Zhang Jingjie, Baigued Huricha, Chen Shana, Borigen Haiyan, Tana Tana, Quan Fu, Yang Dezhi
Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010110, PR China.
Pharmaceutical Laboratory, Inner Mongolia International Mongolian Hospital, Hohhot 010065, PR China.
Access Microbiol. 2024 Oct 11;6(10). doi: 10.1099/acmi.0.000786.v3. eCollection 2024.
The objective is to analyse the physicochemical properties, spatial structure and protein-protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine (MEV). The National Center for Biotechnology Information (NCBI) database was searched for the amino acid sequences of L7/L12 from . In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties: NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyse the PPIs; and the IEDB, ABCpred, SVMTrip and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 was docked to Toll-like receptor 4 (TLR4), B-cell receptor (BCR), Major histocompatibility complex I-T cell receptor (MHC I-TCR) and MHC II-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 6 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16 %, β-turns for 2.42 %, extended strands for 8.87 % and irregular coils for 18.55 % of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cells, two cytotoxic T lymphocytes and three helper T lymphocyte epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC I-TCR and MHC II-TCR complexes and forms stable hydrogen bonds, respectively. L7/L12, which governs the translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing MEVs.
目的是利用生物信息学方法分析L7/L12蛋白的理化性质、空间结构和蛋白质-蛋白质相互作用（PPI），并预测其B细胞和T细胞表位，为开发新型多表位疫苗（MEV）奠定理论基础。在国家生物技术信息中心（NCBI）数据库中搜索来自……的L7/L12的氨基酸序列。此外，使用在线软件ProtParam和ProtScale预测理化性质；使用NetPhos3.1和CD-search预测磷酸化位点和保守结构域；使用SOMPA和SWISS-MODEL预测二级和三级结构；使用STRING数据库分析PPI；使用IEDB、ABCpred、SVMTrip和SYFPEITHI数据库预测B细胞和T细胞表位。分别将L7/L12与Toll样受体4（TLR4）、B细胞受体（BCR）、主要组织相容性复合体I-T细胞受体（MHC I-TCR）和MHC II-TCR复合体对接，并测试L7/L12与靶向受体的结合能力。L7/L12由124个氨基酸组成，被确定为一种稳定的、细胞内的、亲水性蛋白，含有6个磷酸化位点和核糖体蛋白相关的保守结构域。二级结构中α螺旋占70.16%，β转角占2.42%，延伸链占8.87%，无规卷曲占18.55%。PPI表明L7/L12参与核糖体的构成并调节翻译过程的准确性。通过比较多个数据库，最终筛选出3个B细胞、2个细胞毒性T淋巴细胞和3个辅助性T淋巴细胞表位。L7/L12分别与TLR4、BCR、MHC I-TCR和MHC II-TCR复合体结合并形成稳定的氢键。L7/L12负责蛋白质的翻译准确性，具有多个潜在的优势表位，为设计MEV奠定了理论基础。
