Quantum-sized metallic clusters protected by biological ligands represent a new class of luminescent materials; yet the understanding of structural information and photoluminescence origin of these ultra-small clusters remains a challenge. Herein we systematically study the surface ligand dynamics and and ligand-metal core interactions of peptide-protected gold nanoclusters (AuNCs) with combined experimental characterizations and theoretical molecular simulations. We propose that the emission brightness of the resultant nanoclusters is determined by the surface peptide structuring, interfacial water dynamics and ligand-Au core interaction, which can be tailored by controlling peptide acetylation, constituent amino acid electron donating/withdrawing capacity, aromaticity/hydrophobicity and by adjusting environmental pH. Specifically, emission enhancement is achieved through increasing the electron density of surface ligands in proximity to the Au core, discouraging photo-induced quenching, and by reducing the amount of surface-bound water molecules. These findings provide key design principles for maximizing the photoluminescence of metallic clusters through the exploitation of biologically relevant ligand properties.