Protein rigidity and thermophilic adaptation

Abstract

We probe the hypothesis of corresponding states, according to which homologues from mesophilic and thermophilic organisms are in corresponding states of similar rigidity and flexibility at their respective optimal temperatures. For this, the local distribution of flexible and rigid regions in 19 pairs of homologous proteins from meso- and thermophilic organisms is analyzed and related to activity characteristics of the enzymes by constraint network analysis (CNA). Two pairs of enzymes are considered in more detail: 3-isopropylmalate dehydrogenase and thermolysin-like protease. By comparing microscopic stability features of homologues with the help of stability maps, introduced for the first time, we show that adaptive mutations in enzymes from thermophilic organisms maintain the balance between overall rigidity, important for thermostability, and local flexibility, important for activity, at the appropriate working temperature. Thermophilic adaptation in general leads to an increase of structural rigidity but conserves the distribution of functionally important flexible regions between homologues. This finding provides direct evidence for the hypothesis of corresponding states. CNA thereby implicitly captures and unifies many different mechanisms that contribute to increased thermostability and to activity at high temperatures. This allows to qualitatively relate changes in the flexibility of active site regions, induced either by a temperature change or by the introduction of mutations, to experimentally observed losses of the enzyme function. As for applications, the results demonstrate that exploiting the principle of corresponding states not only allows for successful thermostability optimization but also for guiding experiments in order to improve enzyme activity in protein engineering.

Improved insights into protein thermal stability: from the molecular to the structurome scale

“…Instead, interactions between non-charged polar residues seem to disfavour it [13][14][15][16]. Other structural factors that appear related to the thermal resistance are the protein rigidity and the higher packing efficiency [17,18]. These structural features can be achieved for example by shortening some loops, increasing the number of atoms that are buried in the protein core, or filling some buried cavities to optimize the packing.…”

Distinct Roles for Carbohydrate-Binding Modules of Glycoside Hydrolase 10 (GH10) and GH11 Xylanases from Caldicellulosiruptor sp. Strain F32 in Thermostability and Catalytic Efficiency

“…In many cases, a combination of the structural features described above is crucial to achieve increased thermostability (14)(15)(16). These structural changes contribute to the protein thermophilic adaptation of the potential network of noncovalent interaction within the protein, presumably leading to a balance between overall rigidity, which is important for thermostability, and local flexibility, which is important for activity (17).…”

An Interfacial Thermodynamics Model for Protein Stability

“…Nevertheless, the RCD is useful to understand long-time scales, where small amplitude conformational deviations in substructures within a protein are neglected, such as the compression, elongation, bending or twisting of an alpha-helix. The rapid calculations for the RCD by FIRST (requiring tiny fractions of a second) has proved to be useful in making comparative studies across protein families, and to elucidate common structural features regarding flexibility important to function Rader, et al 2004;Fuxreiter, et al 2005;Costa, et al 2006;Radestock & Gohlke 2008;Mamonova et al 2008;Rader, 2010;Heal, et al 2011;Radestock & Gohlke 2011]. It has also been shown there is a statistically significant correlation between the propagation of rigidity between two mutation sites within a protein to non-additive effects in free energy cycles describing double mutant studies [Istomin, et al 2008].…”