At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Abstract

Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, transcription and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way considering basically all reasonable definitions, including (but not limited to) such proposed effects as "coupling between conformational and chemical motions", "landscape searches" and "entropy funnels". It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies.

Protein conformational dynamics dictate the binding affinity for a ligand

“…MBP is therefore likely to have evolved to have optimal dynamics for transporting sugars for the survival of organisms. Along with other studies regarding the connection between protein dynamics and ligand dissociation or enzyme catalysis 26,27 , our results therefore provide direct evidence regarding the dynamics-coupled ligand dissociation at a longer timescale (sub-second to tens of seconds) with a large amplitude (domain movement and reorientation in the nm range).…”

Reply to Karplus: Conformational dynamics have no role in the chemical step

“…3). We agree (3) that rate-determining product release is not an example of chemical catalysis being coupled with dynamics but is a different phenomenon with a very minor relationship to the overall catalytic effect.…”

“…The crossing of the transition state has little to do with catalysis, because the transmission factor, κ, is similar in enzymes and in solution (5); additionally, we have established (2, 3) that fs and ps motions do not lead to rate enhancement, and of course, they do not facilitate millisecond processes, despite the implications that this is so (this issue is addressed in detail in ref. 3).…”

Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins

“…The results indicate that deep tunneling is the rate limiting proton transport event involved in resetting the GFP proton wire for ≲ 295 K. The importance of room temperature deep proton and hydrogen tunneling in biological systems remains a somewhat controversial topic, especially in the context of enzyme reactions 5,11,28,29 . Thus, the experiments presented here, which are the first temperature dependent measurements of tunneling in a biological proton wire and cover a much larger temperature range than previous studies 2,3,5,9 , can help us to better understand this important process.…”