Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

• Published in: Molecular Biology and Evolution
• Main Authors: Koenekoop, Lucien, Åqvist, Johan
• Other Authors: Echave, Julian
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2023
• Subjects: Antarc*; Antarctic
• Online Access: http://dx.doi.org/10.1093/molbev/msad099; https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad099/50127039/msad099.pdf; https://academic.oup.com/mbe/article-pdf/40/5/msad099/50333902/msad099.pdf

Abstract Cold-adapted enzymes from psychrophilic and psychrotolerant species are characterized by a higher catalytic activity at low temperature than their mesophilic orthologs and are also usually found to be more thermolabile. Computer simulations of the catalytic reactions have been shown to be a very powerful tool for analyzing the structural and energetic origins of these effects. Here, we examine the cold adaptation of lactate dehydrogenases from two Antarctic and sub-Antarctic fish species using this approach and compare our results with those obtained for the orthologous dogfish enzyme. Direct calculations of thermodynamic activation parameters show that the cold-adapted fish enzymes are characterized by a lower activation enthalpy and a more negative entropy term. This appears to be a universal feature of psychrophilic enzymes, and it is found to originate from a higher flexibility of certain parts of the protein surface. We also carry out free energy simulations that address the differences in thermal stability and substrate binding affinity between the two cold-adapted enzymes, which only differ by a single mutation. These calculations capture the effects previously seen in in vitro studies and provide straightforward explanations of these experimental results.