Membrane proteins take up about one-third of all human proteins, and they are targets for more than half of all drugs. This thesis will describe how these membrane proteins and peptides can be adapted into miniaturized devices for fundamental research as well as biotechnological applications. The Escherichia coli Cytolysin A (ClyA) is deployed as a label-free nanopore tweezer with a high temporal resolution to resolve protein dynamics at the single-molecule level in real-time. My work identified the anomeric binding modes of maltose-binding protein (MBP) for the first time, derived the kinetics and thermodynamics of the protein-substrate interactions, and shed light on the mechanism of substrate recognition by MBP. I also adapted and improved the traditional droplet-interface bilayer (DIB) techniques for quantitating cell-penetrating peptides (CPPs) assisted macromolecular trafficking. In this work, we discovered the driving force for CPP-assisted translocation and validated a DIB-based approach for high throughput screening of the efficacy of CPPs.