Following evolutionary paths to protein-protein interactions with high affinity and selectivity

TY - JOUR

T1 - Following evolutionary paths to protein-protein interactions with high affinity and selectivity

AU - Levin, Kalia Bernath

AU - Dym, Orly

AU - Albeck, Shira

AU - Magdassi, Shlomo

AU - Keeble, Anthony H.

AU - Kleanthous, Colin

AU - Tawfik, Dan S.

PY - 2009/10

Y1 - 2009/10

N2 - How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (K-d > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity ( against ColE9 inhibition), led to an similar to 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.

AB - How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (K-d > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity ( against ColE9 inhibition), led to an similar to 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.

KW - IMMUNITY PROTEIN

KW - INTERACTION SPECIFICITY

KW - MOLECULAR-MECHANISMS

KW - CRYSTAL-STRUCTURE

KW - DUAL RECOGNITION

KW - COLICIN

KW - EVOLVABILITY

KW - STABILITY

KW - COMPLEXES

KW - IM9

UR - http://www.scopus.com/inward/record.url?scp=70349832423&partnerID=8YFLogxK

U2 - 10.1038/nsmb.1670

DO - 10.1038/nsmb.1670

M3 - Article

C2 - 19749752

SN - 1545-9985

VL - 16

SP - 1049

EP - 1055

JO - Nature structural & molecular biology

JF - Nature structural & molecular biology

IS - 10

ER -