Ancient enzymes can con­trib­ute to green­er chemistry

A research team at Uppsala Uni­ver­sity has resur­rec­ted sev­er­al bil­lion-year-old enzymes and repro­grammed them to cata­lyse com­pletely dif­fer­ent chem­ic­al reac­tions than their mod­ern ver­sions can man­age. The meth­od can be used to devel­op sus­tain­able solu­tions with­in bio­tech­no­logy, such as for enzyme biore­act­ors or to chem­ic­ally degrade envir­on­ment­al tox­ins. The study has been pub­lished in Chem­ic­al Science.

“We use soft­ware to sim­u­late bil­lions of years of evol­u­tion, and we were actu­ally able to devel­op an effect­ive enzyme that can cata­lyse a com­pletely new reac­tion. It’s incred­ibly excit­ing,” says Lynn Kam­er­lin, who is lead­ing the research team at Uppsala University.

Enzymes have the abil­ity to cata­lyse, i.e. speed up, chal­len­ging chem­ic­al reac­tions from mil­lions of years to a frac­tion of a second without being con­sumed them­selves. They are also bio­de­grad­able and have a min­im­al car­bon foot­print. Most enzymes are cata­lysts for a spe­cif­ic chem­ic­al reac­tion, which serves an import­ant func­tion in bio­lo­gic­al pro­cesses, for example in our bodies.

With­in bio­tech­no­logy, intens­ive work is being done to devel­op new enzymes that can cata­lyse unusu­al reac­tions for green chem­istry, sus­tain­able cata­lys­is and the chem­ic­al break­down of envir­on­ment­ally tox­ic substances.

The research team at Uppsala Uni­ver­sity has worked with col­leagues at Uni­ver­sid­ad de Granada in Spain to resur­rect ances­tral enzymes, first on a com­puter, and then in the labor­at­ory. The prim­it­ive enzymes have many char­ac­ter­ist­ics that are desir­able with­in bio­tech­no­logy. They can with­stand extreme tem­per­at­ures and they are struc­tur­ally more flex­ible, mak­ing them easi­er to modi­fy than their mod­ern equivalents.

The research­ers suc­ceeded in repur­pos­ing ancient anti­bi­ot­ic-degrad­ing enzymes to cata­lyse a com­pletely new non-nat­ur­al reac­tion. But even though the repur­posed enzymes sped up the reac­tion sig­ni­fic­antly, it was much slower than most nat­ur­ally occur­ring enzymes.

There­fore, to improve the effi­ciency of the enzyme, the research­ers used power­ful com­puters to cal­cu­late what changes in the struc­ture would res­ult in a faster reac­tion. They used a new meth­od called Fun­cLib, which uses a com­bin­a­tion of evol­u­tion­ary inform­a­tion and cal­cu­la­tions of pro­tein sta­bil­ity, to pre­dict more effect­ive enzyme variants.

A total of 3,000 poten­tial new enzyme vari­ants were pre­dicted by Fun­cLib and the 20 most prom­ising of these were tested in the lab. Of these, four were much faster than the ori­gin­al enzyme. The best was as effect­ive as the aver­age mod­ern, nat­ur­ally occur­ring enzymes.

“Our study shows that it is pos­sible to design new, effect­ive enzymes for a more sus­tain­able future,” says Lynn Kamerlin.

Source: Uni­ver­sity of Uppsala, Press release, 10.06.2020

Pub­lic­a­tion: Valer­ia Risso, et al. (2020) Enhan­cing a De Novo Enzyme Activ­ity by Com­pu­ta­tion­ally-Focused Ultra-Low-Through­put Screen­ing, Chem­ic­al Sci­ence: DOI: 10.1039/D0SC01935F

Con­tact: Lynn Kam­er­lin, pro­fess­or at the Depart­ment of Chem­istry — BMC, Bio­chem­istry, Uppsala Uni­ver­sity, Phone: +46 18 471 4423, Email: lynn.​kamerlin@​kemi.​uu.​se