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. All-atom 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.

Folding without charges

“…3). Even so, the overall limited influence of charge on S6 folding is remarkable considering that the protein functions in a thermophilic bacterium where high charge content is generally believed to reflect an optimization to high thermal stability (39)(40)(41). The principal role of the S6 charges seems rather to be in solubility.…”

Toward Understanding the Cationicity of Defensins

“…In the majority of hyperthermophilic genomes, the excess of positively charged residues is almost entirely due to lysines but not arginines. Berezovsky et al (63) argued that lysines have a much greater number of accessible rotamers than equally buried arginines in folded states of proteins, thus preferentially stabilizing the native state entropically.…”

Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

“…6A). sfAFP's heightened native-state entropy stabilizes the protein by reducing the loss of entropy upon folding, also achievable through the use of specific amino acids (53). Compared with α-helices, the backbone of residues in sfAFP's PP2 helices are slightly more flexible and sample more area in the Ramachandran map during MD simulations (Fig.…”