Sequence and structural parameters enhancing adaptation of proteins to low temperatures

Abstract

A systematic analysis compared sequence and structural parameters distributions between 13 pairs of psychrophilic and mesophilic proteins for elucidating the cold adaptation parameters. The results of statistical test (t-test) revealed that helical content, tight turn content, disulfide bonds and hydrogen bonds do not show significant difference between psychrophilic and mesophilic proteins. However, it was demonstrated in this study that a larger proportion of open β-turn in psychrophilic proteins is an effective parameter in specific activity at low temperature. In addition, substitution of amino acids of charged and aliphatic groups with amino acids of tiny and small groups in protein chains, tight turns and α-helices in the direction from mesophilic to psychrophilic proteins is one of the mechanisms of low temperature adaptation. Such sequence and structural parameter differences would help to develop a strategy for designing cold-adapted proteins.

Introduction

Psychrophilic organisms have the specific ability to grow in environments where the temperature is close to the freezing point of water such as the deep sea, glaciers and mountain regions. Life at low temperatures requires a vast array of adaptation in the form of finely tuned structural changes at the molecular level, particularly in enzymes. Such an adaptation, leads to the ability of psychrophilic enzymes to work as catalysts at low temperatures, and this ability in turn, offers a reduction in energy consumption when used in bioremediation (Timmis and Pieper, 1999; Margesin and Schinner, 1998), biocatalysis under low-water conditions (Bell et al., 1995) and such industries as detergent, food and textile manufacturing. The use of psychrophilic enzymes can be advantageous not only for their high specific activity, thereby reducing the amount of enzyme needed, but also for their easy inactivation. The molecular basis of the cold adaptation is still relatively poorly understood. Identifying and understanding the factors contributing to the enzymes specific activity at low temperatures which is believed to be a consequent of enhanced peptide chain flexibility has been a long-standing problem. The first crystallographic 3D structure of a cold-adapted enzyme isolated from a microorganism, an α-amylase isolated from a gram negative Antarctic bacterium, was described in 1996 (Aghajari et al., 1996), followed by a Ca²⁺−Zn²⁺ protease (Villeret et al., 1997), a triose phosphate isomerase (Alvarez et al., 1998) and a malate dehydrogenase (Kim et al., 1999), all originating from Antarctic bacteria. Since these pioneering efforts, several investigators have focused on the problem of structural and thermodynamic basis of protein cold adaptation.

From historical point of view several studies have performed to compare the individual proteins extracted from psychrophilic and mesophilic organisms. All these efforts have been done to identify the parameters which have contribution in cold-adaptation. (Bae and Phillips, 2004; Russell et al., 1998). Due to adequate frequency of structurally defined thermophilic proteins is much more than psychrophilic proteins, more analysis have been performed to search for parameters thermolability in thermophilic proteins. Although, the number of structurally defined proteins is not significant today, a bank comprising 13 pairs of structurally defined proteins from two mesophilic and psychrophilic groups is collected in this study. Consequently, we compared several sequence and structural parameters between these 13 pairs of psychrophilic and mesophilic proteins to elucidate the cold adaptation parameters. The result suggests possible general rules for protein engineering experiments aimed to produce enzymes catalytically effective at low temperatures.