Abstract
Allostery is fundamentally thermodynamic in nature. Long-range communication in proteins may be mediated not only by changes in the mean conformation with enthalpic contribution but also by changes in dynamic fluctuations with entropic contribution. The important role of protein motions in mediating allosteric interactions has been established by NMR spectroscopy. By using CAP as a model system, we have shown how changes in protein structure and internal dynamics can allosterically regulate protein function and activity. The results indicate that changes in conformational entropy can give rise to binding enhancement, binding inhibition, or have no effect in the expected affinity, depending on the magnitude and sign of enthalpy–entropy compensation. Moreover, allosteric interactions can be regulated by the modulation a low-populated conformation states that serve as on-pathway intermediates for ligand binding. Taken together, the interplay between fast internal motions, which are intimately related to conformational entropy, and slow internal motions, which are related to poorly populated conformational states, can regulate protein activity in a way that cannot be predicted on the basis of the protein’s ground-state structure.
Similar content being viewed by others
References
Bouvignies G, Korzhnev DM, Neudecker P, Hansen DF, Cordes MH, Kay LE (2010) A simple method for measuring signs of (1)H (N) chemical shift differences between ground and excited protein states. J Biomol NMR 47:135–141
Hansen DF, Vallurupalli P, Kay LE (2008a) An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins. J Phys Chem B 112:5898–5904
Hansen DF, Vallurupalli P, Kay LE (2008b) Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states. J Biomol NMR 41:113–120
Kalodimos CG (2012) Protein function and allostery: a dynamic relationship. Ann N Y Acad Sci 1260:81–86
Korzhnev DM, Kloiber K, Kanelis V, Tugarinov V, Kay LE (2004) Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. J Am Chem Soc 126:3964–3973
Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH (2004) Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 14:10–20
Li DW, Bruschweiler R (2009) A dictionary for protein side-chain entropies from NMR order parameters. J Am Chem Soc 131:7226–7227
Loria JP, Rance M, Palmer AG 3rd (1999) A TROSY CPMG sequence for characterizing chemical exchange in large proteins. J Biomol NMR 15:151–155
Marlow MS, Dogan J, Frederick KK, Valentine KG, Wand AJ (2010) The role of conformational entropy in molecular recognition by calmodulin. Nat Chem Biol 6:352–358
Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG (2009) Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc Natl Acad Sci U S A 106:6927–6932
Tugarinov V, Sprangers R, Kay LE (2007) Probing side-chain dynamics in the proteasome by relaxation violated coherence transfer NMR spectroscopy. J Am Chem Soc 129:1743–1750
Tzeng SR, Kalodimos CG (2009) Dynamic activation of an allosteric regulatory protein. Nature 462:368–372
Tzeng SR, Kalodimos CG (2011) Protein dynamics and allostery: an NMR view. Curr Opin Struct Biol 21:62–67
Tzeng SR, Kalodimos CG (2012) Protein activity regulation by conformational entropy. Nature 488:236–240
Tzeng SR, Kalodimos CG (2013) Allosteric inhibition through suppression of transient conformational states. Nat Chem Biol 9:462–465
Tzeng SR, Pai MT, Kalodimos CG (2012) NMR studies of large protein systems. Methods Mol Biol 831:133–140
Yang D, Kay LE (1996) Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol 263:369–382
Compliance with Ethical Standards
Funding
This work was supported by the US National Science Foundation grant MCB1121896 to C.G.K.
Conflict of interest
S.-R. Tzeng and C.G. Kalodimos declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human or animal subjects performed by any of the authors.
Author information
Authors and Affiliations
Corresponding author
Additional information
This article is part of a Special Issue on 'The Role of Protein Dynamics in Allosteric Effects' edited by Gordon Roberts.
Rights and permissions
About this article
Cite this article
Tzeng, SR., Kalodimos, C.G. The role of slow and fast protein motions in allosteric interactions. Biophys Rev 7, 251–255 (2015). https://doi.org/10.1007/s12551-015-0172-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12551-015-0172-8