Boro Nitisha, Alexandrino Fernandes Pedro, Mukherjee Ashis K
Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade De Ciências, Universidade do Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
Heliyon. 2024 Jul 1;10(13):e33895. doi: 10.1016/j.heliyon.2024.e33895. eCollection 2024 Jul 15.
The fibrinolytic enzymes from sp. are proposed as therapeutics in preventing thrombosis. Computational-based analyses of these enzymes' amino acid composition, basic physiological properties, presence of functional domain and motifs, and secondary and tertiary structure analyses can lead to developing a specific enzyme with improved catalytic activity and other properties that may increase their therapeutic potential.
The nucleotide sequences of fibrinolytic enzymes produced by the genus and its corresponding protein sequences were retrieved from the NCBI database and aligned using the PRALINE programme. The varied physiochemical parameters and structural and functional analysis of the enzyme sequences were carried out with the ExPASy-ProtParam tool, MEME server, SOPMA, PDBsum tool, CYS-REC tool, SWISS-MODEL, SAVES servers, TMHMM program, GlobPlot, and peptide cutter software. The assessed data were compared with the published experimental results for validation.
The alignment of sixty fibrinolytic serine protease enzymes (molecular mass 12-86 kDa) sequences showed 49 enzymes possess a conserved domain with a catalytic triad of Asp196, His242, and Ser569. The predicted instability and aliphatic indexes were 1.94-37.77, and 68.9-93.41, respectively, indicating high thermostability. The random coil means value suggested the predominance of this secondary structure in these proteases. A set of 50 amino acid residues representing motif 3 signifies the Peptidase S8/S53 domain that was invariably observed in 56 sequences. Additionally, 28 sequences have transmembrane helices, with two having the most disordered areas, and they pose 25 enzyme cleavage sites. A comparative analysis of the experimental work with the results of study put forward the characteristics of the enzyme sequences JF739176.1 and MF677779.1 to be considered when creating a potential mutant enzyme as these sequences are stable at high pH with thermostability and to exhibit αβ-fibrinogenase activity in both experimental and studies.
来自某菌属的纤溶酶被提议用作预防血栓形成的治疗药物。对这些酶的氨基酸组成、基本生理特性、功能域和基序的存在情况以及二级和三级结构进行基于计算的分析，有助于开发一种具有改进催化活性和其他特性的特定酶，这可能会增加其治疗潜力。
从NCBI数据库中检索某菌属产生的纤溶酶的核苷酸序列及其相应的蛋白质序列，并使用PRALINE程序进行比对。利用ExPASy-ProtParam工具、MEME服务器、SOPMA、PDBsum工具、CYS-REC工具、SWISS-MODEL、SAVES服务器、TMHMM程序、GlobPlot和肽切割软件对酶序列进行各种理化参数以及结构和功能分析。将评估的数据与已发表的实验结果进行比较以进行验证。
六十种纤溶丝氨酸蛋白酶酶（分子量12 - 86 kDa）序列的比对显示，49种酶具有保守结构域，其催化三联体为Asp196、His242和Ser569。预测的不稳定性指数和脂肪族指数分别为1.94 - 37.77和68.9 - 93.41，表明具有高热稳定性。随机卷曲平均值表明这种二级结构在这些蛋白酶中占主导地位。一组代表基序3的50个氨基酸残基表示在56个序列中始终观察到的肽酶S8/S53结构域。此外，28个序列具有跨膜螺旋，其中两个具有最多的无序区域，并且它们有25个酶切割位点。将实验工作的结果与本研究结果进行比较分析，提出在创建潜在突变酶时应考虑酶序列JF739176.1和MF677779.1的特征，因为这些序列在高pH下稳定且具有热稳定性，并且在实验和本研究中均表现出αβ-纤维蛋白原酶活性。
