The kinetics of protein-protein recognition
✍ Scribed by Joël Janin
- Publisher
- John Wiley and Sons
- Year
- 1997
- Tongue
- English
- Weight
- 194 KB
- Volume
- 28
- Category
- Article
- ISSN
- 0887-3585
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✦ Synopsis
We examine a simple kinetic model for association that incorporates the basic features of protein-protein recognition within the rigid body approximation, that is, when no large conformation change occurs. Association starts with random collision at the rate k coll predicted by the Einstein-Smoluchowski equation. This creates an encounter pair that can evolve into a stable complex if and only if the two molecules are correctly oriented and positioned, which has a probability p r . In the absence of long-range interactions, the bimolecular rate of association is p r k coll . Long-range electrostatic interactions affect both k coll and p r . The collision rate is multiplied by q t , a factor larger than 1 when the molecules carry net charges of opposite sign as coulombic attraction makes collisions more frequent, and less than 1 in the opposite case. The probability p r is multiplied by a factor q r that represents the steering effect of electric dipoles, which preorient the molecules before they collide. The model is applied to experimental data obtained by Schreiber and Fersht (Nat. Struct. Biol. 3:427-431, 1996) on the kinetics of barnase-barstar association. When long-range electrostatic interactions are fully screened or mutated away, q t q r <1, and the observed rate of productive collision is p r k coll <10 5 M 21 • s 21 . Under these conditions, p r <1.5 • 10 25 is determined by geometric constraints corresponding to a loss of rotational freedom. Its value is compatible with computer docking simulations and implies a rotational entropy loss DS rot < 22 e.u. in the transition state. At low ionic strength, long-range electrostatic interactions accelerate barnase-barstar association by a factor q t q r of up to 10 5 as favorable charge-charge and charge-dipole interactions work together to make it much faster than free diffusion would allow. Proteins 28: 153-161, 1997.
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