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Enterovirus 71 is the major causative agent of neurovirulent hand, foot and mouth disease. Infection is acute and may culminate in severe neurological and/or cardiovascular complications that have been linked to severe morbidity and death. There currently are no approved vaccines or antivirals to prevent infection or spread of disease, underscoring an urgent need to better understand the molecular determinants underlying this serious threat to public health. EV71 utilizes a type I IRES to promote viral translation in a cap-independent manner through the co-opting of host proteins via a poorly understood mechanism. This thesis seeks to elucidate the molecular determinants regulating cap-independent translation. To that end, studies were pursued using the positive regulator hnRNP A1 and the negative regulator AUF1. Both modulate translation through interactions with the conserved Stem Loop II (SLII) domain of the IRES. Work presented herein shows that hnRNP A1 binds to SLII via a two state thermodynamic transition to the conserved 5nt bulge loop, and the apical portion of the RNA. Mutations that alter sequence and/or structure of these elements destabilized complex formation in vitro and abrogated viral translation and replication in vivo. Site-specific recognition of the bulge loop by hnRNP A1 is facilitated by structural rearrangements in SLII. Calorimetric analysis reveals that hnRNP A1 interacts site-specifically with SLII using a coupled ion-exchange mechanism. Conversely, in a novel RNA recognition mechanism, SLII binding promotes ligand induced folding of AUF1, providing the first structural evidence that AUF1 does not adopt an ordered fold. To assess how SLII structure can coordinate these two distinct translational outcomes, the high resolution solution structures of SLIIWT and a SLIICCC mutant, wherein the conserved 5’-UAG-3’ bulge loop was mutated to 5’-CCC-3’, were determined using an NMR-SAXs based approach. SLIIWT adopts a stable, structured fold in solution wherein the bulge loop determines global topology. SLIIWT adopts an L-shape in solution, mutation of UAG to CCC ablates nucleobase stacking and leads to the adoption of a more rod-like shape in solution. In sum, studies presented in this thesis reveal that biomolecular structure regulates cap-independent translation in EV71 through protein-RNA interactions.