography. These experimental techniques employ an ultrashort laser "pump" pulse (shorter than 10-13 seconds) to trigger a photophysical or photochemical reaction and a variably delayed "probe" pulse that measures the spectral or structural evolution of the protein. This pump-probe technique provides the means to acquire "snapshots" of a protein as it executes its designed function. By monitoring the changes that occur over time, from femtoseconds to milliseconds, we aim to build a foundation for understanding how proteins execute their designed tasks with high efficiency and selectivity. Researchers in the section use this technique to study various model systems, including ligand-binding heme proteins and their mutants, bacteriorhodopsin, and photoactive yellow protein. Using a microfocusing femtosecond spectrometer that is capable of probing protein dynamics in small crystals, researchers can compare dynamics in solution and crystals. This allows us to assess the extent to which crystal contacts influence protein dynamics. Moreover, ultrafast studies of protein photophysics have led to more efficient protocols for chromophore photoactivation, thereby improving the quality of time-resolved X-ray structures.