Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution

Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.

The Influence of Codon Usage, Protein Abundance, and Protein Stability on Protein Evolution Vary by Evolutionary Distance and the Type of Protein

In general, the evolutionary rate of proteins is not primarily related to protein and amino acid functions, and factors such as protein abundance, codon usage, and the protein's T_M are more important. To better understand the factors that affect protein evolution, E. coli MG1655 orthologs were compared to those in closely related bacteria and to more distantly related prokaryotes, eukaryotes, and archaea. Also, the evolution of different types of proteins was studied. The analyses indicate that the amino acid conservation of enzymes that do not use macromolecules (e.g. DNA, RNA, and proteins) as substrates and that carry out metabolic processes involving small molecules (i.e. small molecule enzymes) is different than other enzymes. For example, the small molecule enzymes have a lower percent identity than other enzymes when sequences from closely related bacteria are compared. Analyses indicate the lower percent identity is not a result of the amino acid or codon usage of the small molecule enzymes. The small molecule enzymes also don't have a significantly lower protein abundance indicating that is also not likely an important factor driving differences in amino acid conservation. Analyses indicate different methods to measure the T_M of proteins have different relationships between amino acid conservation over different evolutionary distances. In totality, the results demonstrate that the relationship between the factors thought to affect protein evolution (protein abundance, codon usage, and proteins T_Ms) and protein evolution are complex and depend on the factor, the organisms, and the type of proteins being analyzed.

Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles

The bilobal protein kinase-like fold in pseudokinases lack one or more catalytic residues, conserved in canonical protein kinases, and are considered enzymatically deficient. Tertiary structures of pseudokinases reveal that their loops topologically equivalent to activation segments of kinases adopt contracted configurations, which is typically extended in active conformation of kinases. Herein, anisotropic network model based normal mode analysis (NMA) was conducted on 51 active conformation structures of protein kinases and 26 crystal structures of pseudokinases. Our observations indicate that although backbone fluctuation profiles are similar for individual kinase-pseudokinase families, low intensity mean square fluctuations in pseudo-activation segment and other sub-structures impart rigidity to pseudokinases. Analyses of collective motions from functional modes reveal that pseudokinases, compared to active kinases, undergo distinct conformational transitions using the same structural fold. All-atom NMA of protein kinase-pseudokinase pairs from each family, sharing high amino acid sequence identities, yielded distinct community clusters, partitioned by residues exhibiting highly correlated fluctuations. It appears that atomic fluctuations from equivalent activation segments guide community membership and network topologies for respective kinase and pseudokinase. Our findings indicate that such adaptations in backbone and side-chain fluctuations render pseudokinases competent for catalysis-independent roles.

Evolutionary coupling range varies widely among enzymes depending on selection pressure

Recent studies proposed that enzyme-active sites induce evolutionary constraints at long distances. The physical origin of such long-range evolutionary coupling is unknown. Here, I use a recent biophysical model of evolution to study the relationship between physical and evolutionary couplings on a diverse data set of monomeric enzymes. I show that evolutionary coupling is not universally long-range. Rather, range varies widely among enzymes, from 2 to 20 Å. Furthermore, the evolutionary coupling range of an enzyme does not inform on the underlying physical coupling, which is short range for all enzymes. Rather, evolutionary coupling range is determined by functional selection pressure.

Quantifying evolutionary importance of protein sites: A Tale of two measures

A key challenge in evolutionary biology is the accurate quantification of selective pressure on proteins and other biological macromolecules at single-site resolution. The evolutionary importance of a protein site under purifying selection is typically measured by the degree of conservation of the protein site itself. A possible alternative measure is the strength of the site-induced conservation gradient in the rest of the protein structure. However, the quantitative relationship between these two measures remains unknown. Here, we show that despite major differences, there is a strong linear relationship between the two measures such that more conserved protein sites also induce stronger conservation gradient in the rest of the protein. This linear relationship is universal as it holds for different types of proteins and functional sites in proteins. Our results show that the strong selective pressure acting on the functional site in general percolates through the rest of the protein via residue-residue contacts. Surprisingly however, catalytic sites in enzymes are the principal exception to this rule. Catalytic sites induce significantly stronger conservation gradients in the rest of the protein than expected from the degree of conservation of the site alone. The unique requirement for the active site to selectively stabilize the transition state of the catalyzed chemical reaction imposes additional selective constraints on the rest of the enzyme.

Sites within proteins which are important for stability or function are under stronger selective pressure and evolve more slowly than other sites. Catalytic sites in enzymes are such highly conserved sites with relatively low evolutionary rates. Recently, catalytic sites were shown to induce a strong gradient of conservation such that the closer a residue is to the catalytic site, the more conserved it is. Here we show that there is a universal linear relationship between the degree of evolutionary conservation of a protein site and the conservation gradient it induces in the protein tertiary structure, applicable to all types of sites. Our findings suggest that selective pressure acting on a protein site generally percolates through the rest of the protein via residue-residue contacts. Remarkably however, catalytic sites induce significantly stronger conservation gradients than expected from their degree of conservation alone. Our results indicate that the strong conservation gradient induced by catalytic sites is driven by the unique function of enzyme catalysis, which requires the participation of many residues beyond the few key catalytic residues. Our results provide insights into evolutionary conservation patterns of and surrounding proteins functional sites, with implications for functional site prediction and protein design.

Exploring mutable conserved sites and fatal non-conserved sites by random mutation of esterase from Sulfolobus tokodaii and subtilisin from Thermococcus kodakarensis

Homologous proteins differ in their amino acid sequences at several positions. Generally, conserved sites are recognized as not suitable for amino acid substitution, and thus in evolutionary protein engineering, non-conserved sites are often selected as mutation sites. However, there have also been reports of possible mutations in conserved sites. In this study, we explored mutable conserved sites and immutable non-conserved sites by testing random mutations of two thermostable proteins, an esterase from Sulfolobus tokodaii (Sto-Est) and a subtilisin from Thermococcus kodakarensis (Tko-Sub). The subtilisin domain of Tko-Sub needs Ca²⁺ ions and the propeptide domain for stability, folding and maturation. The results from the two proteins showed that about one-third of the mutable sites were detected in conserved sites and some non-conserved sites lost enzymatic activity at high temperatures due to mutation. Of the conserved sites in Sto-Est, the sites on the loop, on the surface, and far from the active site are more resistant to mutation. In Tko-Sub, the sites flanking Ca²⁺-binding sites and propeptide were undesirable for mutation. The results presented here serve as an index for selecting mutation sites and contribute to the expansion of available sequence range by introducing mutations at conserved sites.