Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

TY - JOUR

T1 - Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

AU - Haq, S Raza

AU - Chi, Celestine N

AU - Bach, Anders

AU - Dogan, Jakob

AU - Engström, Åke

AU - Hultqvist, Greta

AU - Karlsson, O. Andreas

AU - Lundström, Patrik

AU - Montemiglio, Linda Celeste

AU - Strømgaard, Kristian

AU - Gianni, Stefano

AU - Jemth, Per

PY - 2012/1/11

Y1 - 2012/1/11

N2 - Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K d correlate with changes in k off.

AB - Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K d correlate with changes in k off.

KW - Former Faculty of Pharmaceutical Sciences

U2 - 10.1021/ja209341w

DO - 10.1021/ja209341w

M3 - Journal article

C2 - 22129097

SN - 0002-7863

VL - 134

SP - 599

EP - 605

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

IS - 1

ER -