Study of alpha-amylase and gold nanoparticles interaction at two different temperatures through molecular dynamics

The interaction of alpha-amylase with gold nanoparticles was studied at the two different temperatures of 25 and 75 °C through molecular dynamics simulation. To this end, 3-nm diameter spherical gold nanoparticles were designed. According to root mean square deviation results, at a high temperature, enzyme stability decreased in the absence of nanoparticles and increased in the presence of nanoparticles. Root mean square fluctuation results obtained for alpha-amylase residues indicated that the flexibility of residues 150-160 was affected more by the temperature in the presence and absence of nanoparticles. In addition, loop and helix regions in the secondary structure were affected more by the temperature. Results of enzyme contact maps in the designed systems showed that, in the absence of nanoparticles, a great number of contacts between residues were removed at high temperatures. The radius of gyration showed that the contact between the residues of amylase were removed in the absence of nanoparticles due to the enzyme expansion. Also Molecular dynamics simulation of α-amylase was performed in the presence of fifty 3- to 7-carbon sugar molecules at 25 and 75 °C. The results showed that the structure of α-amylase beta sheets is not affected by sugars. Docking of 3- to 7-carbon sugars with amylase sampled from simulations revealed that the affinity of sugars to the enzyme decreased at high temperatures in the absence of nanoparticles, while the presence of nanoparticles increased the affinity. Docking also showed that van der Waals and hydrophobic interactions contributed more than hydrogen interactions to the sugars-amylase interactions.