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David Goldenberg

Professor of Biology

A.B. Whitman College

Ph.D. Massachusetts Institute of Technology

Research

References

 

David Goldenberg's Lab Page

David Goldenberg's PubMed Literature Search

Research

The long-range goal of research in my laboratory is to understand the mechanisms by which polypeptide chains fold into stable structures and assemble into functional complexes. We are particularly interested in understanding the role of protein dynamics in determining the stabilities of protein structures, the specificity of their formation and their functional properties.

Our current efforts are focused on two aspects of protein dynamics. The first is the characterization of unfolded proteins. Although it is usually the well-defined folded structures of proteins that are associated with biological function, there is growing interest in the properties of unfolded proteins, which are best described as broad ensembles of rapidly interconverting structures. These ensembles serve as the starting point for folding and as the reference state for most measurements of protein stability. In addition, non-native states are now known to play important roles in normal cellular processes, including protein localization and degradation, as well as pathological processes such as the formation of amyloid fibers associated with many neurodegenerative diseases. We are using a combination of computational and experimental techniques to obtain a more complete understanding of the distributions of conformations that make up an unfolded state. We are particularly interested in determining how the properties of unfolded proteins change in response to solution conditions and the presence of high concentrations of other macromolecules, as found intracellularly.

The second focus of our work is the interaction between a protease, trypsin, and a natural inhibitor of this enzyme, bovine pancreatic trypsin inhibitor (BPTI). BPTI is a member of a large class of natural protease inhibitors that act by binding to the active sites of their targets, much as a substrate would, but are resistant to hydrolysis. By blocking the access of potential substrates to the active sites, these inhibitors play critical biological roles in preventing unregulated proteolysis. We have found that amino acid replacements at specific sites in BPTI can, at the same time, increase the flexibility of the free inhibitor, decrease the stability of the complex it forms with trypsin and increase its likelihood of being hydrolyzed by the enzyme. Together, these observations suggest that flexibility, or the lack thereof, is a critical factor in the function of this and other protease inhibitors. We are currently using NMR spectroscopy, thermodynamic and kinetic measurements and x-ray crystallography to learn more about the factors that determine flexibility in the context of an enzyme-substrate complex and about the nature of the motions that are necessary for catalytic function.

Structure of a serine protease poised to resynthesize a peptide bond. Zakharova et al. (2009).

References