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Why is catalase so fast? A preliminary network hypothesis to explain ultra-fast enzyme-catalysed reactions

Institute of Dentistry

Applications accepted all year round Self-Funded PhD Students Only

About the Project

Biochemistry’s reductionist framework underpins much of today’s biomedical practice. But is it right? Consider the classical view of enzyme catalysis. This is based on the view that cellular reactions are the result of random, diffusion-controlled, molecular collisions, i.e., as occurs in laboratory glassware. All a cell’s biochemical complexity amounts to apparently, is meaningless responses to random molecular events [Dawkins, 1988]. And then there are the catalases.

They are some of the most efficient enzymes known, disproportionating tens of millions of hydrogen peroxide molecules per second. Such a huge turnover means H2O2 molecules need to travel extremely rapidly into and react with active sites deep within catalases’ protein structures, far removed from the bulk intracellular aqueous milieu in which they function. This suggests catalases operate with kinetics impossibly faster than H2O2 molecular diffusion rates in water.

Although several mechanisms have been invoked to explain this phenomenon, it is difficult to reconcile the speed, precision, and subtlety of catalases with the classical reductionist narrative of diffusion-controlled random molecular collisions.

Proposed hypothesis:
That the classical view of enzyme action is fundamentally incorrect. Instead, it is proposed that, in enzymes with very large turn-over numbers, (e.g., the catalases), the enzyme acts as a ‘hub’ for ultra-fast reactivity that, via a giant dynamically hydrogen-bonded network of water and H2O2 molecules, spreads out rapidly into the intra-cellular aqueous milieu [Milgrom, 2016, 2018]. Thus, without contradicting catalase’s experimentally determined enzyme kinetics, this proposed mechanism predicts the vast majority of catalysed reactions occurs outside of the enzyme.

If experimentally demonstrated, such a coherent network mechanism is a ‘game changer’ because it effectively expands the focus of enzyme activity from the conventional concentration on active sites and enzyme-substrate complexes, to include the enzyme’s aqueous intracellular environment. Ironically however, this is not in itself new.

Prior to the now accepted lock-and-key [Stryer et al. 2002] and induced fit models [Koshland, 1958], early ideas of enzyme action imagined they induced changes in the surrounding water, which then accelerated reactions in molecules nearby [Kohler, 1973]. Interestingly, such a notion of essentially coherent operation has recently been suggested to explain the enzymic action of endonucleases reading DNA sequences [Kurian et al, 2014].

In catalase, some of its surface amino acids are hydrophilic polar/charged, and it is thought this helps concentrate H2O2 molecules near and into the channels leading to the enzyme’s active sites [Dominguez, 2010]. But these are precisely the conditions that could generate so-called Exclusion Zone (EZ) layers near the catalase enzyme’s surface [Pollack, 2013].

EZ layer formation also generates free solvated protons, which in the presence of transition metal ions such as Fe(II)/Fe(III), provide catalytic environments for H2O2 redox chemistry [Baker, 2007]. Consequently, “ biological catalysis may resemble generic catalysis, involving little more than high concentrations of EZ-generated protons.” [Pollack, 2013]. Therefore, given the network hypothesis does not appear to violate known biochemistry, the game-changing notion that enzyme activity might be in coherence with its cytoplasmic aqueous milieu, does not seem too far-fetched.

How the hypothesis will be tested
One way would be to use the well-known chemiluminescence reaction of H2O2-derived oxygen with luminol [Huntress et al. 1934]. In crime-scene forensics, luminol is used to detect the presence of blood; the iron in the haemoglobin leading to disproportionation of H2O2, whose oxygen release generates luminol chemiluminescence [James and Eckert 1998].
To observe exo-enzymatic H2O2 disproportionation, it would however be necessary to use immobilised catalase [Yoon et al. 2007] and ensure the H2O2-reaction solution containing the luminol underwent the minimum of disturbance. This would be to make sure that H2O2 disproportionation really is occurring at a distance from the immobilised enzyme and is not being carried away from it by random mixing of the solution that would occur if the solution is disturbed.

If correct, the hypothesis shifts the emphasis back to water’s central role in catalase activity, and challenges biochemistry to give more serious consideration to water in all biological function. Or as Albert Szent-Gyorgyi put it, “Water is the mater and matrix, the mother and medium of life.” [Collins, 2000].

Funding Notes

We will consider applications from prospective students with a source of funding to cover tuition fees and bench fees for three years full-time or 6 years part-time. Both self-funded and sponsored students will be considered.

UK and EU nationality self-funded students might be eligible for both the cost of tuition fees and a yearly stipend over the course of the PhD programme from the Student Finance England: View Website

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