Proteins are sustainable as they keep their function in time and in different conditions. As a first approximation of functional behavior, we investigate how the structure design yields sustainability, concentrating on the problem of diagnosing of structural and dynamical perturbations caused by mutations of amino-acid, basic components of proteins. This is relevant to decipher how diseases arise from mutations. We also open the possibility of designing sustainable urban systems bio-inspired from proteins. Proteins and cities are modeled using weighted spatial networks that measure space occupancy by amino acids and buildings, respectively. This allows inferring the empty space available for the dynamics. Proteins have empty space that we assume to be exploited for the accommodation of mutations. In contrast, in the city high packing is present, suggesting spatial unsustainability (impossibility to change). We verify the relation between local packing and the impact of mutations on the protein structure and dynamics. We find that mutations keeping structural integrity require links rearrangement at diverse scales that will perturb the protein dynamics depending on the impacted structural level (2D, 3D, 4D). We propose a tool to describe the direction of the perturbations and extract the impact of multiple mutations acting collectively. This work contributes to the decoding of the protein's design for sustainability, opening perspectives in the fields of biomedicine and the design of sustainable bio-inspired systems.