Origin of Metal Cluster Tuning Enzyme Activity at the Bio-Nano Interface

Detailed understanding of how the bio-nano interface orchestrates the function of both biological components and nanomaterials remains ambiguous. Here, through a combination of experiments and molecular dynamics simulations, we investigated how the interface between Candida Antarctic lipase B and palladium (Pd) nanoparticles (NPs) tunes the structure, dynamics, and catalysis of the enzyme. Our simulations show that the metal binding to protein is a shape matching behavior and there is a transition from saturated binding to unsaturated binding along with the increase in the size of metal NPs. When we engineered the interface with the polymer, not only did the critical size of saturated binding of metal NPs become larger, but also the disturbance of the metal NPs to the enzyme function was reduced. In addition, we found that an enzyme–metal interface engineered with the polymer can boost bio-metal cascade reactions via substrate channeling. Understanding and control of the bio-nano interface at the molecular level enable us to rationally design bio-nanocomposites with prospective properties.


Enzyme Activity Assays of Pd/CALB-P
The hydrolytic activities of CALB, CALB-P and Pd/CALB-P were assayed by a standard method using p-NPB as the substrate. Triton X-100 (0.25g) was dissolved in Na 2 HPO 4 /NaH 2 PO 4 buffer (20 mL, 50 mM, pH 7.0) and then added to a 50 mL beaker with magnetic stirring. p-NPB was dissolved in acetone (1 mL) and then added to the above-mentioned Trition X-100 solution dropwisely. The mixture was stirred for 5 min at room temperature. The reaction was started by adding 50 μL of enzyme sample solution (50 μg/mL protein in 10 mM phosphate buffer, pH 7.0) to 950 μL of the substrate solution. The increase in absorbance was detected at 348 nm by a UV/Vis spectrophotometer SHIMADZU UV-2600.

Quantity Formula
Total atom number of each particle (NT) Surface atom number of each particle (NS) The diameter of Pd atom (d Pd atom) is 0.274 nm. Between the particle size (d) and the number of atoms involved in one truncated cuboctahedron shaped Pd particle follows the relationship of . m is the number of atoms lying on an equivalent edge (corner atoms included). Table S3. The total atom number of each particle (NT), surface atom number of each particle (NS), the ratio of NS and NT, and the diameter of four Pd NPs in our simulation. Figure S2. The parameters of LJ potential of atom Pd and some common atoms in the protein of Pos-3 had the highest binding affinity and it was selected to do the following simulation.   for Pd19/CALB). Two drawing methods "NewCartoon" and "QuickSurf" were used to show the structure of CALB. Pd atoms were shown as yellow spheres. The residues interacting with Pd NPs were shown with blue color and the catalytic triad was also shown.           divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified two pathways connecting the Pd19 binding site to the active site.   divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified two pathways connecting the Pd55 binding site to the active site.   divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified a pathway connecting the Pd201 binding site to the active site.

Figure S26. Visualization of Jensen-Shannon (JS) divergence of the probability distribution of side-chain torsion-angle between Pd459/CALB and wild CALB. (a)
The residues with JS divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) As the Pd459 binding site was close to the active site, no pathway was given. The residues surrounding the active site with high JS divergence were shown.  Figure S28. The simulation procedure of CALB-P to find the equilibrium structure.
Step-2: 200 ns NPT simulation in water at 600 K.
From green to red, the JS divergence gradually increases. divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified a pathway connecting the Pd55 binding site to the active site.  divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified a pathway connecting the Pd201 binding site to the active site.  divergence bigger than 0.5 ("responsive" residues) were displayed as "QuickSurf" drawing methods.
From green to red, the JS divergence gradually increases. (b) According to the results of (a), we identified a pathway connecting the Pd459 binding site to the active site.