基于计算机虚拟技术研究牦牛乳硬质干酪苦味肽的抑菌活性差异

Study on Difference of Antibacterial Activity of Bitter Peptide from Yak Milk Hard Cheese Based on Computer Virtual Technology

摘要:

为研究牦牛乳硬质干酪中苦味肽的抑菌活性差异及其与不同微生物菌体蛋白相互作用的氨基酸和位置信息。运用生物信息学方法计算牦牛乳硬质干酪中4种苦味肽RPKHPIK（RK7）、TPVVVPPFL（TL9）、VYPFPGPIPN（VN10）和SLVYPFPGPIPN（SN12）的分子特性，利用分子对接工具从分子层面研究肽的抑菌活性、研究肽段和不同菌体蛋白（大肠杆菌5BNS、金黄色葡萄球菌4ALM、沙门氏菌6CH3）之间相互作用的分子机制，通过BIOPEP数据库比对表征肽段抑菌活性。研究结果表明：RK7所带净电荷为3.1，疏水性氨基酸比例为42.86%；TL9所带净电荷为0，疏水性氨基酸比例为88.89%；VN10和SN12的疏水力矩分别为0.189和0.372，疏水性氨基酸比例为70.00%和66.67%。RK7和TL9均能和5BNS、4ALM、6CH3形成配体-受体复合物构象，VN10和SN12仅能和4ALM、6CH3形成配体-受体复合物构象；将RK7、TL9、VN10和SN12与抗菌肽数据库比对后发现RK7为抑菌活性已知的肽段，最高相似度为100%，TL9、VN10和SN12为潜在的具有抑菌活性的新型抗菌肽。结合肽段分子特性分析、分子对接和数据库比对预测4种苦味肽的抑菌活性，大肠杆菌抑制活性：RK7 > TL9，金黄色葡萄球菌抑制活性：RK7 > VN10 > TL9 > SN12，沙门氏菌抑制活性：RK7 > TL9 > VN10 > SN12。该研究为分子层面研究牦牛乳硬质干酪苦味肽结构特征及其抑菌活性提供了理论参考。

Abstract:

The difference in antibacterial activity of bitter peptides in yak milk hard cheese and the amino acid and position information of their interaction with different bacterial proteins were studied. The bioinformatic methods were used to calculate the molecular characteristics of four bitter peptides including RPKHPIK (RK7), TPVVVPPFL (TL9), VYPFPGPIPN (VN10) and SLVYPFPGPIPN (SN12) in yak milk hard cheese. The molecular docking tool was used to study the antibacterial activity of peptides and the molecular mechanism of the interaction between peptides and different bacterial proteins (E. coli 5BNS, Staphylococcus aureus 4ALM, Salmonella 6CH3) at the molecular level. BIOPEP database comparison was used to characterize the antibacterial activity of peptides. The results showed that the net charge of RK7 was 3.1, and the proportion of hydrophobic amino acids was 42.86%. The net charge of TL9 was 0, and the proportion of hydrophobic amino acids was 88.89%. The hydrophobic moments of VN10 and SN12 were 0.189 and 0.372, respectively, and the proportion of hydrophobic amino acids was 70.00% and 66.67%, respectively. Both RK7 and TL9 could form ligand-receptor complex conformations with 5BNS, 4ALM and 6CH3, while VN10 and SN12 could only form ligand-receptor complex conformations with 4ALM and 6CH3. After comparing RK7, TL9, VN10 and SN12 with the antibacterial peptide database, it was found that RK7 was a peptide with known antibacterial activity with the highest similarity of 100%, and TL9, VN10 and SN12 were potential new antibacterial peptides with antibacterial activity. The antibacterial activity of four bitter peptides was predicted through analysis of peptide molecular characteristics, molecular docking and database comparison. The inhibitory activity of E. coli was RK7 > TL9, while RK7 > VN10 > TL9 > SN12 for that of Staphylococcus aureus and RK7 > TL9 > VN10 > SN12 for that of Salmonella inhibitory activity. This study could provide a theoretical reference for studying the structural characteristics and antibacterial activity of bitter peptides from yak milk hard cheese at the molecular level.