Was binding of free amino acids an early innovation in the evolution of allostery?

Rüdiger Ettrich¹, Rebecca Strawn², Milan Melichercik¹, Tomas Stockner³ and Jannette Carey²

¹Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, Zámek 136, 373 33 Nové Hrady

²Chemistry Dept. Princeton University Princeton NJ 085441009 USA

³Dept. of Health & Environment Austrian Research Centers GmbHARC, Vienna Austria

ettrich@nh.usbe.cas.cz

Interpretation of thermodynamic ligand-binding data through the lens of molecular dynamics (1) has led to a structural and energetic description of the molecular mechanism of allostery for the hexameric E. coli arginine repressor, the master feedback regulator of transcription in L-arginine metabolism, which displays strong negative cooperativity of L-arginine binding. A controversial prediction of the famous allostery model of Monod, Wyman, and Changeux is that constraints imposed on protein subunits by multimerization are relaxed by ligand binding, but with conservation of symmetry in partially-liganded states. Molecular dynamics simulations reveal that conserved Arg and Asp sidechains in each L-arginine binding pocket promote rotational oscillation of apoArgR trimers by engagement and release of salt bridges. Binding of exogenous L-arginine displaces resident Arg residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting subunit motions that generate an entropic driving force while maintaining symmetry in partially-liganded states.The results indicate that partially-liganded states can be structurally symmetric despite their conceptual asymmetry. The symmetric relaxed state is visualized as a multimer with all subunits anchored near the center, and with motions transferred to the periphery like a bouquet of balloons in strong wind. Thus, even during sequential filling of binding sites, symmetry can be maintained by exploiting the dynamics of the assembly and the distributed nature of its cohesive energy. The mechanism suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery (2).

Acknowledgements - The access to METACentrum supercomputing facilities provided under the research intent MSM6383917201 is acknowledged. We gratefully acknowledge support from the Ministry of Education, Youth and Sports of the Czech Republic (LC06010), Academy of Sciences of the Czech Republic (AVOZ60870520), Grant Agency of the Czech Republic (203/08/0114 to R.E), , and joint Czech US National Science Foundation International Research Cooperation (INT0309049 and ME09016) is acknowledged.

References

1. R.Strawn, T. Stockner, M. Melichercik, L Jin, J. Carey, R. Ettrich (2010)  Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery.   In: Methods in Enzymology, Biothermodynamics C Edited by:Michael L. Johnson, Jo M. Holt , Gary K. Ackers. , in press

2. R.Strawn, M. Melichercik, Green M., T. Stockner, J. Carey, R. Ettrich (2010) Symmetric allosteric mechanism of hexameric E. coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues, submitted.