Calorimetric dissection of colicin DNase--immunity protein complex specificity.
We explore the thermodynamic strategies used to achieve specific, high-affinity binding within a family of conserved protein-protein complexes. Protein-protein interactions are often stabilized by a conserved interfacial hotspot that serves as the anchor for the complex, with neighboring variable residues providing specificity. A key question for such complexes is the thermodynamic basis for specificity given the dominance of the hotspot. We address this question using, as our model, colicin endonuclease (DNase)-immunity (Im) protein complexes. In this system, cognate and noncognate complexes alike share the same mechanism of association and binding hotspot, but cognate complexes (K(d) approximately 10(-)(14) M) are orders of magnitude more stable than noncognate complexes (10(6)-10(10)-fold discrimination), largely because of a much slower rate of dissociation. Using isothermal titration calorimetry (ITC), we investigated the changes in enthalpy (DeltaH), entropy (-TDeltaS), and heat capacity (DeltaC(p)) accompanying binding of each Im protein (Im2, Im7, Im8, and Im9) to the DNase domains of colicins E2, E7, E8, and E9, in the context of both cognate and noncognate complexes. The data show that specific binding to the E2, E7, and E8 DNases is enthalpically driven but entropically driven for the E9 DNase. Analysis of DeltaC(p), a measure of the change in structural fluctuation upon complexation, indicates that E2, E7, and E8 DNase specificity is coupled to structural changes within cognate complexes that are consistent with a reduction in the conformational dynamics of these complexes. In contrast, E9 DNase specificity appears coupled to the exclusion of water molecules, consistent with the nonpolar nature of the interface of this complex. The work highlights that although protein-protein interactions may be centered on conserved structural epitopes the thermodynamic mechanism underpinning binding specificity can vary considerably.
Keeble
Anthony H
AH
Department of Biology (Area 10), Post Office Box 373, University of York, Heslington, York YO10 5YW, United Kingdom.
Kirkpatrick
Nadine
N
Shimizu
Seishi
S
Kleanthous
Colin
C
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002151:Calorimetry / Q000379:methods*; D003087:Colicins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D003851:Deoxyribonucleases / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D001426:Bacterial Proteins; D003087:Colicins; C007104:colicin immunity proteins; D003851:Deoxyribonucleases