Protein Dynamics and Enzymatic Catalysis

Abstract

This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

Figure 1.

Chemical reaction catalyzed by lactate dehydrogenase. The reaction involves the hydride transfer of the NC4 hydrogen of NADH from the pro-R side of the reduced nicotinamide ring to the C2 carbon of pyruvate and protein transfer from the imidozole group of His-193 to pyruvate’s keto oxygen.

Figure 2.

Promoting vibration in human heart LDH. This protein motion is along the donor–acceptor axis for hydride transfer, and compression always proceeds reaction.

Figure 3.

Structure factor S(k, ω) for k = 0.2 Å⁻¹ along the PV axis (black line) and along an axis perpendicular to the promoting vibration. There is strong anisotropy. The sharpness of the peak at 125 cm⁻¹ means that there are stable fluctuations along the PV axis for that frequency.

Figure 4.

Different spherical shells containing members of the promoting vibration. The highlighted residues represent the different members of the promoting vibration.

Figure 5.

Chemical reaction catalyzed by human purine nucleoside phosphorylase. The promoting vibration compresses O₄′ and O₅′.

Figure 6.

Constrained PNP Chain A (red) and active site (green). The loop is held open by constraining the α carbon of Glu250 to the α carbon of Pro122. The unconstrained loop is shown in blue. The difference in loop positions is less than 2 Å.

Figure 7.

Free energy profile for the unconstrained (left) and constrained (right) PNP systems calculated using the TPS based method. Standard deviations are calculated using the bootstrapping method and denoted as blue error bars, while the continuous black curve represents the polynomial fitting function.

Figure 8.

Region of the most evolved variant, that introduced protein dynamics shown in both panels (A) and (B) with key interactions highlighted. (A) has internal residues associated with decreased hydrogen bonding compared to variant IV highlighted in orange; the direction of the rate promoting vibration is out of the page. (B) has internal residues associated with increased hydrogen bonding compared to variant IV highlighted in purple and pink; the direction of the rate promoting vibration is going from right to left. The substrate and QM residues (the active site) are highlighted in red.