In the next decade the interactions between macromolecular components with proteins, drug molecules and genetic material will be exploited for the creation of novel functional nano-structures with advanced properties. Control of the organization of matter at the nano-scale is the key issue in modern applications of nano-medicine (drug-loaded nanoparticles), food science (enriched food matrices), tissue engineering (nanocomposite hydrogels) and biotechnology (protein separation). Macromolecular components offer versatile templates for creation of functional, stimuli-responsive and often bioactive systems via self-assembly. Modifications by physical self-assembly and temperature treatment is in cases preferred against chemical modification e.g. when the introduction of a chemically modified substance is a time consuming process. In a broader sense exploitation of physical interactions between natural components is a route to acceptable novel products. Small angle scattering methods and spatially sensitive measurements of viscoelasticity (i.e. microrheological techniques) are going to play central role in the imminent developments as they provide information at the relevant length scales. In this talk previous work on self-organization of synthetic and biological macromolecules, their interactions with proteins and the response of such systems to external stimuli will be presented. In more detail the role of electrostatic and hydrophobic interactions, the effect of thermal response and the hierarchical organization in synthetic, biological and hybrid aqueous solutions will be explored. The open questions in polymer/protein interactions will be illustrated and the potential of producing novel soft-materials by controlling these interactions will be presented.