How special is the biochemical function of native proteins?

Abstract

Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation.

Keywords: Enzymatic active sites; Protein structure; biochemical function; native proteins; protein conformation; protein interactions.

Figure 1.

Cumulative fraction of enzymes whose active sites match pocket residues in ( A) other classes of enzymes in native structures with different first two digit Enzyme Commission (EC) numbers, ( B) in non-enzymes, and ( C) in ART structures. For each target enzyme, we count the number of alternative enzyme classes that contain at least a hit by the target enzyme at various root-mean-square-deviation (RMSD) cut-offs.

Figure 2.. Root-mean-square-deviation (RMSD) of native enzymatic to ART pockets versus the number of pocket residues aligned.

The number of residues in the native active site pocket, N, is shown in the figure legend.

Figure 3.. Artificial protein-protein, protein-DNA complexes.

( A) Statistics of putative artificial protein-protein complexes. Joint probability density of interaction energy E _PP and the p-value of the interface similarity (IS)-score ^, between an artificial complex and its corresponding native template. Darker blue indicates higher density, with the 100 lowest density spots represented by grey spheres. A vertical/horizontal dashed line is placed at E _PP = -15 (a cut-off for high likelihood of interaction) and P = 1×10 ^-3. ( B) Protein-binding propensity scores (>0 implies favorable binding) of native protein-protein interfaces versus putatively attractive ( E _PP <-15) and repulsive ( E _PP >10) artificial protein-protein interfaces. ( C) Example of an ART protein-protein complex. The complex was built by superimposing two artificial structures (cyan and orange) onto a native dimeric template (Protein Data Bank [PDB] code 2f4m, chain A and B, colored in green and purple). Interface alignment according to iAlign . Both structures are shown in line representations, with the non-interfacial regions of the native template shown in transparent mode for clarity. ( D) Statistics of artificial DNA-protein complexes. Joint probability density of DNA-protein interaction energy, E _DP , and the interfacial template modeling (TM)-score between an ART protein and its corresponding native template. A vertical/horizontal dashed line is placed at E _DP = -10 and iTM-score = 0.4. ( E) DNA-binding propensity scores (>0 implies favorable binding) of native DNA-protein interfaces versus putatively attractive ( E _DP <-10) and repulsive ( E _DP >10) artificial DNA-protein interfaces. ( F) Example of an artificial DNA-protein complex. The complex was built by superimposing the ART structure (red) onto a native template (PDB code 1akh, the native protein and DNA are colored in green and cyan, respectively).