UC Santa Barbara

Conservative estimates indicate that 30% of known proteins contain long (>40 residues) intrinsically disordered regions (IDRs). In contrast to globular proteins, IDRs adopt multiple distinct conformations in their native state, similar to a random-walk polymer in a good solvent. While the sequence properties of IDRs have been extensively studied, their physical properties are still poorly understood. Characterizing these physical properties is an important step towards understanding the numerous biological functions and diseases associated with IDRs. Recently, Magnetic Tweezers (MTs) have emerged as a powerful tool for determining the structural properties of polymers in a manner that is orthogonal to other approaches, e.g., scattering experiments. With MTs, researchers use the thermodynamic effects of applied tension to study the conformations of single polymers via their end-to-end extension. This approach is particularly desirable for IDRs because many of them are found in the cellular cytoskeleton, where they play a critical structural and mechanical role. In the first part of this dissertation, I present my work on improving the MT technique with the aim of studying IDRs. I develop a computational tool for the robust calibration of forces and their uncertainty, an important but often overlooked aspect of these experiments. I also study the effects of surfaces on the low-force entropic elastic response of polymers, showing that they can be used to extract the radius of gyration. In the second part of this dissertation, I present the unexpected finding of glassy dynamics in a model IDR system, a polyprotein of the disordered neurofilament light tail (NFLt) domain. The NFLt is part of a large group of IDRs in neurons that are responsible for the structure and mechanics of the axon. Glassy dynamics in globular proteins was a major finding nearly 50 years ago that emphasized the importance of protein dynamics. However, it is attributed to conformational behaviors that are missing from IDRs. Nevertheless, using MT experiments, I show that a NFLt polyprotein’s extension changes, in response to a change in applied tension, with a nonexponential time dependence that is history dependent, two characteristic features of glassy systems. I show that the extension changes can be predicted using a phenomenological framework adapted from bulk glassy systems. Finally, I show that the glassy dynamics can be understood in terms of multiple, independent, and heterogeneous globules within a single NFLt. This mechanism for glassy dynamics is novel and likely to apply broadly to other IDRs.