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Deniz Lab Single Molecule Biophysics

Research

Structural Studies of Intrinsically Disordered Proteins

In contrast with a common view of proteins as having a well-defined 3-dimensional structure that encodes their functions in the cell, IDPs have long stretches of sequence relatively devoid of structure. The special biophysics of these systems is believed to play a key role in function and health roles in the cell. In addition, misfolding and amyloid formation of some IDPs has been linked to diseases such as Parkinson’s disease. Our early studies (see chapter) have intriguingly revealed that IDPs can be rather compact and yet rapidly flicker between different structures (see paper), and how binding of apparently simple partners can result in folding into multiple shapes (see paper) on complex (see paper) and tunable (see paper) energy landscapes.

Mechanisms of Folding, Assembly and Function

We investigate mechanism and complexity in biological folding and RNAi. For example, our work has explored the effects of symmetry on the folding landscape of the dimeric RNA-binding Rop protein (see paper). Our results directly validate computational predictions and also provide new insight into the complex folding behavior of this protein. In addition, we have also used multicolor ensemble fluorescence imaging to probe the pathways of RNAi in cells (see paper). Our data reveal differences in the RNAi pathways for different target RNAs, and also provide evidence for a dual role for components of the RNAi machinery that can be coopted by viruses.

Advances in single-molecule biophysics methods

We continue to develop and improve single-molecule methodologies as needed by our biophysical studies. For example, we have made advances in multicolor single-molecule FRET (see paper), a powerful extension aimed at providing more global information about biological folding and binding. In addition, new advances in single-molecule mixing technology (see paper) are allowing us to probe the time-evolution of protein conformational landscapes during binding to partners. To facilitate these studies, we have also developed improved methods for data collection via microfluidics (see paper), and site-specific FRET labeling (see paper).