The rapid development of nanoparticles (NPs) has impacted many fields including energy efficiency, material science, biosensing, and medical therapeutics. Recently, NPs have been utilized to immobilize enzymes. The so-formed enzyme- NP complex show great potential to increase the reusability of enzymes and catalytic efficiencies. Enzyme-NP complex can also advance enzyme delivery for therapeutics where NPs serve as the enzyme carrier. In all applications, the contact of NPs with biomacromolecules, especially proteins, is either necessary or inevitable, which can lead to alterations in adsorbed enzyme structure and function. In biocatalysis, such changes often reduce the desired catalytic activity; in living organisms these changes can even cause protein malfunction, raising concerns about public health and nanotoxicity. Therefore, understanding the correlation of enzyme structure and activity upon contact with NPs is essential. While enzyme activities can often be determined, the details of enzyme structural changes caused by NPs are underexplored for most enzyme-NP complexes. Obtaining the structural information is challenging due to the relatively large size of the complexes, high heterogeneity in enzyme binding, and complexities caused by the presence of NPs which limit most structure determination approaches. These challenges were overcome using a set of biophysical techniques especially site-directed spin labeling (SDSL) with Electron Paramagnetic Resonance (EPR). SDSL-EPR can measure site-specific structural information in the native state of enzyme/NP systems, regardless of the complexity, primarily due to its “penetrating” power which is only sensitive to the motion of the spin label. The focus of this dissertation was on T4 lysozyme (T4L), a representing model enzyme proven useful in many works. Gold Nanoparticles (AuNPs), Gold Nanorods (AuNRs), Silica Nanoparticles (SiNPs), and Carbon Nanotubes (CNTs) were the studied NPs. The interaction of T4L with each NPs was unique. The local structural information and the orientation of T4L in each NP was revealed based on which the possible docking mechanism for each case was proposed. The ultimate goals to reveal the structure-function relationship of enzymes on NPs and utilize this information to fine-tune enzyme adsorption on various NPs to 1) avoid NPs aggregation and 2) optimize NPs as enzyme carriers were met.