Bio-nano hybrid materials feature eco-friendly synthesis, various self-assembly patterns and numerous possibilities for surface functionalization. With these unique advantages, biological scaffolds have been regarded as green alternatives to fabricate metallic nanomaterials. Herein, a bulky tobacco mosaic virus coat protein (TMVCP) was employed as a versatile template to synthesize metallic nanoparticles at room temperature. These materials exhibited exceptional performance for organic transformations under green conditions. Remarkably, while Au NPs showed rapid kinetics in pollutant 4-nitrophenol reduction, Pd NPs demonstrated superior catalytic activity towards hydrogenation of unsaturated alcohols. The enhanced performance is likely related to the protein. To ascertain the protein structure-function effect on the catalytic performance, an in-depth analysis was performed for a TMVCP-Pd NP system via molecular dynamic (MD) simulations. Our results suggest that due to minimal passivation of bulky protein, a large portion of the Pd NP surface remains approachable for the reactants, thus resulting in high reaction rate.