A Biophysical Perspective on Enzyme Catalysis

Abstract

Even after a century of investigations, our knowledge of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve the high catalytic efficiency still remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bringing together and properly orienting the participants so that the reaction can proceed; therefore, only viewing enzymes as passive participants in the catalyzed reaction. Increasing evidence shows that enzymes are not rigid structures but they are constantly undergoing a wide range of internal motions and conformational fluctuations. In this perspective, based on studies from our group, we discuss the emerging biophysical model for enzyme catalysis that provides detailed understanding of the interconnection between internal protein motions, conformational sub-states, enzyme mechanisms and catalytic efficiency of enzymes. For a number of enzymes, networks of conserved residues have been discovered that span from the surface of the enzyme all the way to the active-site. These networks are hypothesized to serve as pathways of energy transfer that enables thermodynamical coupling of surrounding solvent with enzyme catalysis, and play a role in promoting the enzyme function. Additionally, the role of enzyme structure and electrostatic effects is already well known for quite some time. Collectively, the recent knowledge gained about enzyme mechanisms suggest that the conventional paradigm of enzyme structure encodes function is incomplete and needs to be extended to structure encodes dynamics and the catalytic rate-acceleration, and together these enzyme features encode function.

Protein Flexibility and Stiffness Enable Efficient Enzymatic Catalysis

“…In these cases the results of biophysical studies on protein dynamics may not be relevant to the explanation for the enzymatic rate acceleration. 111 Now the only protein motions clearly relevant to the rate acceleration are those associated with the creation and breakdown of E C ·S during the steps for k c , k –c , and k ′ –c in Scheme 7 . These motions may affect the reaction rate, if they occur together with conversion of enzyme-bound substrate to product in a single reaction stage.…”

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles

“…For example, enzymes commonly contain loops that close to interact with substrates, and emerging results provide evidence that the most reactive sub-states in enzymatic reactions are not the most populated (Callender and Dyer, 2015;Klinman, 2009Klinman, , 2013Reddish et al, 2014). It has been also suggested that the ability to adopt reactive conformations may be dynamically linked to surface residues and solvent (Agarwal, 2004(Agarwal, , 2019Agarwal et al, 2002Agarwal et al, , 2004Meadows et al, 2014;Ramanathan and Agarwal, 2011) and further proposed that catalytic rates are gated by collective dynamic events of the protein (Silva et al, 2011;Suarez and Schramm, 2015).…”

Enzyme Dynamics: Looking Beyond a Single Structure

“…For several decades, the pioneering work of Frauenfelder and coworkers indicated that hydration shell solvent motions have a direct and strong influence on internal protein residue motions . Driven by the temperature‐associated fluctuations, the motions of solvent molecules at surface enslave the motions of protein surface residues, which in turn influences how the longer time‐scale motion sampling occurs …”

“…Another excellent article by Schwartz builds a consensus view emerging from experimental and computational techniques, particularly on the role of fast motions in enzyme reactions . Agarwal also summarized a biophysical model of enzymes based on enzyme and solvent dynamics with focus on pathways of energy transfer between the dynamical surface loop regions and the active‐site of several enzymes …”