Fundamental processes of life are carried out within cells by nm-scale molecular machines. There are diverse families of protein molecular motors that burn chemical fuel to exert forces and move along DNA tracks in order to modify molecular structures (e.g., helicases ripping open the DNA double helix) or copy information (e.g., polymerases transcribing DNA into messenger RNA). In order to study such motors, we have recently built a new single molecule biophysics instrument that combines angstrom resolution optical trapping and single molecule fluorescence microscopy (Comstock et al., Nature Methods, 2011). Being able to simultaneously measure and correlate two degrees of freedom at high resolution allows us to directly and unambiguously reveal fundamental properties of these molecular motors (e.g., the connection between motor configuration or quantity and capability). However many essential molecular properties depend not on just two but rather three, four… degrees of freedom. Most molecular motors within the cell do not work alone but rather function within coordinated heterogeneous complexes of many molecules which directly affect their function. I will discuss how we can expand the fluorescence and sample handling capabilities of our instrument to be able to directly observe multi-component and multi-degree of freedom molecular machine systems and thereby more faithfully reveal how they function within the cell. Second, the fuel-to-motion conversion process of molecular motors is at the core of their function and yet remains mysterious. I will discuss how advances in technique and instrumentation will allow us to directly observe and thereby understand this essential process. Finally I will discuss how we can take advantage of our powerful new instrumentation developments and the knowledge thereby gained in order to engineer novel molecular machine capabilities such as remote optical control.
