Entropic stabilization of proteins and its proteomic consequences

Abstract

Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However, it is sometimes difficult to discern their causes without a clear understanding of underlying physical mechanisms of thermal stabilization of proteins. For example, it is well-known that hyperthermophiles feature a greater proportion of charged residues, but, surprisingly, the excess of positively charged residues is almost entirely due to lysines but not arginines in the majority of hyperthermophilic genomes. Allatom simulations show that lysines have a much greater number of accessible rotamers than arginines of similar degree of burial in folded states of proteins. This finding suggests that lysines would preferentially entropically stabilize the native state. Indeed, we show in computational experiments that arginine-to-lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanism as a complement to electrostatic stabilization in its strategies of thermophilic adaptation, then hyperthermostable organisms would have much greater content of lysines in their proteomes than comparably sized and similarly charged arginines. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias toward arginine-to-lysine replacement in hyperthermophilic organisms and overall much greater content of lysines than arginines in hyperthermophiles. This finding cannot be explained by genomic GC compositional biases or by the universal trend of amino acid gain and loss in protein evolution. We discovered here a novel entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state and demonstrated its immediate proteomic implications. Our study provides an example of how analysis of a fundamental physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why amino acid compositions of hyperthermophilic proteomes are significantly biased toward lysines but not similarly charged arginines.

Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles

“…We interpret SdiffN as related to conformational flexibility, for sidechains, so that the current result is roughly in accord with the observation [48] that any increase in sidechain flexibility in thermophile proteins compared to mesophile proteins is small. It has been hypothesised that the basis for thermophile proteins containing a greater proportion of Lys over Arg, is a difference in the number of accessible rotameric states [48]. In a subsequent section we look at variations in dehydration energy that could contribute to changes in the percentages of charged residue classes.…”

“…The greatest difference in amino acid composition between mesophile and hyperthermophile proteins was their proportion of titratable residues (Figure 4a), being higher for hyperthermophiles [16,18,22], with the largest changes for Glu and Lys [48,69]. We see a small decrease in the proportion of Asn [8], in common with other polar residues that do not carry net charge.…”

“…iii) Aspects of the general amino acid composition [48]. More specifically a decrease in the number of thermolabile residues e.g.…”

Optimization of electrostatics as a strategy for cold-adaptation: A case study of cold- and warm-active elastases

“…1 and Table 1), which is in agreement with a low relative arginine content [Arg/(Arg + Lys)], a typical characteristic of several cold-adapted enzymes [2,4,5,7]. It has been suggested that lysine residues stabilize the folded state through increased rotameric states and thereby reducing the entropic penalty of going from the unfolded to the folded state when compared to arginine [38]. SE has 7 Lys and 6 Arg residues while the corresponding numbers are 3 and 12 for PE, and from an entropic point of view this will increase the stability of the SE relative to PE.…”

New opportunities revealed by biotechnological explorations of extremophiles

“…Similar to the situation in cold adaptation, the intrinsic properties of nucleic acids, lipids and enzymes/proteins allow thermophiles to flourish in high temperature environments, and specific composition biases and structural adaptations have been identified [16,[28][29][30][31]. Recent publications describing the genomes of two hyperthermophilic archaea (Nanoarchaeum equitans and Thermococcus kodakaraensis [32 ,33]), one archaeal thermoacidophile (Sulfolobus acidocaldarius) [34] and one thermophilic bacterium (Carboxydothermus hydrogenoformans) [35], although not significantly changing the perception of high temperature adaptation, bring together several exciting novelties on various aspects of the biology, genome evolution and metabolic versatility in specific thermophilic environments.…”