Varela-Rodríguez H, Guzman-Pando A, Camarillo-Cisneros J
Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua (UACH), Chihuahua 31125, Chihuahua, Mexico.
Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua (UACH), Chihuahua 31125, Chihuahua, Mexico.
Comput Biol Chem. 2024 Dec;113:108276. doi: 10.1016/j.compbiolchem.2024.108276. Epub 2024 Nov 13.
As cold-blooded organisms living in damp and dark environments, amphibians have evolved robust defense mechanisms to protect themselves from predators and infections. Among the wide repertoire of bioactive compounds they produce are antimicrobial peptides (AMPs), which are required as part of innate immunity. One important class of AMPs is cathelicidins, known for their broad-spectrum activity against pathogens and their immunoregulatory roles. However, despite their promising biomedical potential and the increasing availability of omics data, few cathelicidins have been studied in amphibians, mostly through conventional experimental techniques. Here, we present 210 novel cathelicidin sequences from amphibian transcriptomes, identified through a comprehensive computational pipeline, which employed HMMER and BLAST tools to screen cathelicidin domains. These sequences reveal a typical tripartite domain architecture that was confirmed by SignalP and InterProScan analysis. Phylogenetic inference with IQ-TREE classified the sequences into six categories based on evolutionary relationships. Compared to cathelicidins from other vertebrates, amphibian mature peptides exhibit longer average lengths (around 50 amino acids), fewer aromatic and hydrophobic residues, and reduced thermal stability. Furthermore, these amphibian cathelicidins were characterized for their physicochemical and biological properties, revealing significant antimicrobial potential with lower hemolytic capability, especially in anurans, which suggests a balance between their antimicrobial and hemolytic activities predicted through AMPlify, ampir, AmpGram, and HemoPI. Secondary structure estimations, including three-dimensional modeling using AlphaFold2, indicate that amphibian cathelicidins predominantly feature α-helices and coils. Some representative models also display a high α-helix composition with amphipathic topology, facilitating interactions with simulated bacterial membranes as assessed by the PPM approach. Thus, these findings highlight the functional role of cathelicidins in amphibian immunity and their promising biomedical applicability, emphasizing the importance of applying computational methods to expand the scope and reveal the diverse landscape of cathelicidins across vertebrates.
作为生活在潮湿阴暗环境中的冷血生物，两栖动物进化出了强大的防御机制来保护自己免受捕食者和感染。它们产生的多种生物活性化合物中包括抗菌肽（AMPs），这是先天免疫的一部分。一类重要的抗菌肽是cathelicidins，以其对病原体的广谱活性及其免疫调节作用而闻名。然而，尽管它们具有潜在的生物医学价值，且组学数据的可用性不断增加，但在两栖动物中，很少有cathelicidins通过传统实验技术进行研究。在这里，我们展示了来自两栖动物转录组的210个新的cathelicidin序列，这些序列是通过一个综合计算流程鉴定出来的，该流程使用HMMER和BLAST工具筛选cathelicidin结构域。这些序列揭示了典型的三方结构域架构，这一点通过SignalP和InterProScan分析得到了证实。使用IQ-TREE进行的系统发育推断根据进化关系将这些序列分为六类。与其他脊椎动物的cathelicidins相比，两栖动物的成熟肽平均长度更长（约50个氨基酸），芳香族和疏水残基更少，热稳定性降低。此外，对这些两栖动物的cathelicidins的物理化学和生物学特性进行了表征，结果显示它们具有显著的抗菌潜力，溶血能力较低，尤其是在无尾两栖类动物中，这表明它们在通过AMPlify、ampir、AmpGram和HemoPI预测的抗菌和溶血活性之间达到了平衡。二级结构预测，包括使用AlphaFold2进行的三维建模，表明两栖动物的cathelicidins主要以α-螺旋和卷曲为特征。一些代表性模型还显示出具有两亲拓扑结构的高α-螺旋组成，通过PPM方法评估，这有利于与模拟细菌膜相互作用。因此，这些发现突出了cathelicidins在两栖动物免疫中的功能作用及其潜在的生物医学适用性，强调了应用计算方法扩大范围并揭示脊椎动物中cathelicidins多样性的重要性。
