DNA聚合酶在活细胞中产生互补的DNA链,对基因组传递和维持至关重要。这些酶具有类似的人类右手褶皱,包含拇指,手指,和棕榈亚结构域,并有助于聚合活性。这些酶分为七个进化家族,A,B,C,D,X,Y,RT,基于氨基酸序列分析和生化特性。家族ADNA聚合酶存在于广泛的生物体中,包括嗜温,嗜热,和嗜热细菌,参与DNA复制和修复,在分子生物学和生物技术中有着广泛的应用。在这项研究中,我们试图检测在该家族成员的热稳定性特性中起作用的因素,尽管它们在结构和功能上具有显着相似性。为此,氨基酸序列的异同,结构,并对这些酶的动力学进行了检查。我们的结果表明,嗜热和超嗜热酶具有更多的电荷,芳香,和极性残基比中温性残基,因此显示出进一步的静电和阳离子-pi相互作用。此外,在嗜热酶中,脂肪族残基比嗜温酶更倾向于处于埋藏状态。在它们的脂肪族部分中的这些残基增加了疏水性核心填充,因此增强了这些酶的热稳定性。此外,嗜热腔体积的减少有助于蛋白质紧密度的增强。此外,分子动力学模拟结果表明,升高温度对嗜温酶的影响比对极性和脂肪族残基表面积和氢键变化的嗜热酶的影响更大。
DNA polymerases create complementary DNA strands in living cells and are crucial to genome transmission and maintenance. These enzymes possess similar human right-handed folds which contain thumb, fingers, and palm subdomains and contribute to polymerization activities. These enzymes are classified into seven evolutionary families, A, B, C, D, X, Y, and RT, based on amino acid sequence analysis and biochemical characteristics. Family A DNA polymerases exist in an extended range of organisms including mesophilic, thermophilic, and hyper-thermophilic bacteria, participate in DNA replication and repair, and have a broad application in molecular biology and biotechnology. In this
study, we attempted to detect factors that play a role in the thermostability properties of this family member despite their remarkable similarities in structure and function. For this purpose, similarities and differences in amino acid sequences, structure, and dynamics of these enzymes have been inspected. Our results demonstrated that thermophilic and hyper-thermophilic enzymes have more charged, aromatic, and polar residues than mesophilic ones and consequently show further electrostatic and cation-pi interactions. In addition, in thermophilic enzymes, aliphatic residues tend to position in buried states more than mesophilic enzymes. These residues within their aliphatic parts increase hydrophobic core packing and therefore enhance the thermostability of these enzymes. Furthermore, a decrease in thermophilic cavities volumes assists in the protein compactness enhancement. Moreover, molecular dynamic simulation results revealed that increasing temperature impacts mesophilic enzymes further than thermophilic ones that reflect on polar and aliphatic residues surface area and hydrogen bonds changes.