Routes to covalent catalysis by reactive selection for nascent protein nucleophiles.
Reactivity-based selection strategies have been used to enrich combinatorial libraries for encoded biocatalysts having revised substrate specificity or altered catalytic activity. This approach can also assist in artificial evolution of enzyme catalysis from protein templates without bias for predefined catalytic sites. The prevalence of covalent intermediates in enzymatic mechanisms suggests the universal utility of the covalent complex as the basis for selection. Covalent selection by phosphonate ester exchange was applied to a phage display library of antibody variable fragments (scFv) to sample the scope and mechanism of chemical reactivity in a naive molecular library. Selected scFv segregated into structurally related covalent and noncovalent binders. Clones that reacted covalently utilized tyrosine residues exclusively as the nucleophile. Two motifs were identified by structural analysis, recruiting distinct Tyr residues of the light chain. Most clones employed Tyr32 in CDR-L1, whereas a unique clone (A.17) reacted at Tyr36 in FR-L2. Enhanced phosphonylation kinetics and modest amidase activity of A.17 suggested a primitive catalytic site. Covalent selection may thus provide access to protein molecules that approximate an early apparatus for covalent catalysis.
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10, Miklukho-Maklaya str, Moscow, 117871, Russia.
Andrey V
AV
Reshetnyak
Maria Francesca
MF
Armentano
Natalia A
NA
Ponomarenko
Domenica
D
Vizzuso
Oxana M
OM
Durova
Rustam
R
Ziganshin
Marina
M
Serebryakova
Vadim
V
Govorun
Gennady
G
Gololobov
Herbert C
HC
Morse
Alain
A
Friboulet
Sudesh P
SP
Makker
Alexander G
AG
Gabibov
Alfonso
A
Tramontano
D002384:Catalysis; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
D011506:Proteins