Computational design of the temperature optimum of an enzyme reaction

• Published in: Science Advances
• Main Authors: van der Ent, Florian, Skagseth, Susann, Lund, Bjarte A., Socan, Jaka, Griese, Julia J., Brandsdal, Bjorn O., Åqvist, Johan
• Format: Article in Journal/Newspaper
• Language: English
• Published: Uppsala universitet, Beräkningsbiologi och bioinformatik 2023
• Subjects: Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; Antarctic; Antarc*
• Online Access: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-508544; https://doi.org/10.1126/sciadv.adi0963

Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic a-amylase from an Antarctic bacterium, the inactivation is thought to originate from a specific enzyme-substrate interaction that breaks around room temperature. Here, we report a computational redesign of this enzyme aimed at shifting its temperature optimum upward. A set of mutations designed to stabilize the enzyme-substrate interaction were predicted by computer simulations of the catalytic reaction at different temperatures. The predictions were verified by kinetic experiments and crystal structures of the redesigned a-amylase, showing that the temperature optimum is indeed markedly shifted upward and that the critical surface loop controlling the temperature dependence approaches the target conformation observed in a mesophilic ortholog.