Unique properties that occur at the nanoscale drive development of nanoparticles as carriers for efficient delivery of various therapeutically active compounds [1,2]. Nanoparticles carrying peptides derived from pathogen microorganisms can improve the peptides delivery to a desirable site of action and thus, e.g. in the case of HIV, can accelerate development of a preventive vaccine [2].

Complexation of therapeutically active peptides with nanoparticles depends on the physicochemical properties of nanoparticles such as surface chemistry, charge, size, shape etc. As a next step, when nanoparticle-based delivery system enters a human blood or cellular environment, it gets into the contact with variety of other biomacromolecules including proteins. Protein-nanoparticle interactions are similarly governed by material characteristics [3].

Studying of complex formation between nanoparticles and cargo peptides followed by protein interaction in biological medium is important for assessment of binding affinity, nanoparticle fate and its (non)safety behavior.

To achieve this aim, different biophysical methods can be employed. We will focus onto fluorescence polarization and circular dichroism methods. These methods have been successfully applied to the analysis of various molecular interactions [4], such as potein-ligand, protein-protein, protein-DNA binding. Thus, it is expected that these methods may bring useful information also in the case of protein/peptide – nanoparticle interaction studies.

Fluorescence polarization (FP) measurements are based on the fact, that when a fluorescently labeled molecule (peptide) is excited by polarized light, it emits light with a degree of polarization that is inversely proportional its molecular rotation. Quantitatively, FP is defined as the difference of the emission light intensity parallel and perpendicular to the excitation light plane normalized by the total fluorescence emission intensity [5].

An increase in fluorescence polarization indicates a decrease in mobility of the dye attached to the peptide upon the interaction/ peptide binding to the surface of nanoparticle [2].

Circular dichroism (CD) is a method that can be used for conformation analysis of optically active biomomolecules, in particular peptides/proteins by measuring their ability to differentially absorb circularly polarized light. CD can determine secondary structure (α-helix, β-sheets, random coil) in far-UV region (190-250nm), where the chromophore is a peptide bond [6].

Changes in the CD spectra represent conformation changes in peptide/protein secondary structures upon the absorption/stable interaction of nanoparticles [2].