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Abstract
Structures and functions of proteins are closely related, and variations in amino acid sequences are a result of their evolutionary adaptations. Since substitutions are not only found at the active site but also on the distal surfaces of the proteins; and a majority of biological reactions occur in an aqueous environment, the contribution of water molecules to protein function will be discussed. Comparison of proteins from different populations or species is advantageous to our understanding of the molecular mechanism of adaptation. For this purpose, I compared mutations observed in natural variants with functional properties of protein. In this study, hemoglobin and deoxyuridine triphosphatase (dUTPase) were chosen as model systems. Hemoglobin is an oxygen-transporting protein that that maintains a low redox-level. Hemoglobins from deer mice living at highland and lowland populations were compared. The surface interactions between amino acids and water molecules were observed to govern the allostery. dUTPase is a hydrolase that maintains a cellular balanced in pyrimidine. Comparative studies of dUTPases from various species, including Arabidopsis, revealed a contribution of water molecules in the enzyme’s substrate affinity. These studies show that alteration of hydrogen bonding is a key factor contributing to functional variations.
