Elucidating the protein cold-adaptation: Investigation of the parameters enhancing protein psychrophilicity

Abstract

To investigate the role of the critical parameters in adaptation of proteins to low temperatures, a comparative systematic analysis was performed. Several parameters were proposed to have contribution to cold adaptation of proteins. Among proposed parameters, total values of residual structure states, secondary structure states and oligomeric states were alike in both psychrophilic and mesophilic proteins. In addition, our results provided new quantitative information about the trends in the substitution preference of Ile, Phe, Tyr, Lys, Arg, His, Glu and Leu with most of amino acids and substitution avoidance of Gly, Thr and Ala with most of amino acids. These findings would help future efforts propose a strategy for designing psychrophilic proteins.

Introduction

Cold-adapted proteins surprisingly enable some organisms to grow in environments where the temperature is close to the freezing point of water. Microbial life in super-cooled droplets in high altitudes, or below 3500 m of ice in the Antarctic Lake Vostok, or algae colonies, mainly Chlamydomonas, are some instances of the organisms with such a capability (Lonhienne et al., 2000). Adaptation to such conditions requires extensive and finely tuned structural changes at the molecular level, especially in the enzymes. The plausible reason for enhanced catalytic activity of psychrophilic enzymes is generally believed to be an increase in structural flexibility, leading to a reduction of their thermostability (Vihinen, 1987). The low stability of cold-adapted enzymes is therefore the consequence of structural-based changes, which arise from the strong selection pressure allowing a viable physiological activity at low temperatures. Such an adaptation makes them attractive targets as components of industrial products. For instance, these proteins are expected to work as catalysts at low temperatures where such ability offers a reduction in the energy consumption, especially when used in bioremediation (Margesin and Schinner, 1998) and such industries as detergent, food and textile manufacturing. Hence, researchers are interested in identifying the parameters in charge of protein cold-adaptation. Historically, several experimental and theoretical methods have been employed to investigate and compare the individual proteins extracted from psychrophilic and mesophilic organisms. All these efforts have been made to identify the parameters contributing to protein cold-adaptation (Russell et al., 1998; Bae and Phillips, 2004; Altermark et al., 2007).

In our two previous works, we devoted the investigation to elucidate the cold-adaptation parameters (Jahandideh et al., 2007a, Jahandideh et al., 2007b). The candidate parameters were sequence and structural parameters of psychrophilic and mesophilic proteins. In the present study, we constructed a new dataset making use of the existent updated databases. Fifteen homologous pairs of psychrophilic and mesophilic proteins are present in the collected dataset. These pairs represented 15 different families of proteins, in which the individual protein pairs were selected based on the sequence identity. For each amino acid type, the substitution preference and avoidance from mesophilic to psychrophilic type were scrutinized. Besides, other structural properties were compared, including the distribution of the residue structural states, distribution of the secondary structure states and oligomeric states between 15 pairs of psychrophilic and mesophilic proteins. Making advantage of these complementary analyses will in turn serve us with evolutionary information required for the design of psychrophilic proteins.