Adaptations of protein structure and function to temperature: there is more than one way to ‘skin a cat’

Abstract

Sensitivity to temperature helps determine the success of organisms in all habitats, and is caused by the susceptibility of biochemical processes, including enzyme function, to temperature change. A series of studies using two structurally and catalytically related enzymes, A 4 -lactate dehydrogenase (A 4 -LDH) and cytosolic malate dehydrogenase (cMDH) have been especially valuable in determining the functional attributes of enzymes most sensitive to temperature, and identifying amino acid substitutions that lead to changes in those attributes. The results of these efforts indicate that ligand binding affinity and catalytic rate are key targets during temperature adaptation: ligand affinity decreases during cold adaptation to allow more rapid catalysis. Structural changes causing these functional shifts often comprise only a single amino acid substitution in an enzyme subunit containing approximately 330 residues; they occur on the surface of the protein in or near regions of the enzyme that move during catalysis, but not in the active site; and they decrease stability in cold-adapted orthologs by altering intra-molecular hydrogen bonding patterns or interactions with the solvent. Despite these structure-function insights, we currently are unable to predict a priori how a particular substitution alters enzyme function in relation to temperature. A predictive ability of this nature might allow a proteome-wide survey of adaptation to temperature and reveal what fraction of the proteome may need to adapt to temperature changes of the order predicted by global warming models. Approaches employing algorithms that calculate changes in protein stability in response to a mutation have the potential to help predict temperature adaptation in enzymes; however, using examples of temperatureadaptive mutations in A 4 -LDH and cMDH, we find that the algorithms we tested currently lack the sensitivity to detect the small changes in flexibility that are central to enzyme adaptation to temperature.

Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C

“…Biochemical adaptation of proteins to temperature has been documented for a variety of proteins across a diversity of ectothermic taxa (Tattersall et al, 2012;Fields et al, 2015;Lim et al, 2016). A key factor that underlies these temperature-adaptive differences is the need for an appropriate degree of structural stability at normal cellular temperatures (Somero et al, 2017).…”

“…Efforts to identify adaptive variation in physiological and biochemical systems not only can help to account for current distribution patterns of species, but also can be helpful in predicting the consequences of global change. A major focal point in studies of biochemical adaptation to the environment has been on temperature effects on proteins (Somero, 2010;Fields et al, 2015). Adaptive variation in functional properties, for example, ligand binding, as indexed by the Michaelis-Menten constant (K M ), and structural stability, has been documented in many comparative studies of orthologous proteins from differently thermally adapted species (e.g.…”

“…Adaptive variation in functional properties, for example, ligand binding, as indexed by the Michaelis-Menten constant (K M ), and structural stability, has been documented in many comparative studies of orthologous proteins from differently thermally adapted species (e.g. Fields et al, 2015). Studies that have extended these lines of analysis to elucidate the underlying molecular mechanisms of adaptation have shown that a relatively small number of amino acid substitutions -as little as a single substitution in some cases (Dong and Somero, 2009) -can account for adaptive differences in function and stability.…”

“…These adaptive amino acid substitutions lead to alterations in weak bonding interactions (hydrogen bonds, ionpair interactions and hydrophobic interactions) that alter stabilities of proteins (Scandurra et al, 1998;Xiao and Honig, 1999;Fitter and Haber-Pohlmeier, 2004;Dong and Somero, 2009). An important conclusion from these analyses is that proteins are under selection to maintain a balance between stability and flexibility (Kohen et al, 1999;Fields, 2001;Somero, 2010;Fields et al, 2015), which leads to corresponding states of protein structural stability at normal cellular temperatures of different species (Somero et al, 2017). Whereas this general stability-flexibility balance has been repeatedly demonstrated, the precise regions of the protein for which this balance is most important remain to be clearly elucidated.…”

“…The predicted differences in net free energy of protein stabilization resulting from the minor variation in sequences among closely related congeners are small. The effects of minor variations in sequence on stability may not be great enough to allow a priori predictions of whether an amino acid substitution at a particular site will lead to a predictable change in thermal stability (Fields et al, 2015).…”