Cold-active enzymes studied by comparative molecular dynamics simulation
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Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included α-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.
KeywordsCold-active enzymes Psychrophiles Extremophiles Molecular dynamics Flexibility
This work was supported by the Academy of Sciences of the Czech Republic (GAAV KJB 500500512) and the Ministry of Education, Youth and Sports (MSM 6046137305). The authors would like to acknowledge colleagues from the Department of Biochemistry and Microbiology, Institute of Chemical Technology Prague who have lent their personal computers during holiday periods for performing some of the computations presented herein. They are listed on the following web site: biomikro.vscht.cz/groups/lab211/holiday.
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