Temperature affects protein structure and function [18]. A comparison of enzyme structures and amino acid sequences across the entire thermal range has shown certain conserved strategies for maintaining optimal stability and activity under different conditions.
Methods employed by proteins to cope with high temperatures include increased ionic interactions and hydrogen bonds, increased hydrophobicity, decreased flexibility at room temperature, and smaller surface loops. The enzyme glutamate dehydrogenase provides a striking example of this. A comparison of the Pyrococcus furiosus glutamate dehydrogenase with the same enzyme from mesophiles revealed that the hyperthermophilic enzyme contained a sequence of ion-pairs that were formed by regions of the protein containing a high density of charged residues, but these were absent in the mesophilic enzymes. The ion-pair networks formed clusters at the inter-domain and inter-subunit surfaces [34]. Hyperthermophile proteins have very high temperature optima, higher than their growth temperatures. For example, a hyperthermophilic starch-degrading enzyme, amylopullanase, wasisolated and showed activity up to 142°C [39]. Chaperone proteins, which assist in protein folding, are particularly important in thermophiles. In Pyrodictium occultum grown at 108°C, 2°C below its upper growth limit, 80% of the soluble protein consists of a chaperone protein complex called the thermosome, which maintains the other cellular proteins in a functional conformation [28].
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At low temperatures, proteins tend to become less rigid, implying that increases in flexibility can increase function. This is indeed observed in psychrophilic proteins, which tend to show decreases in ionic interactions and hydrogen bonds, fewer hydrophobic groups and more charged groups on the protein surface, and longer surface loops [17]. Cold adaptation is accomplished by regulation of membrane fluidity by increasing the proportion of unsaturated fatty acids, the synthesis of cold-shock and antifreeze proteins, the regulation of ion channel permeability, alterations in enzyme kinetics that make the enzymes more efficient, and stabilising the polymerisation of microtubules [19].
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Halophile proteins employ other adaptations, notably an excess of negatively-charged amino acids (glutamate and aspartate) on the protein surface. The surface binds hydrated ions and reduces the surface hydrophobicity, decreasing the tendency to aggregate at high salt concentrations [21]. Halophiles respond to increases in osmotic pressure in different ways. The extremely halophilic archaea, the Halobacteriaceae, accumulat K+. Other bacteria accumulate compatible solutes (e.g., glycine betaine, sugars, polyols, amino acids and ectoines), helping them to maintain an environment isotonic with the growth medium. These substances also help to protect cells against stresses like high temperature, desiccation and freezing [11].
Acidophiles and alkaliphiles use proton pumps to keep their internal pH values close to neutral, but how their extracellular proteins operate at pH extremes is, as yet, poorly understood. Alkaliphiles have negatively charged cell-wall polymers in addition to peptidoglycan [3] and these may reduce the pH value at the cell surface, which helps to stabilise the cell membrane. Acidophiles employ a range of mechanisms to enablethem to withstand low pH, including a positively charged surface [25], high internal buffer capacity, overexpression of H+ export enzymes, and unique transpor ters [36]. Piezophile adaptations are as yet relatively unknown but, in some of these organisms, gene expression is known to be pressure-regulated [1].
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