Many biomaterials can adapt to changes in the local biological environment (such as pH, temperature, or ionic composition) in order to regulate function or deliver a payload. Such adaptation to environmental perturbation is typically a hierarchical process that begins with a response at a local structural level and then propagates to supramolecular and macromolecular scales. Understanding fast structural dynamics that occur upon perturbation is important for rational design of functional biomaterials. However, few nanosecond time-resolved methods can probe both intra- and intermolecular scales simultaneously with a high structural resolution. Here, we utilize time-resolved X-ray scattering to probe nanosecond to microsecond structural dynamics of poly-l-glutamic acid undergoing protonation via a pH jump initiated by photoexcitation of a photoacid. Our results provide insights into the protonation-induced hierarchical changes in packing of peptide chains, formation of a helical structure, and the associated collapse of the peptide chain.