Protein encapsulated gold nanoclusters has attracted great attention for their excellent fluorescent properties and potential biomedical applications. Glucose Binding Protein (GBP) has a high sensitivity and selectivity to glucose binding that makes them ideal for biosensor development. It is anticipated that GBP encapsulated gold nanoclusters could be a promising glucose sensor. Here we investigated the growth of gold nanoclusters in GBP using Molecular Dynamics (MD) simulation. To facilitation the nucleation of gold nanoclusters at specific sites, cysteine mutations were introduced in GBP. It is found that the nucleation site of gold nanoclusters inside mutant GBP are different from those in native GBP. Gold nanoclusters were formed near the mutated cysteine and tyrosine residues. Glucose remained in the binding site of a mutant GBP with gold nanoclusters although no conformational change was observed in MD simulation, similar to a native GBP. This work suggests the possibility of growing gold nanoclusters in the designed site within GBP and a new glucose sensor based on mutated GBP protected gold nanoclusters.