Comparative Analyses Of The Structural Parameters Between Differently Temperature-adapted Enzymes

Enzymes are proteins produced by organisms with the capacity to speed up chemical reactions and,take part in almost all life activities and physiological processes.The extremophilic enzymes produced by the organisms that live in the extreme temperature conditions is thought to play a crucial role in the temperature adaptation of the extreme organisms;as a result,investigating the temperature adaptation mechanisms of the extremophilic enzymes not only provides a direct and effective way for probing the mechanisms by which the organisms adapt to the extreme temperatures,but also is of great significance to the enzyme engineering and industrial applications.In order to ascertain the structural factors significantly related to the enzyme temperature adaptation,in this thesis we constructed a high-quality non-redundant structural data set within which the different enzyme families consist of the differently temperature-adapted members(i.e.,psychrophilic,mesophilic,and thermophilic enzyme member),based on which the amino acid contents and a series of structural parameters were calculated and statistically analyzed.Specifically,by using the keyword search approach,we collected 21 enzyme families that simultaneously contain the structures of the psychrophilic,mesophilic,and thermophilic members(with the total number of 63 crystal structures)from PDB(protein data bank).For each structure within the data set,the amino acid content and various structural parameters,including the number of hydrogen bonds,the number of salt bridges,the number,volume and surface area of cavities,solvent accessible surface area(SASA),relative solvent accessibility surface area(R-SASA),hydrophobicity,and the contents of the regular and irregular secondary structure elements,were quantitatively calculated,followed by pair-wise comparison and statistical analysis of the amino acid content and the above structural parameters between differently temperature-adapted enzyme groups.The main results are as follows: i)the group of thermophilic enzymes tended to contain more Arg and Glu,while the groups of psychrophilic and mesophilic enzymes group tend to contain more Asp,Thr,Asn,and Gln;ii)the group of thermophilic enzymes have significantly more number of salt bridges than the groups of psychrophilic and mesophilic enzymes,despite no significant difference in the number of salt bridges between the groups of psychrophilic and mesophilic enzymes;iii)The groups of thermophilic and mesophilic enzymes have significantly more number of hydrogen bonds than the group of psychrophilic enzymes,but there is no significant difference in the number of hydrogen bonds between the groups of thermophilic and mesophilic enzymes;iv)there are no significant differences in the number,volume,and surface area of cavities among differently temperature-adapted enzyme groups;v)although there is no significant difference in SASA between differently temperatureadapted enzyme groups,R-SASA detected in the psychrophilic enzyme group is significantly higher than in the thermophilic enzyme group;vi)there are no significant differences in the hydrophobicity values(characterized by the ratio of the buried hydrophobic/non-polar area to the total hydrophobic/non-polar surface area of an enzyme)among differently temperature-adapted enzyme groups;vii)for the regular secondary structure content,thermophilic enzyme group has a significant higher content of helical secondary structures than psychrophilic group,despite no significant differences in the helical content existed between the mesophilic and thermophilic groups and between the mesophilic and psychrophilic groups,and no significant differences in the content of the sheet-like regular secondary structures detected among differently temperature-adapted enzyme group;viii)the content of the irregular secondary structure is significantly higher in the psychrophilic group than in the thermophilic group,whereas no significant differences in the content of the irregular secondary structure were detected between the mesophilic group and the psychrophilic and thermophilic groups.The above results indicate that the number of hydrogen bonds,the number of salt bridges,R-SASA,and the contents of the helical and irregular secondary structures are very likely to be the key structural factors in determining the temperature adaptability of enzymes,while the number,volume,and surface area of cavities and the content of sheet-like secondary structures are probably not directly related to the temperature adaptability of enzymes.Combining the above results of statistical analyses with the basic knowledge of structural biology,we deduce that: i)the thermophilic enzymes could maintain their structural stability and rigidity at high temperatures via increasing the numbers of hydrogen bonds and salt bridges(which may be related to more contents of Arg and Glu)and the helical content,and at the same time reducing the solventexposed degree and the content of irregular secondary structure;ii)the psychrophilic enzymes could maintain their conformation flexibility and hence guarantee the lowtemperature catalytic activity via reducing the numbers of hydrogen bonds and salt bridges,increasing the solvent-exposed degree(which may be related to more contents of a negative residue Asp and the uncharged strong-polar residues Thr,Asn,and Gln)and the content of the irregular secondary structure;iii)a stronger plasticity in the temperature adaptation(i.e.,an ability to maintain structural stability and catalytic activity in a wider range of temperature)of mesophilic enzymes may explain why the contents of certain amino acid residues and the quantitative values of some structural parameters calculated for the mesophilic enzymes are closer to those for the psychrophilic enzymes,whereas the calculated contents/values of the other residues/structural parameters are more closer to those for the thermophilic enzymes.The results presented in this thesis are not only helpful to understand general adaptation strategies adopted by the extreme temperature enzymes,but also provide clues and ideas for the engineering modification of extremophilic enzymes.